No protocol specified
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/maotai.Rcheck/00install.out’ for details.
prepare_Rd: RGL: unable to open X11 display
prepare_Rd: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
Namespaces in Imports field not imported from:
  ‘gtools’ ‘reshape’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Note: found 3058 marked UTF-8 strings
Note: found 11396 marked UTF-8 strings
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    mapdata  33.4Mb
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.6Mb
    htmlwidgets   2.2Mb
    libs         14.7Mb
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.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rgdal’ ‘rlang’ ‘testthat’
  All declared Imports should be used.
'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.
mapping_bar: no visible global function definition for ‘plot’
mapping_bar : <anonymous>: no visible global function definition for
  ‘plot’
mapping_choro: no visible global function definition for ‘plot’
mapping_typo: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Note: found 10032 marked UTF-8 strings
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   8.1Mb
    libs   3.1Mb
Note: found 55 marked UTF-8 strings
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 114-119 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Note: found 996 marked UTF-8 strings
Note: found 13084 marked UTF-8 strings
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 ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
No protocol specified
  No protocol specified
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/marginalizedRisk.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘betareg’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘kableExtra’ ‘knitr’
  All declared Imports should be used.
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    examples   2.7Mb
    libs      11.5Mb
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
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.
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.
Packages required but not available: 'GO.db', 'org.Hs.eg.db'

Packages required and available but unsuitable versions:
  'AnnotationDbi', 'GOstats'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/MASSExtra.Rcheck/00install.out’ for details.
MASSunite: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Note: found 1 marked UTF-8 string
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   8.6Mb
with.mimids: no visible global function definition for ‘deparse1’
with.wimids: no visible global function definition for ‘deparse1’
Undefined global functions or variables:
  deparse1
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.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/matlib.Rcheck/00install.out’ for details.
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.
GNU make is a SystemRequirements.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Package suggested but not available for checking: ‘qvalue’
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Note: found 17 marked UTF-8 strings
Note: found 66 marked UTF-8 strings
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.
Namespaces in Imports field not imported from:
  ‘effsize’ ‘psych’
  All declared Imports should be used.
MFIerror: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘formatR’ ‘utf8’
  All declared Imports should be used.
Note: found 6 marked Latin-1 strings
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘lars’ ‘methods’ ‘parallel’ ‘smoothmest’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/mcca.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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 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’
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs  12.0Mb
Errors in running code in vignettes:
when running code in ‘mcemGLM-vignette.Rnw’
  ...
         6      :  6   6      :  6   Max.   :1.000  
         (Other):324   (Other):324                  

> fitBernoulli <- mcemGLMM(fixed = Mate ~ 0 + Cross, 
+     random = list(~0 + Female, ~0 + Male), data = salamander, 
+     family = "bernoulli", vcD .... [TRUNCATED] 

Execution halted

... incomplete output.  Crash?

  ‘mcemGLM-vignette.Rnw’... failed to complete the test
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.
Namespace in Imports field not imported from: ‘boot.heterogeneity’
  All declared Imports should be used.
Note: found 46 marked UTF-8 strings
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
.hybrid.template: no visible global function definition for ‘plot’
.runMCMCdemo : plot.density: no visible global function definition for
  ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
installed size is 29.9Mb
  sub-directories of 1Mb or more:
    libs  28.8Mb
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
Namespace in Imports field not imported from: ‘generics’
  All declared Imports should be used.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘parallelMap’ ‘reshape2’
  All declared Imports should be used.
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.
plot.nsga2: no visible global function definition for ‘plot’
plot.nsga2.collection: no visible binding for global variable ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'library' or 'require' 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.
Checking should be performed on sources prepared by ‘R CMD build’.
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘covr’ ‘curl’ ‘devtools’ ‘gh’ ‘git2r’ ‘grDevices’ ‘httr’
  ‘knitr’ ‘openssl’ ‘pkgbuild’ ‘rlang’ ‘rmarkdown’ ‘roxygen2’
  ‘spelling’ ‘testthat’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Package suggested but not available for checking: ‘RGtk2’
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/MDSMap.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/mdsOpt.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘datasets’ ‘dplyr’ ‘psych’ ‘shiny’
  All declared Imports should be used.
Note: found 2866 marked UTF-8 strings
installed size is 26.2Mb
  sub-directories of 1Mb or more:
    libs  24.5Mb
Note: found 7757 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘R6’ ‘ggplot2’ ‘lavaan’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘vroom’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/MEDseq.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
.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.
Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘RODBC’ ‘dplyr’ ‘foreign’ ‘formattable’ ‘ggplot2’
  ‘haven’ ‘mem’ ‘openxlsx’ ‘plotly’ ‘readxl’ ‘shinyBS’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stringi’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shinyBS’ ‘shinycssloaders’
  All declared Imports should be used.
'library' or 'require' calls in package code:
  ‘adegenet’ ‘geosphere’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
codomToPropShared: no visible global function definition for
  ‘df2genind’
codomToPropShared: no visible global function definition for
  ‘propShared’
mgLandscape: no visible global function definition for ‘SpatialPoints’
mgQuick: no visible global function definition for ‘distm’
mgQuick: no visible binding for global variable ‘distMeeus’
Undefined global functions or variables:
  SpatialPoints df2genind distMeeus distm propShared
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/memify.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.1Mb
Namespace in Imports field not imported from: ‘urca’
  All declared Imports should be used.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
Running examples in ‘MendelianRandomization-Ex.R’ failed
The error most likely occurred in:

> ### Name: mr_forest
> ### Title: Draw a forest plot of causal estimates
> ### Aliases: mr_forest mr_forest,MRInput-method
> 
> ### ** Examples
> 
> mr_forest(mr_input(bx = ldlc, bxse = ldlcse, by = chdlodds, byse = chdloddsse),
+   alpha = 0.01, ordered = TRUE)
Error in `levels<-`(`*tmp*`, value = as.character(levels)) : 
  factor level [13] is duplicated
Calls: mr_forest -> mr_forest -> factor
Execution halted
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   5.7Mb
Package suggested but not available for checking: ‘INLA’
Package suggested but not available for checking: ‘GenABEL’
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.
installed size is 89.6Mb
  sub-directories of 1Mb or more:
    libs  88.9Mb
GNU make is a SystemRequirements.
Note: found 37 marked UTF-8 strings
Package required but not available: ‘BiocStyle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘ggrepel’ ‘reshape’ ‘svglite’
  All declared Imports should be used.
Package required but not available: ‘ChemmineR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘gbm’ ‘ggplot2’ ‘graphics’ ‘randomForest’
  All declared Imports should be used.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘BiocStyle’
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘DT’ ‘GEOmetadb’ ‘RMySQL’ ‘RSQLite’ ‘gplots’ ‘pheatmap’
  ‘readr’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘MetaIntegrator.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 29-30 (MetaIntegrator.Rmd) 
Error: processing vignette 'MetaIntegrator.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
--- failed re-building ‘MetaIntegrator.Rmd’

--- re-building ‘MetaIntegratorRealExample.Rmd’ using rmarkdown_notangle
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘MetaIntegratorRealExample.Rmd’

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

Error: Vignette re-building failed.
Execution halted
No protocol specified
No protocol specified
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking:
  'org.Hs.eg.db', 'annaffy', 'hgu133plus2.db', 'hgu133a.db',
  'hgu95av2.db'
installed size is  9.5Mb
  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.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/metamicrobiomeR.Rcheck/00install.out’ for details.
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.7Mb
Found the following significant warnings:
  Warning: package ‘AnnotationDbi’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/MetaPath.Rcheck/00install.out’ for details.
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').
Namespaces in Imports field not imported from:
  ‘ade4’ ‘dendextend’ ‘ggforce’ ‘ggrepel’ ‘stringr’ ‘tidyverse’
  All declared Imports should be used.
installed size is 77.9Mb
  sub-directories of 1Mb or more:
    libs  77.6Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
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.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   3.1Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   2.4Mb
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.
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Note: found 5 marked UTF-8 strings
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    5.4Mb
    libs  19.2Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
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.
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    libs  18.4Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘ECoL’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/MFHD.Rcheck/00install.out’ for details.
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.
Namespaces in Imports field not imported from:
  ‘boot’ ‘energy’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/mgcViz.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
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.
'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').
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  21.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘mgwrsar-basic_examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 91-94 (mgwrsar-basic_examples.Rmd) 
Error: processing vignette 'mgwrsar-basic_examples.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘mgwrsar-basic_examples.Rmd’

SUMMARY: processing the following file failed:
  ‘mgwrsar-basic_examples.Rmd’

Error: Vignette re-building failed.
Execution halted
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.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘copula’
  All declared Imports should be used.
Package suggested but not available for checking: ‘structSSI’
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   8.5Mb
Note: found 9345 marked UTF-8 strings
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/miclust.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘biotools’
Package unavailable to check Rd xrefs: ‘biotools’
Running examples in ‘micompr-Ex.R’ failed
The error most likely occurred in:

> ### Name: assumptions.cmpoutput
> ### Title: Get assumptions for parametric tests performed on output
> ###   comparisons
> ### Aliases: assumptions.cmpoutput
> 
> ### ** Examples
> 
> 
> # Create a cmpoutput object from the provided datasets
> cmp <- cmpoutput("All", 0.9, pphpc_ok$data[["All"]], pphpc_ok$obs_lvls)
> 
> # Get the assumptions for the parametric tests performed in cmp
> acmp <- assumptions(cmp)
sROC 0.1-2 loaded
MANOVA assumptions require 'MVN' and 'biotools' packages.
Error in `*tmp*`[[i]] : subscript out of bounds
Calls: assumptions -> assumptions.cmpoutput
Execution halted
Running ‘testthat.R’ [20s/46s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  subscript out of bounds
  1: assumptions(mic1a) at testthat/test_micomp.R:281
  2: assumptions.micomp(mic1a)
  3: lapply(obj, function(x) assumptions(x))
  4: FUN(X[[i]], ...)
  5: assumptions(x)
  6: assumptions.cmpoutput(x)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 363 SKIPPED: 0 FAILED: 2
  1. Error: assumptions.cmpoutput creates the correct object (@test_cmpoutput.R#214) 
  2. Error: micomp assumptions have the correct properties (@test_micomp.R#281) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘paper.Rnw’ using knitr
Quitting from lines 341-342 (paper.Rnw) 
Error: processing vignette 'paper.Rnw' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘paper.Rnw’

--- re-building ‘tolatex-examples.Rnw’ using knitr
Warning in wilcox.test.default(x = c(-2.17390550005803e-11, -2.17097451127302e-11,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(2.13309370167281e-11, 2.12594386539422e-11,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(1.99236183107132e-11, 1.97388771994156e-11,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(1.00897068477934e-12, 1.02406971791424e-12,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(8.95727936267576e-13, 8.4909856923332e-13,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(9.80548975348938e-13, 8.81072992342524e-13,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(5.90887339058099e-11, 6.09077233093558e-11,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(9.97119053991469e-15, 9.92695509127728e-15,  :
  cannot compute exact p-value with ties
--- finished re-building ‘tolatex-examples.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'dada2', 'DECIPHER'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘microcontax.data’
Package unavailable to check Rd xrefs: ‘microcontax.data’
Namespaces in Imports field not imported from:
  ‘DT’ ‘ggiraph’ ‘ggplot2’ ‘grid’ ‘gtools’ ‘scales’ ‘shinyBS’
  ‘shinyWidgets’ ‘tidyr’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Hsapiens.UCSC.hg19',
  'BSgenome.Mmusculus.UCSC.mm10'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/MicroSEC.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘config’ ‘desc’ ‘dplyr’ ‘glue’ ‘withr’
  All declared Imports should be used.
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    doc    6.0Mb
    lib    6.9Mb
    libs   3.1Mb
Namespaces in Imports field not imported from:
  ‘AzureAuth’ ‘R6’ ‘curl’ ‘jsonlite’ ‘utils’ ‘vctrs’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
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.
Package suggested but not available for checking: ‘gWidgets2RGtk2’
.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').
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
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.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘softImpute’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
Note: found 5 marked UTF-8 strings
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.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
rminimax: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘markdown’ ‘metafor’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cluster’ ‘dendextend’ ‘npmv’ ‘utils’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/MIRES.Rcheck/00install.out’ for details.
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.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   6.3Mb
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
render.standard: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
Running examples in ‘misc3d-Ex.R’ failed
The error most likely occurred in:

> ### Name: slices3d
> ### Title: Interactive Image Slices of 3D or 4D Volume Data
> ### Aliases: slices3d
> ### Keywords: hplot
> 
> ### ** Examples
> 
>   #Example 1: View of a mixture of three tri-variate normal densities
>   nmix3 <- function(x, y, z, m, s) {
+       0.4 * dnorm(x, m, s) * dnorm(y, m, s) * dnorm(z, m, s) +
+       0.3 * dnorm(x, -m, s) * dnorm(y, -m, s) * dnorm(z, -m, s) +
+       0.3 * dnorm(x, m, s) * dnorm(y, -1.5 * m, s) * dnorm(z, m, s)
+   }
>   x<-seq(-2, 2, len=40)
>   g<-expand.grid(x = x, y = x, z = x)
>   v<-array(nmix3(g$x,g$y,g$z, .5,.5), c(40,40,40))
>   slices3d(vol1=v, main="View of a mixture of three tri-variate normals", col1=heat.colors(256))
Loading required namespace: tkrplot
No protocol specified
No protocol specified
Warning: loading Rplot failed
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: slices3d ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Packages suggested but not available for checking: 'mixAK', 'BRugs'
Package unavailable to check Rd xrefs: ‘mixAK’
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘mcmcr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘corrplot’ ‘sbm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
'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.
Missing or unexported objects:
  ‘rvest::html_element’ ‘rvest::html_elements’ ‘rvest::read_html’
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    libs  23.3Mb
prepare_Rd: <connection>:4: unexpected END_OF_INPUT '
'
Missing link or links in documentation object 'nonparamHankel.Rd':
  ‘[base]{plot}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      4.1Mb
    libs   1.6Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Package which this enhances but not available for checking: ‘pbdMPI’
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘MASS’ ‘RODBC’ ‘tcltk’ ‘tcltk2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fit.mixtNB: no visible global function definition for ‘dnbinom’
fit.mixtNB: no visible global function definition for ‘nlminb’
wald.test: no visible global function definition for ‘pnorm’
wald.test: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  dnbinom nlminb p.adjust pnorm
Consider adding
  importFrom("stats", "dnbinom", "nlminb", "p.adjust", "pnorm")
to your NAMESPACE file.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Namespaces in Imports field not imported from:
  ‘ashr’ ‘fdrtool’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/MKclass.Rcheck/00install.out’ for details.
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.
Package required and available but unsuitable version: ‘inline’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
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.
Namespace in Imports field not imported from: ‘reticulate’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘R6’
  All declared Imports should be used.
plot.mlbench: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/MLDAShiny2.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘DiscriMiner’ ‘MASS’ ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘klaR’
  ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
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.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/mlergm.Rcheck/00install.out’ for details.
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').
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Package suggested but not available for checking: ‘IlluminaHumanMethylation450kmanifest’
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.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/mlpack.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
listGenoToTable: no visible binding for global variable ‘dummy’
Undefined global functions or variables:
  dummy
Package suggested but not available for checking: ‘mlr3extralearners’
Namespaces in Imports field not imported from:
  ‘DT’ ‘data.table’ ‘e1071’ ‘mlr3’ ‘mlr3learners’ ‘mlr3measures’ ‘plyr’
  ‘purrr’ ‘ranger’ ‘readxl’ ‘shinyWidgets’ ‘shinyalert’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stats’ ‘stringr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
Namespaces in Imports field not imported from:
  ‘QuantPsyc’ ‘corrgram’ ‘dplyr’ ‘forecast’ ‘psych’ ‘shinyAce’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘QuantPsyc’ ‘corrgram’ ‘dplyr’ ‘forecast’ ‘psych’ ‘shinyAce’
  All declared Imports should be used.
installed size is 34.6Mb
  sub-directories of 1Mb or more:
    libs  34.2Mb
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    libs  21.6Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    images   1.1Mb
    shiny   14.5Mb
Namespaces in Imports field not imported from:
  ‘Cairo’ ‘DT’ ‘XML’ ‘caTools’ ‘data.table’ ‘dplyr’ ‘ggplot2’
  ‘htmltools’ ‘leaflet’ ‘lubridate’ ‘plotly’ ‘shinyjs’ ‘stringr’ ‘xts’
  ‘zoo’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘plotrix’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘doParallel’ ‘parallel’
  All declared Imports should be used.
Package suggested but not available for checking: ‘ALL’
Running examples in ‘MMDvariance-Ex.R’ failed
The error most likely occurred in:

> ### Name: gsMMD.v
> ### Title: Gene selection based on variances by using a mixture of marginal
> ###   distributions
> ### Aliases: gsMMD.v
> ### Keywords: classif
> 
> ### ** Examples
> 
>       t1 = proc.time()
>       library(ALL)
Error in library(ALL) : there is no package called ‘ALL’
Execution halted
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.
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').
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
Error(s) in re-building vignettes:
--- re-building ‘mnlogit.Rnw’ using Sweave
Package: mnlogit
Version: 1.2.6
Multinomial Logit Choice Models.
Scientific Computing Group, Sentrana Inc.
Loading required package: Formula
Loading required package: zoo

Attaching package: 'zoo'

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

    index

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

    as.Date, as.Date.numeric

Loading required package: lmtest

Attaching package: 'mlogit'

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

    hmftest, scoretest
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘e1071’ ‘nnet’ ‘shiny’ ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Package suggested but not available for checking: ‘doMPI’

Package which this enhances but not available for checking: ‘MoBPSmaps’
Namespace in Imports field not imported from: ‘sads’
  All declared Imports should be used.
Package required but not available: ‘doMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
Missing or unexported object: ‘rstanarm::posterior_epred’
Note: found 12 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘DALEX’ ‘DT’ ‘auditor’ ‘breakDown’ ‘drifter’ ‘svglite’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘lattice’
  All declared Imports should be used.
Note: found 18 marked Latin-1 strings
Namespaces in Imports field not imported from:
  ‘crayon’ ‘dials’ ‘glmnet’ ‘parsnip’ ‘progressr’ ‘utils’
  All declared Imports should be used.
Running ‘testthat.R’ [97s/96s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
      █
   1. ├─`%>%`(...) test-recursive.R:41:4
   2. ├─modeltime::recursive(...)
   3. └─modeltime.ensemble:::recursive.mdl_time_ensemble(...)
  ── Error (test-recursive.R:169:5): recursive ensemble 2 - panel / function / parsnip + workflow ──
  Error: long vectors not supported yet: ../../../../R-3.6.2/src/main/subassign.c:1814
  Backtrace:
      █
   1. ├─`%>%`(...) test-recursive.R:169:4
   2. ├─modeltime::recursive(...)
   3. └─modeltime.ensemble:::recursive.mdl_time_ensemble(...)
  
  [ FAIL 2 | WARN 2 | SKIP 0 | PASS 125 ]
  Error: Test failures
  Execution halted
Namespaces in Imports field not imported from:
  ‘crayon’ ‘dials’ ‘glue’ ‘parsnip’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'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.
Note: found 20578 marked UTF-8 strings
.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.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/MoEClust.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/molaR.Rcheck/00install.out’ for details.
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    doc  23.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘molaR_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: alphahull
Loading required package: rgl
Loading required package: Rvcg
Quitting from lines 58-60 (molaR_vignette.Rmd) 
Error: processing vignette 'molaR_vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘molaR_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      2.8Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
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  8.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    1.7Mb
    libs   4.6Mb
Note: found 16 marked UTF-8 strings
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    htmlwidgets  14.6Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  as.numeric(solution3[[1]]$summary[4, 2]) not equal to 17.
  1/1 mismatches
  [1] 2 - 17 == -15
  ── Failure (test_solutions.R:132:3): Multifurcating solution3 is accurate ──────
  as.numeric(solution3[[1]]$summary[5, 2]) not equal to 13.
  1/1 mismatches
  [1] 1 - 13 == -12
  ── Failure (test_solutions.R:133:3): Multifurcating solution3 is accurate ──────
  as.numeric(solution3[[1]]$summary[6, 2]) not equal to 2.
  1/1 mismatches
  [1] 3 - 2 == 1
  
  [ FAIL 44 | WARN 0 | SKIP 0 | PASS 52 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: ‘ztable’
  All declared Imports should be used.
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.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/morphomap.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Morpho.Rcheck/00install.out’ for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   6.4Mb
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.
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘international-mortality-tables-overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 302-305 (international-mortality-tables-overview.Rmd) 
Error: processing vignette 'international-mortality-tables-overview.Rmd' failed with diagnostics:
object 'EttlPagler.male' not found
--- failed re-building ‘international-mortality-tables-overview.Rmd’

--- re-building ‘using-the-mortalityTables-package.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
--- finished re-building ‘using-the-mortalityTables-package.Rmd’

SUMMARY: processing the following file failed:
  ‘international-mortality-tables-overview.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘ggformula’ ‘magrittr’ ‘rlang’
  All declared Imports should be used.
Note: found 7 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggridges’ ‘ggstance’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘NlcOptim’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs     3.0Mb
    raster   2.2Mb
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.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.4Mb
Package required and available but unsuitable version: ‘elevatr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘corpus.useR.2008.abstracts’
Package suggested but not available for checking: ‘CGHcall’
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.
Note: found 6 marked UTF-8 strings
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.
plot.binom.diag: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
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.
No protocol specified
No protocol specified
'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.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
ppersp: no visible global function definition for ‘colorRampPalette’
Undefined global functions or variables:
  colorRampPalette
Consider adding
  importFrom("grDevices", "colorRampPalette")
to your NAMESPACE file.
installed size is 65.4Mb
  sub-directories of 1Mb or more:
    libs  65.2Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
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.
plot.hmrfout: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  14.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Package required but not available: ‘WGCNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/mrregression.Rcheck/00install.out’ for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘UsageOfMrSGUIDE.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 119-120 (UsageOfMrSGUIDE.Rmd) 
Error: processing vignette 'UsageOfMrSGUIDE.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘UsageOfMrSGUIDE.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘msaR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 25-32 (msaR.Rmd) 
Error: processing vignette 'msaR.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘msaR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Note: found 26 marked UTF-8 strings
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').
Namespaces in Imports field not imported from:
  ‘MASS’ ‘moments’ ‘mvtnorm’
  All declared Imports should be used.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   3.9Mb
    libs   3.1Mb
installed size is 46.6Mb
  sub-directories of 1Mb or more:
    libs  46.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R   6.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘msir.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
Warning in normalizePath(f2) :
  path[1]="webshotd75b1bd36747.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotd75b1bd36747.png': No such file or directory
Quitting from lines 101-103 (msir.Rmd) 
Error: processing vignette 'msir.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘msir.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘datasets’ ‘grDevices’ ‘graphics’ ‘iterators’ ‘methods’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/MSQC.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs  17.6Mb
Running examples in ‘mssqlR-Ex.R’ failed
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.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/mStats.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/mstDIF.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
plot_bidev: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/mtk.Rcheck/00install.out’ for details.
'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.
Note: found 2 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘capushe’ ‘shiny’
  All declared Imports should be used.
Note: found 2632 marked UTF-8 strings
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
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').
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/mully.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘shape’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/MultBiplotR.Rcheck/00install.out’ for details.
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.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Packages suggested but not available for checking:
  'switchBox', 'BiocStyle', 'leukemiasEset'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/multiclassPairs.Rcheck/00install.out’ for details.
calculate_direction: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘cowsay’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ez’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
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 96.9Mb
  sub-directories of 1Mb or more:
    libs  96.7Mb
installed size is 105.3Mb
  sub-directories of 1Mb or more:
    doc    5.9Mb
    libs  98.3Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘rPorta’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
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  5.1Mb
  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.
Namespaces in Imports field not imported from:
  ‘stats’ ‘utils’
  All declared Imports should be used.
Note: found 6 marked UTF-8 strings
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 42.1Mb
  sub-directories of 1Mb or more:
    libs  42.0Mb
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').
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
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.
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.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/mvmesh.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
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.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘grDevices’ ‘knitr’ ‘utils’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘vignette_mvord2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: minqa
Loading required package: BB
Loading required package: ucminf
Loading required package: dfoptim
--- finished re-building ‘vignette_mvord2.Rmd’

--- re-building ‘vignette_mvord.Rnw’ using Sweave
Loading required package: minqa
Loading required package: BB
Loading required package: ucminf
Loading required package: dfoptim
Error: processing vignette 'vignette_mvord.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'vignette_mvord.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'vignette_mvord.Rnw'

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

Error: Vignette re-building failed.
Execution halted
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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘mvSLOUCH_Carnivorans.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 148-149 (mvSLOUCH_Carnivorans.Rmd) 
Error: processing vignette 'mvSLOUCH_Carnivorans.Rmd' failed with diagnostics:
Failed to open file /Users/urbanek/Library/Caches/R/rdryad/10_5061_dryad_77tm4.zip.
--- failed re-building ‘mvSLOUCH_Carnivorans.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
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.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/MXM.Rcheck/00install.out’ for details.
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
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.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
GNU make is a SystemRequirements.
Note: found 50 marked UTF-8 strings
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Namespaces in Imports field not imported from:
  ‘Kendall’ ‘perm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘mlr3learners’
  All declared Imports should be used.
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.
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    data     1.9Mb
    libs    23.3Mb
    models   1.1Mb
Note: found 47936 marked UTF-8 strings
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘lifecycle’ ‘lme4’ ‘methods’
  All declared Imports should be used.
Running ‘POSIXt.R’ [1s/1s]
  Running ‘data.frame.R’ [1s/1s]
  Running ‘simpleTests.R’ [1s/1s]
  Running ‘tinytest.R’ [4s/4s]
Running the tests in ‘tests/tinytest.R’ failed.
Last 13 lines of output:
   diff| The error message:
   diff| 'c++ exception (unknown reason)'
   diff| does not match pattern 'cannot parse nanoperiod'
  ----- FAILED[xcpt]: test_nanoperiod.R<40--40>
   call| expect_error(as.nanoperiod("1ym00:01:01"), "cannot parse nanoperiod")
   diff| The error message:
   diff| 'c++ exception (unknown reason)'
   diff| does not match pattern 'cannot parse nanoperiod'
  ----- FAILED[xcpt]: test_nanoperiod.R<41--41>
   call| expect_error(as.nanoperiod("1dm00:01:01"), "cannot parse nanoperiod")
   diff| The error message:
   diff| 'c++ exception (unknown reason)'
   diff| does not match pattern 'cannot parse nanoperiod'
  Error: 9 out of 1184 tests failed
  Execution halted
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/nat.nblast.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/nat.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/nat.templatebrains.Rcheck/00install.out’ for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    1.9Mb
Namespace in Imports field not imported from: ‘tuneR’
  All declared Imports should be used.
Note: found 140 marked UTF-8 strings
Package suggested but not available for checking: ‘DEXSeq’
Package unavailable to check Rd xrefs: ‘DEXSeq’
Package unavailable to check Rd xrefs: ‘sSeq’
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.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/NBShiny3.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
No protocol specified
No protocol specified
Namespace in Imports field not imported from: ‘bookdown’
  All declared Imports should be used.
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.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
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.
Namespaces in Imports field not imported from:
  ‘Deriv’ ‘compiler’ ‘stringi’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Running ‘testthat.R’ [19s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   5.         └─value[[3L]](cond)
  ── Error (test-CRAN-subject.R:21:3): capture_first_df does not use s arg for subject ──
  Error: problem for subject column x: Error in stop_for_subject(subject): subject has class=factor and length=1 but should be a character vector with length>0
  
  Backtrace:
      █
   1. └─nc::capture_first_df(subject, x = list(s = "\\S+$")) test-CRAN-subject.R:21:2
   2.   └─base::tryCatch(...)
   3.     └─base:::tryCatchList(expr, classes, parentenv, handlers)
   4.       └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   5.         └─value[[3L]](cond)
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 543 ]
  Error: Test failures
  Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.1Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.
Note: found 7332 marked UTF-8 strings
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Package required but not available: ‘ConsensusClusterPlus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘ez’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘igraph’ ‘rlang’ ‘tidyselect’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘downloader’ ‘jsonlite’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/neonstore.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘igraph’
  All declared Imports should be used.
clustConfigurations: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
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  9.4Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   5.5Mb
EnvInd: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Package suggested but not available for checking: ‘fastshp’
Note: found 1 marked UTF-8 string
.e.pi: no visible global function definition for ‘proportions’
Undefined global functions or variables:
  proportions
Running examples in ‘NetMix-Ex.R’ failed
The error most likely occurred in:

> ### Name: covFX
> ### Title: Generate estimated monadic covariate effects for estimated mmsbm
> ###   model
> ### Aliases: covFX
> 
> ### ** Examples
> 
> library(NetMix)
> ## Load datasets
> data("lazega_dyadic")
> data("lazega_monadic")
> ## Estimate model with 2 groups
> lazega_mmsbm <- mmsbm(SocializeWith ~ Coworkers,
+                       ~  Age,
+                       senderID = "Lawyer1",
+                       receiverID = "Lawyer2",
+                       nodeID = "Lawyer",
+                       data.dyad = lazega_dyadic,
+                       data.monad = lazega_monadic,
+                       n.blocks = 2,
+                       mmsbm.control = list(seed = 123, 
+                                            conv_tol = 1e-2, 
+                                            hessian = FALSE))
> 
> ## Compute effect of decreasing every lawyers' age by 10 years
> fx_list <- covFX(lazega_mmsbm, cov = "Age", shift = -10)
Error in proportions(pi_l[[1]], 2) : 
  could not find function "proportions"
Calls: covFX -> predict -> predict.mmsbm -> .e.pi
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.6Mb
Namespace in Imports field not imported from: ‘CoDiNA’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'limma', 'DESeq2', 'edgeR', 'org.Hs.eg.db'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
simulate.sisnetwork: no visible global function definition for ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
Note: found 2 marked Latin-1 strings
Malformed Description field: should contain one or more complete sentences.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/neuroim.Rcheck/00install.out’ for details.
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.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘xml2’
  All declared Imports should be used.
Note: found 318 marked UTF-8 strings
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Note: found 4485 marked UTF-8 strings
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.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘curl’ ‘mathjaxr’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘nflsimulator-basics.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 34-36 (nflsimulator-basics.Rmd) 
Error: processing vignette 'nflsimulator-basics.Rmd' failed with diagnostics:
level sets of factors are different
--- failed re-building ‘nflsimulator-basics.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
Running examples in ‘nhdplusTools-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_vaa_names
> ### Title: Available NHDPlusV2 Attributes
> ### Aliases: get_vaa_names
> 
> ### ** Examples
> 
> get_vaa_names()
didn't find data, downloading.
Error in curl::curl_fetch_disk(url, x$path, handle = handle) : 
  Failed to open file /Users/urbanek/Library/Caches/nhdplus-vaa/nhdplusVAA.fst.
Calls: get_vaa_names ... request_fetch -> request_fetch.write_disk -> <Anonymous>
Execution halted
Running ‘testthat.R’ [45s/83s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
      █
   1. └─nhdplusTools::discover_nhdplus_id(nldi_feature = nldi_nwis) test_get_functions.R:188:2
   2.   └─nhdplusTools::get_nldi_feature(nldi_feature)
   3.     └─dataRetrieval::findNLDI(origin = nldi_feature)
   4.       └─base::lapply(...)
   5.         └─dataRetrieval:::FUN(X[[i]], ...)
   6.           └─dataRetrieval:::get_nldi(...)
   7.             └─httr::RETRY("GET", url, times = 3, pause_cap = 60)
  
  [ FAIL 2 | WARN 0 | SKIP 28 | PASS 241 ]
  Error: Test failures
  In addition: Warning message:
  In i :
    closing unused connection 4 (https://waterservices.usgs.gov/nwis/site/?format=mapper&bBox=-119.845811,34.4145911,-119.845789,34.4146089&siteType=ST&siteStatus=active)
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘nhdplusTools.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘nhdplusTools.Rmd’

--- re-building ‘nhdplushr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in file(con, "w") :
  cannot open file '/Users/urbanek/Library/Caches/nhdplusTools__packages': No such file or directory
Quitting from lines 30-61 (nhdplushr.Rmd) 
Error: processing vignette 'nhdplushr.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘nhdplushr.Rmd’

--- re-building ‘plot_nhdplus.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘plot_nhdplus.Rmd’

--- re-building ‘point_indexing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in file(con, "w") :
  cannot open file '/Users/urbanek/Library/Caches/nhdplusTools__packages': No such file or directory
Quitting from lines 30-39 (point_indexing.Rmd) 
Error: processing vignette 'point_indexing.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘point_indexing.Rmd’

SUMMARY: processing the following files failed:
  ‘nhdplushr.Rmd’ ‘point_indexing.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    extdata   6.8Mb
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘sp’
  All declared Imports should be used.
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    CppCode        1.2Mb
    R              5.6Mb
    classic-bugs   1.5Mb
    include        5.5Mb
    libs          19.0Mb
    tests          1.9Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/NIPTeR.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Note: found 170 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rjson’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
Package suggested but not available for checking: ‘ALL’
Found the following significant warnings:
  Warning: package ‘AnnotationDbi’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/nlcv.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘geocode.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 127-133 (geocode.Rmd) 
Error: processing vignette 'geocode.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘geocode.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
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.
installed size is 22.0Mb
  sub-directories of 1Mb or more:
    libs  20.3Mb
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
Found the following significant warnings:
  clang-7: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
  DIRsubrout.c:505:10: warning: explicitly assigning value of variable of type 'integer' (aka 'int') to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/nloptr.Rcheck/00install.out’ for details.
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.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.2Mb
Namespace in Imports field not imported from: ‘deSolve’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘jsonlite’
  All declared Imports should be used.
Package suggested but not available for checking: ‘INLA’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
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: ‘doMPI’
Namespace in Imports field not imported from: ‘BiocManager’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/nmm.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘KernelKnn’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘uroot’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘multicool’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lwgeom’ ‘s2’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/NNS.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘hurricaneexposuredata’
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘choroplethr’ ‘choroplethrMaps’ ‘data.table’ ‘forcats’
  ‘hurricaneexposure’ ‘plyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘crayon’ ‘digest’ ‘hash’
  All declared Imports should be used.
Running examples in ‘node2vec-Ex.R’ failed
The error most likely occurred in:

> ### Name: node2vecR
> ### Title: Algorithmic Framework for Representational Learning on Graphs
> ### Aliases: node2vecR
> 
> ### ** Examples
> 
> #Parameters can be customized as needed
> data(gene_edges)
> use_data<-gene_edges
> emb<-node2vecR(use_data,p=2,q=1,num_walks=5,walk_length=5,dim=10)
[1] "The normalized probabilities finished."
[1] 1
Warning in `[[<-.factor`(`*tmp*`, i, value = 0.0909090909090909) :
  invalid factor level, NA generated
Warning in `[[<-.factor`(`*tmp*`, i, value = 0.181818181818182) :
  invalid factor level, NA generated
Warning in `[[<-.factor`(`*tmp*`, i, value = 0.181818181818182) :
  invalid factor level, NA generated
Warning in `[[<-.factor`(`*tmp*`, i, value = 0.181818181818182) :
  invalid factor level, NA generated
Warning in `[[<-.factor`(`*tmp*`, i, value = 0.181818181818182) :
  invalid factor level, NA generated
Warning in `[[<-.factor`(`*tmp*`, i, value = 0.181818181818182) :
  invalid factor level, NA generated
Error in if (q[i] > 1) { : missing value where TRUE/FALSE needed
Calls: node2vecR -> get_alias_1node_edge -> alias_setup
Execution halted
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.
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
Running examples in ‘noisyr-Ex.R’ failed
The error most likely occurred in:

> ### Name: calculate_distance_matrices_transcript
> ### Title: Calcualte the distance matrices using the BAM files
> ### Aliases: calculate_distance_matrices_transcript
> 
> ### ** Examples
> 
> bams <- rep(system.file("extdata", "ex1.bam", package="Rsamtools", mustWork=TRUE), 2)
> genes <- data.frame("id" = 1:2,
+                     "gene_id" = c("gene1", "gene2"),
+                     "seqid" = c("seq1", "seq2"),
+                     "start" = 1,
+                     "end" = 1600)
> obj <- calculate_distance_matrices_transcript(
+   bams = bams,
+   genes = genes,
+   mapq.unique = 99
+ )
Calculating distances...
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘GenomeInfoDbData’
Calls: calculate_distance_matrices_transcript ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘e1071’ ‘pROC’ ‘purrr’ ‘randomForest’ ‘rlang’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/nonlinearTseries.Rcheck/00install.out’ for details.
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.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘e1071’ ‘glmnet’
  All declared Imports should be used.
Note: found 3 marked UTF-8 strings
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
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.
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.
.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:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/NPCirc.Rcheck/00install.out’ for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
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.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘CAMAN’ ‘Hmisc’ ‘latexpdf’ ‘spatstat’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘rts’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
nps.test: no visible global function definition for ‘qnorm’
nps.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
'library' or 'require' call to ‘parallel’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
npst: no visible global function definition for ‘mclapply’
Undefined global functions or variables:
  mclapply
Package suggested but not available for checking: ‘PMA’
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.
Namespace in Imports field not imported from: ‘xgboost’
  All declared Imports should be used.
.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.
Note: found 1 marked UTF-8 string
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Rdpack’ ‘base’ ‘graphics’ ‘parallel’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘forecast’ ‘rlang’ ‘tsibble’ ‘viridis’
  All declared Imports should be used.
installed size is 22.0Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs  16.1Mb
Package suggested but not available for checking: ‘BiocStyle’
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  7.0Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
Note: found 6409 marked UTF-8 strings
Note: found 1 marked UTF-8 string
Note: found 7284 marked UTF-8 strings
Package required and available but unsuitable version: ‘methods’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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').
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.
Namespaces in Imports field not imported from:
  ‘ape’ ‘bit64’ ‘knitr’ ‘magrittr’
  All declared Imports should be used.
Note: found 6 marked UTF-8 strings
Namespace in Imports field not imported from: ‘units’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.5Mb
    test_files   4.2Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/OceanView.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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 12.8Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    data   1.0Mb
    doc    2.0Mb
    help   3.4Mb
    libs   3.2Mb
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/OCNet.Rcheck/00install.out’ for details.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
odds.n.ends: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘graphics’
  All declared Imports should be used.
installed size is 86.2Mb
  sub-directories of 1Mb or more:
    libs  85.7Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
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.
Note: found 2444 marked UTF-8 strings
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.
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Expected match: "The length value"
  Actual message: "c++ exception (unknown reason)"
  
  ── 2. Failure: OLC encoding throws an error with odd-numbered requested lengths 
  `x` threw an error with unexpected message.
  Expected match: "The length value"
  Actual message: "c++ exception (unknown reason)"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 34 SKIPPED: 1 FAILED: 2
  1. Failure: OLC encoding throws an error with odd-numbered requested lengths below 8 (@test_encoding.R#20) 
  2. Failure: OLC encoding throws an error with odd-numbered requested lengths below 8 (@test_encoding.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gt’
  All declared Imports should be used.
installed size is 35.2Mb
  sub-directories of 1Mb or more:
    libs  34.3Mb
Namespaces in Imports field not imported from:
  ‘bayesplot’ ‘ggplot2’
  All declared Imports should be used.
GNU make is a SystemRequirements.
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.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘fs’ ‘pdp’
  All declared Imports should be used.
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
run_core_mtx_algo : <anonymous>: no visible binding for global variable
  ‘list2DF’
Undefined global functions or variables:
  list2DF
GNU make is a SystemRequirements.
Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  Writing CSC data.
  Writing CSR data.
  
  Writing CSC data.
  Writing CSR data.
  
  Writing CSC data.
  Writing CSR data.
  
  Writing CSC data.
  Writing CSR data.
  Error in list2DF(.) : could not find function "list2DF"
  Calls: test_check ... create_ondisc_matrix_from_mtx -> run_core_mtx_algo -> lapply -> FUN -> %>%
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial_odm_class.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 43-48 (tutorial_odm_class.Rmd) 
Error: processing vignette 'tutorial_odm_class.Rmd' failed with diagnostics:
could not find function "list2DF"
--- failed re-building ‘tutorial_odm_class.Rmd’

--- re-building ‘tutorial_other_classes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 30-45 (tutorial_other_classes.Rmd) 
Error: processing vignette 'tutorial_other_classes.Rmd' failed with diagnostics:
could not find function "list2DF"
--- failed re-building ‘tutorial_other_classes.Rmd’

SUMMARY: processing the following files failed:
  ‘tutorial_odm_class.Rmd’ ‘tutorial_other_classes.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘R6’ ‘safer’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/onemap.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
plot.BayesCP: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   1.7Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
Note: found 32 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘randomForest’ ‘ranger’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘digest’ ‘dplyr’ ‘miniUI’ ‘text2vec’
  All declared Imports should be used.
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 ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/OOS.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/OpenCL.Rcheck/00install.out’ for details.
No protocol specified
Missing or unexported object: 'tools::R_user_dir'
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
Note: found 4 marked UTF-8 strings
GNU make is a SystemRequirements.
installed size is 25.7Mb
  sub-directories of 1Mb or more:
    libs   15.9Mb
    share   9.7Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   6.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
Note: found 2518 marked UTF-8 strings
Error(s) in re-building vignettes:
  ...
--- re-building ‘openland_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'https://zenodo.org/record/3685230/files/SaoLourencoBasin.rda?download=1'
Content type 'application/octet-stream' length 5309066 bytes (5.1 MB)
==================================================
downloaded 5.1 MB

Quitting from lines 264-269 (openland_vignette.Rmd) 
Error: processing vignette 'openland_vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘openland_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/openMSE.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘Rmpi’
installed size is 197.9Mb
  sub-directories of 1Mb or more:
    R         2.6Mb
    libs    187.6Mb
    models    4.7Mb
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’
Namespaces in Imports field not imported from:
  ‘formattable’ ‘rintrojs’ ‘shinyBS’ ‘shinyFeedback’ ‘shinyWidgets’
  ‘shinycssloaders’ ‘shinydashboard’ ‘shinydashboardPlus’ ‘shinyjs’
  ‘shinythemes’ ‘splines’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/OpenRepGrid.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘BiocStyle’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/OpenSpecy.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   3.1Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.0Mb
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').
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Missing or unexported object: ‘RcppSimdJson::fparse’
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      4.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/opitools.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'gurobi', 'Rsymphony'
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
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.
Package required but not available: ‘rpanel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'GO.db', 'org.At.tair.db'
Malformed Title field: should not end in a period.
Package which this enhances but not available for checking: ‘gurobi’
No protocol specified
plot.W_base_object: no visible global function definition for ‘plot’
plot.optimal_rerandomization_obj: no visible global function definition
  for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘geometry’
  All declared Imports should be used.
print.optimbase: no visible global function definition for ‘str’
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/optiSel.Rcheck/00install.out’ for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.1Mb
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/optiSolve.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘boot’ ‘splines’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘optparse.Rrst’ using knitr
sh: +RTS: command not found
Warning in system(command) : error in running command
Error: processing vignette 'optparse.Rrst' failed with diagnostics:
pandoc document conversion failed with error 127
--- failed re-building ‘optparse.Rrst’

SUMMARY: processing the following file failed:
  ‘optparse.Rrst’

Error: Vignette re-building failed.
Execution halted
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.
Package which this enhances but not available for checking: ‘graph’
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.
'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.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Packages suggested but not available for checking: 'IsoGene', 'Biobase'
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘gridExtra’ ‘scales’ ‘tools’
  All declared Imports should be used.
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.
File ‘OriGen/libs/OriGen.so’:
  Found ‘__gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__gfortran_st_read’, possibly from ‘read’ (Fortran)
    Object: ‘OriGen.o’

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.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
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.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    nifti   3.8Mb
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
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.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/orthoDr.Rcheck/00install.out’ for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
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.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tibble’
  All declared Imports should be used.
plotPower: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
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.
Note: found 80 marked UTF-8 strings
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc    4.3Mb
    libs   5.8Mb
Note: found 263 marked UTF-8 strings
No protocol specified
No protocol specified
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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  9.2Mb
  sub-directories of 1Mb or more:
    doc   7.8Mb
Package suggested but not available for checking: ‘Rcplex’
Namespaces in Imports field not imported from:
  ‘R6’ ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘quantreg’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘Rcpp_API.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘Rcpp_API.Rmd’

--- re-building ‘customisation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘customisation.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 185-198 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘introduction.Rmd’

--- re-building ‘overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘overview.Rmd’

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

Error: Vignette re-building failed.
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.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
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.
Namespaces in Imports field not imported from:
  ‘jsonlite’ ‘praise’ ‘withr’
  All declared Imports should be used.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
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.
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘graph_packing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘graph_packing.Rmd’

--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘intro.Rmd’

--- re-building ‘progressive_packing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 204-226 (progressive_packing.Rmd) 
Error: processing vignette 'progressive_packing.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘progressive_packing.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
Namespaces in Imports field not imported from:
  ‘flexsurv’ ‘nlme’ ‘tibble’ ‘tidyverse’ ‘tm’
  All declared Imports should be used.
plot_return_residual_cox: no visible global function definition for
  ‘plot’
plot_return_residual_survival: no visible global function definition
  for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Running examples in ‘packDAMipd-Ex.R’ failed
The error most likely occurred in:

> ### Name: microcosting_liquids_long
> ### Title: Function to estimate the cost of liquids when IPD is in long
> ###   format
> ### Aliases: microcosting_liquids_long
> 
> ### ** Examples
> 
> med_costs_file <- system.file("extdata", "average_unit_costs_med_brand.csv",
+ package = "packDAMipd")
> data_file <- system.file("extdata", "medication_liq.xlsx",
+ package = "packDAMipd")
> ind_part_data <- load_trial_data(data_file)
> med_costs <- load_trial_data(med_costs_file)
> conv_file <- system.file("extdata", "Med_calc.xlsx",
+ package = "packDAMipd")
> table <- load_trial_data(conv_file)
> names <- colnames(ind_part_data)
> ending <- length(names)
> ind_part_data_long <- tidyr::gather(ind_part_data, measurement, value,
+ names[2]:names[ending], factor_key = TRUE)
> the_columns <- c("measurement", "value")
> res <- microcosting_liquids_long(the_columns,
+ ind_part_data_long = ind_part_data_long,
+ name_med = "liq_name", brand_med =  NULL, dose_med = "liq_strength",
+ unit_med = NULL, bottle_size = "liq_bottle_size",bottle_size_unit = NULL,
+ bottle_lasts = "liq_lasts",bottle_lasts_unit = NULL,preparation_dose = NULL,
+ preparation_unit = NULL,timeperiod = "4 months",unit_cost_data = med_costs,
+ unit_cost_column = "UnitCost",cost_calculated_per = "Basis",
+ strength_column = "Strength",list_of_code_names = NULL,
+ list_of_code_brand = NULL,list_of_code_dose_unit = NULL,
+ list_of_code_bottle_size_unit = NULL,list_of_code_bottle_lasts_unit = NULL,
+ list_preparation_dose_unit = NULL,eqdose_covtab = table,
+ basis_strength_unit = NULL)
Error in microcosting_liquids_wide(ind_part_data_wide, name_med, brand_med,  : 
  The used dosage is not in costing table
Calls: microcosting_liquids_long -> microcosting_liquids_wide
Execution halted
Running ‘testthat.R’ [72s/72s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ans$brand not equal to "a".
  'current' is not a factor
  ── Failure (test-help_cost_analysis_functions.R:15:4): testing to get the subset of data compared to list of string ──
  ans$brand not equal to "a".
  'current' is not a factor
  ── Failure (test-help_cost_analysis_functions.R:24:3): testing to get the subset of data compared to list of string ──
  ans$xx not equal to c("bb", "aa").
  'current' is not a factor
  ── Failure (test-help_parameter_estimation_survival.R:94:3): testing creating a new dataset based on given one ──
  unique(new$check) not equal to "no".
  'current' is not a factor
  
  [ FAIL 9 | WARN 0 | SKIP 0 | PASS 994 ]
  Error: Test failures
  Execution halted
[,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'
Namespace in Imports field not imported from: ‘ape’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pacviz.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘optparse’
  All declared Imports should be used.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
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.
Namespaces in Imports field not imported from:
  ‘network’ ‘scales’ ‘sna’
  All declared Imports should be used.
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.
Packages suggested but not available for checking:
  'GO.db', 'org.Dr.eg.db', 'org.Hs.eg.db', 'org.Mm.eg.db', 'p2data',
  'scde'
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   5.6Mb
my.heatmap2: no visible global function definition for ‘plot’
score.cells.puram: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Package suggested but not available for checking: ‘DECIPHER’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pagoo.Rcheck/00install.out’ for details.
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.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
Package which this enhances but not available for checking: ‘CorShrink’
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘lattice’ ‘vegan’
  Please remove these calls from your code.
Note: found 1 marked UTF-8 string
Note: found 9 marked UTF-8 strings
Namespace in Imports field not imported from: ‘iterators’
  All declared Imports should be used.
No protocol specified
Note: found 34 marked UTF-8 strings
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
No protocol specified
No protocol specified
No protocol specified
Namespaces in Imports field not imported from:
  ‘rjson’ ‘rstudioapi’
  All declared Imports should be used.
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
No protocol specified
  No protocol specified
Running ‘testthat.R’ [12s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Warning message:
  In fun(libname, pkgname) : couldn't connect to display ":0"
  > 
  > test_check("PAMpal")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-processPps.R:64:5): Test process time ─────────────────────────
  id(exTime[[1]]) not equal to grp$id.
  Types not compatible: character is not integer
  ── Failure (test-workStudy.R:79:5): Test working with AcousticStudy object ─────
  species(exData[[1]])$id not equal to "c".
  'current' is not a factor
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 119 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: ‘smoothmest’
  All declared Imports should be used.
Package required but not available: ‘GO.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 57.0Mb
  sub-directories of 1Mb or more:
    doc    9.3Mb
    libs  47.3Mb
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
--- re-building ‘PandemicLP.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 28-30 (PandemicLP.Rmd) 
Error: processing vignette 'PandemicLP.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘PandemicLP.Rmd’

--- re-building ‘PandemicLP_SumRegions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'http://github.com/CovidLP/PandemicLP/raw/master/temp/PandemicLP_SumRegions.rda'
Content type 'application/octet-stream' length 13851069 bytes (13.2 MB)
==================================================
downloaded 13.2 MB

trying URL 'http://github.com/CovidLP/PandemicLP/raw/master/temp/PandemicLP_SumRegions.rda'
Content type 'application/octet-stream' length 13851069 bytes (13.2 MB)
==================================================
downloaded 13.2 MB

Quitting from lines 172-175 (PandemicLP_SumRegions.Rmd) 
Error: processing vignette 'PandemicLP_SumRegions.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘PandemicLP_SumRegions.Rmd’

SUMMARY: processing the following files failed:
  ‘PandemicLP.Rmd’ ‘PandemicLP_SumRegions.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘evals.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-19 (evals.Rmd) 
Error: processing vignette 'evals.Rmd' failed with diagnostics:
package or namespace load failed for 'futile.logger' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'formatR'
--- failed re-building ‘evals.Rmd’

--- re-building ‘knitr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘knitr.Rmd’

--- re-building ‘pander.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

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

    format.pval, units

--- finished re-building ‘pander.Rmd’

--- re-building ‘pandoc_table.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘pandoc_table.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Running examples in ‘PantaRhei-Ex.R’ failed
The error most likely occurred in:

> ### Name: check_balance
> ### Title: Checks the mass balance of the flows involved
> ### Aliases: check_balance
> 
> ### ** Examples
> 
> nodes <- data.frame(ID=c("A","B","C"), x=1:3, y=1:3, dir=c("right","right","stock"))
> flows <- data.frame(from=c("A","B"), to=c("B","C"), quantity=c(10,10))
> check_balance(nodes,flows)
Error in nchar(nodes$ID) : 'nchar()' requires a character vector
Calls: check_balance -> parse_nodes
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘panta-rhei.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 51-70 (panta-rhei.Rmd) 
Error: processing vignette 'panta-rhei.Rmd' failed with diagnostics:
operator '/' not meaningful for units
--- failed re-building ‘panta-rhei.Rmd’

SUMMARY: processing the following file failed:
  ‘panta-rhei.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    extdata   8.8Mb
Namespaces in Imports field not imported from:
  ‘caret’ ‘geoR’ ‘gstat’ ‘randomForest’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
Packages suggested but not available for checking: 'pcalg', 'Rgraphviz'
Running examples in ‘ParallelPC-Ex.R’ failed
The error most likely occurred in:

> ### Name: IDA_parallel
> ### Title: Estimate Total Causal Effects using the IDA_parallel Algorithm
> ### Aliases: IDA_parallel
> 
> ### ** Examples
> 
> ##########################################
> ## Using IDA_parallel without mem.efficeient
> ##########################################
> library(bnlearn)

Attaching package: ‘bnlearn’

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

    sigma

> library(pcalg)
Error in library(pcalg) : there is no package called ‘pcalg’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-parallelplot.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 25-26 (introduction-to-parallelplot.Rmd) 
Error: processing vignette 'introduction-to-parallelplot.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction-to-parallelplot.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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 suggested but not available for checking: ‘M3C’
Namespace in Imports field not imported from: ‘survey’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘tibble’
  All declared Imports should be used.
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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-parcoords-.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 27-30 (introduction-to-parcoords-.Rmd) 
Error: processing vignette 'introduction-to-parcoords-.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction-to-parcoords-.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
Note: found 16 marked UTF-8 strings
Package suggested but not available for checking: ‘Rsymphony’
Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/parseRPDR.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
Running ‘tests.R’ [11s/11s]
Running the tests in ‘tests/tests.R’ failed.
Last 13 lines of output:
  \begin{tabular}{crrr}
   & \multicolumn{3}{c}{NULL: Random Walk} \\ 
    & \multicolumn{1}{c}{p=0.01} & \multicolumn{1}{c}{p=0.05} & \multicolumn{1}{c}{p=0.10}\\ 
  \hline 
  n=50   &      -4.7  &      -2.9  &      -2.2  \\ 
  n=100   &      -4.7  &      -3.0  &      -2.2  \\ 
  n=250   &      -4.6  &      -3.0  &      -2.2  \\ 
  n=500   &      -4.7  &      -3.2  &      -2.4  \\ 
  n=1000   &      -4.8  &      -3.1  &      -2.4  \\ 
  n=2500   &      -4.8  &      -3.1  &      -2.4  \\ 
  \end{tabular}
  
  
  Error in test_par(TRUE) : ERRORS! 1 tests failed
  Execution halted
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.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
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.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.9Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘goftest’ ‘tidyverse’
  All declared Imports should be used.
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.
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  as.character(func_out_date) not equal to test_dates$Ans[curr_row].
  Types not compatible: character is not integer
  ── Failure (test-utility-funcs.R:34:5): utility function: get_date_tues ────────
  as.character(func_out_date) not equal to test_dates$Ans[curr_row].
  Types not compatible: character is not integer
  ── Failure (test-utility-funcs.R:34:5): utility function: get_date_tues ────────
  as.character(func_out_date) not equal to test_dates$Ans[curr_row].
  Types not compatible: character is not integer
  ── Failure (test-utility-funcs.R:34:5): utility function: get_date_tues ────────
  as.character(func_out_date) not equal to test_dates$Ans[curr_row].
  Types not compatible: character is not integer
  
  [ FAIL 5 | WARN 0 | SKIP 0 | PASS 6 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: ‘logger’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pathfindR.data.Rcheck/00install.out’ for details.
Packages required but not available: 'pathfindR.data', 'org.Hs.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘glue’ ‘logging’ ‘purrr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
Checking should be performed on sources prepared by ‘R CMD build’.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/patternize.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Packages required but not available: 'jetset', 'Mfuzz', 'WGCNA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
No protocol specified
No protocol specified
Packages required but not available: 'pbdMPI', 'pbdSLAP'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘pbdPROF’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pbdMPI.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pbdPROF.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘ade4’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘pbdMPI’
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
'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.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc        1.3Mb
    examples   1.7Mb
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pca3d.Rcheck/00install.out’ for details.
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  5.6Mb
  sub-directories of 1Mb or more:
    extdata   2.7Mb
    libs      2.2Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pander’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pcaL1.Rcheck/00install.out’ for details.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   7.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Namespace in Imports field not imported from: ‘fda’
  All declared Imports should be used.
PCDReg.wf: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  optimize
Consider adding
  importFrom("stats", "optimize")
to your NAMESPACE file.
installed size is 106.8Mb
  sub-directories of 1Mb or more:
    doc     2.9Mb
    libs  103.4Mb
GNU make is a SystemRequirements.
Found the following significant warnings:
  Warning: package ‘AnnotationDbi’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/PCGSE.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pchc.Rcheck/00install.out’ for details.
installed size is 35.6Mb
  sub-directories of 1Mb or more:
    libs  34.4Mb
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/PCRedux.Rcheck/00install.out’ for details.
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  9.3Mb
  sub-directories of 1Mb or more:
    doc   8.1Mb
Note: found 11 marked UTF-8 strings
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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 18.5Mb
  sub-directories of 1Mb or more:
    libs    6.5Mb
    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').
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘car’ ‘sandwich’
  All declared Imports should be used.
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.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Error(s) in re-building vignettes:
--- re-building ‘pdxTrees-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

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

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshotf78651f8a951.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotf78651f8a951.png': No such file or directory
Quitting from lines 93-133 (pdxTrees-vignette.Rmd) 
Error: processing vignette 'pdxTrees-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘pdxTrees-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Note: found 118 marked UTF-8 strings
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.
Running examples in ‘pedbuildr-Ex.R’ failed
The error most likely occurred in:

> ### Name: reconstruct
> ### Title: Pedigree reconstruction
> ### Aliases: reconstruct
> 
> ### ** Examples
> 
> #-----------------
> # Example 1: Trio
> #-----------------
> 
> data(trioData)
> 
> x = as.ped(trioData, locusAttributes = "snp-12")
> summary(x)
List of 3 singletons.
Labels: 1 (male), 2 (male), 3 (male).
100 attached markers.
> 
> res = reconstruct(x, inferPO = TRUE, age = "1 > 2", linearInb = FALSE)
Pairwise estimation:
  PO: 2-2 
  non-PO: 1-2 

Pedigree parameters:
  ID labels: 1, 2, 3
  Sex: 1, 1, 1
  Extra: parents
  Age info: 1>2
  Known PO: 2-2
  Known non-PO: 1-2
  No children: -
  Connected only: TRUE
  Symmetry filter: TRUE
  Linear inbreeding: FALSE

Building pedigree list:
  Undirected adjacency matrices: 4 
  Directed adjacency matrices: 0 
  After adding parents: 0 
  Connected solutions: 0 
Error: Empty pedigree list
Execution halted
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘RcppArmadillo’ ‘ggplot2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
AssoTestProc: no visible global function definition for ‘rbinom’
AssoTestProc: no visible global function definition for ‘princomp’
AssoTestProc: no visible global function definition for ‘loadings’
AssoTestProc: no visible global function definition for ‘lm’
CNVtypeAnay: no visible global function definition for ‘cov’
ClusProc: no visible global function definition for ‘princomp’
ClusProc: no visible global function definition for ‘prcomp’
ClusProc0: no visible global function definition for ‘kmeans’
ClusProc0: no visible global function definition for ‘cov’
Inde: no visible global function definition for ‘lm’
Inde: no visible global function definition for ‘var’
STE: no visible global function definition for ‘pchisq’
STIM: no visible global function definition for ‘cor’
STIM: no visible global function definition for ‘pchisq’
plot.clust: no visible global function definition for ‘princomp’
plot.clust: no visible global function definition for ‘loadings’
plot.clust: no visible global function definition for ‘qplot’
plot.clust: no visible global function definition for ‘geom_histogram’
plot.clust: no visible global function definition for ‘aes_string’
plot.clust: no visible global function definition for ‘barplot’
plot.clust: no visible global function definition for ‘title’
plot.clust: no visible global function definition for ‘mtext’
plot.clust: no visible global function definition for ‘text’
Undefined global functions or variables:
  aes_string barplot cor cov geom_histogram kmeans lm loadings mtext
  pchisq prcomp princomp qplot rbinom text title var
Consider adding
  importFrom("graphics", "barplot", "mtext", "text", "title")
  importFrom("stats", "cor", "cov", "kmeans", "lm", "loadings", "pchisq",
             "prcomp", "princomp", "rbinom", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
blup: no visible global function definition for ‘model.matrix’
blup: no visible global function definition for ‘model.frame’
blup: no visible global function definition for ‘read.table’
calcG: no visible global function definition for ‘as’
gblup: no visible global function definition for ‘model.matrix’
gblup: no visible global function definition for ‘model.frame’
Undefined global functions or variables:
  as model.frame model.matrix read.table
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "model.frame", "model.matrix")
  importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
No protocol specified
No protocol specified
Note: found 7240 marked UTF-8 strings
Running examples in ‘pegas-Ex.R’ failed
The error most likely occurred in:

> ### Name: cophenetic.haploNet
> ### Title: Cophenetic Matrix on Haplotype Networks
> ### Aliases: cophenetic.haploNet
> ### Keywords: manip
> 
> ### ** Examples
> 
> example(mst)

mst> data(woodmouse)

mst> d <- dist.dna(woodmouse, "n")

mst> (r <- mst(d))
Haplotype network with:
  15 haplotypes
  14 links
  link lengths between 2 and 14 steps

Use print.default() to display all elements.

mst> plot(r)

mst> ## a case where the RMST and the MJN are identical:
mst> x <- c(">A", "TAAGTGCAT", ">B", "TAAATGCAT", ">C", "TAGGTGCAT", ">D", "TAAGTACAT",
mst+        ">E", "TAAGTGTAT", ">F", "TAAGTACAC", ">G", "TAAGTACGT", ">H", "CAAGTACAC",
mst+        ">I", "CAAGCACAC", ">J", "CAAGTACAT", ">K", "CGAGTACAT", ">L", "TAAGTACGC",
mst+        ">M", "CAAGCACAT")

mst> fl <- tempfile()

mst> cat(x, file = fl, sep = "\n")

mst> x <- read.dna(fl, "f")

mst> tr <- rmst(dist.dna(x, "n"))

Iteration: 1   Number of links: 12
Iteration: 2   Number of links: 15
Iteration: 3   Number of links: 15
Iteration: 4   Number of links: 15
Iteration: 5   Number of links: 15
Iteration: 6   Number of links: 15

mst> ts <- mjn(x)
Adding median vectors:Error in class(res) <- clx : 
  invalid to set the class to matrix unless the dimension attribute is of length 2 (was 0)
Calls: example ... withVisible -> eval -> eval -> mjn -> funVariableCol -> latag2n
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/PELVIS.Rcheck/00install.out’ for details.
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.
Package suggested but not available for checking: ‘globaltest’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Namespace in Imports field not imported from: ‘lhs’
  All declared Imports should be used.
Package suggested but not available for checking: ‘ptmixed’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pencal.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 47.2Mb
  sub-directories of 1Mb or more:
    libs  46.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/percentiles.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
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’
Namespace in Imports field not imported from: ‘rms’
  All declared Imports should be used.
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').
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/PERMANOVA.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/permGPU.Rcheck/00install.out’ for details.
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  7.6Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
Malformed Description field: should contain one or more complete sentences.
Note: found 63777 marked UTF-8 strings
Note: found 1 marked UTF-8 string
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc    6.3Mb
    help   1.2Mb
    libs   3.7Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.8Mb
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.
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.
Namespaces in Imports field not imported from:
  ‘jsonlite’ ‘memoise’
  All declared Imports should be used.
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  5.5Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.1Mb
Running examples in ‘phonfieldwork-Ex.R’ failed
The error most likely occurred in:

> ### Name: srt_to_df
> ### Title: Subtitles .srt file to dataframe
> ### Aliases: srt_to_df
> 
> ### ** Examples
> 
> srt_to_df(system.file("extdata", "test.srt", package = "phonfieldwork"))
Error in strsplit(result[, "times"], " --> ") : non-character argument
Calls: srt_to_df -> cbind -> do.call -> strsplit
Execution halted
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ● On CRAN (6)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-srt-to-df.R:2:3): srt_to_df ─────────────────────────────────────
  Error: non-character argument
  Backtrace:
      █
   1. └─phonfieldwork::srt_to_df(system.file("extdata", "test.srt", package = "phonfieldwork")) test-srt-to-df.R:2:2
   2.   ├─base::cbind(...)
   3.   ├─base::do.call(rbind, strsplit(result[, "times"], " --> "))
   4.   └─base::strsplit(result[, "times"], " --> ")
  
  [ FAIL 1 | WARN 6 | SKIP 6 | PASS 36 ]
  Error: Test failures
  Execution halted
Note: found 1 marked Latin-1 string
Packages required and available but unsuitable versions:
  'graphics', 'grDevices', 'stats', 'utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 37.2Mb
  sub-directories of 1Mb or more:
    libs  36.4Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/PHSMM.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘Advanced_Usage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="webshotc4dc454c7107.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotc4dc454c7107.png': No such file or directory
Quitting from lines 20-27 (Advanced_Usage.Rmd) 
Error: processing vignette 'Advanced_Usage.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Advanced_Usage.Rmd’

--- re-building ‘Basic_Use.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 30-32 (Basic_Use.Rmd) 
Error: processing vignette 'Basic_Use.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Basic_Use.Rmd’

SUMMARY: processing the following files failed:
  ‘Advanced_Usage.Rmd’ ‘Basic_Use.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/phylolm.Rcheck/00install.out’ for details.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘rgeos’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘intergraph’
  All declared Imports should be used.
Package suggested but not available for checking: ‘INLA’
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   9.6Mb
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.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Namespace in Imports field not imported from: ‘FrF2.catlg128’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/piecewiseSEM.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘debugme.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘debugme.Rmd’

--- re-building ‘extending.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘extending.Rmd’

--- re-building ‘printing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 64-65 (printing.Rmd) 
Error: processing vignette 'printing.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘printing.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 2048 marked UTF-8 strings
Note: found 36 marked UTF-8 strings
Running examples in ‘pipenostics-Ex.R’ failed
The error most likely occurred in:

> ### Name: m325tracebw
> ### Title: Minenergo-325. Trace backwards thermal-hydraulic regime for
> ###   district heating network
> ### Aliases: m325tracebw
> 
> ### ** Examples
> 
> # It is possible to run without specification of argument values:
> m325tracebw()

2021-04-09 13:14:35 m325tracebw | start backward tracing; segments 1;
2021-04-09 13:14:35 m325tracebw | start job; job 0;
2021-04-09 13:14:35 m325tracebw | now process; 1 node(s); [7]
2021-04-09 13:14:35 m325tracebw | trace temperature;;
2021-04-09 13:14:35 m325tracebw | trace pressure;;
2021-04-09 13:14:35 m325tracebw | finish job; job 0; processed node(s) 1
2021-04-09 13:14:35 m325tracebw | finish backward tracing;;
       node  trace backward aggregation temperature pressure consumption job
1         7 sensor     TRUE    identity          70 0.588399          20   0
span      7 sensor     TRUE        span           0 0.000000          20   0
median    7 sensor     TRUE      median          70 0.588399          20   0
mean      7 sensor     TRUE        mean          70 0.588399          20   0
> 
> # Get isomorphic representation of district heating network graph:
> nx <- pipenostics::m325testbench
> nx$d <- 1e3*nx$d  # convert [m] to [mm]
> 
> # When tracing large network graphs put screen log to file
> output <- do.call("m325tracebw", c(as.list(nx), verbose = TRUE))

2021-04-09 13:14:35 m325tracebw | start backward tracing; segments 26;
2021-04-09 13:14:35 m325tracebw | start job; job 0;
2021-04-09 13:14:35 m325tracebw | now process; 13 node(s); [1,10,15,17,19,2,21,24,25,26,3,7,9]Error in m325tracebw(sender = c(4L, 4L, 5L, 8L, 6L, 8L, 6L, 11L, 6L, 11L,  : 
  Assertion on 'all(acceptor[is_processed_pipe] %in% regime[["node"]]) && all(regime[["node"]] %in% acceptor[is_processed_pipe])' failed: Must be TRUE.
Calls: do.call ... m325tracebw -> <Anonymous> -> makeAssertion -> mstop
Execution halted
Running ‘testthat.R’ [70s/70s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   8.             └─checkmate::makeAssertion(x, res, .var.name, add)
   9.               └─checkmate:::mstop(...)
  ── Error (testm325.R:69:1): (code run outside of `test_that()`) ────────────────
  Error: Assertion on 'all(acceptor[is_processed_pipe] %in% regime[["node"]]) && all(regime[["node"]] %in% acceptor[is_processed_pipe])' failed: Must be TRUE.
  Backtrace:
      █
   1. ├─base::do.call("m325tracebw", nx) testm325.R:69:0
   2. └─pipenostics::m325tracebw(...)
   3.   └─checkmate::assert_true(...)
   4.     └─checkmate::makeAssertion(x, res, .var.name, add)
   5.       └─checkmate:::mstop(...)
  
  [ FAIL 2 | WARN 0 | SKIP 1 | PASS 42 ]
  Error: Test failures
  Execution halted
plot.pred.int: no visible global function definition for ‘plot.default’
plot.pred.int: no visible global function definition for ‘axis’
plot.pred.int: no visible global function definition for ‘box’
plot.pred.int : cidist: no visible global function definition for
  ‘ecdf’
plot.pred.int : negcidist: no visible global function definition for
  ‘ecdf’
plot.pred.int : pi.col.fun: no visible global function definition for
  ‘gray’
plot.pred.int: no visible global function definition for ‘segments’
plot.pred.int: no visible global function definition for ‘points’
plot.pred.int: no visible global function definition for ‘abline’
pred.int: no visible binding for global variable ‘sd’
prop.test.mult: no visible global function definition for ‘qnorm’
sim.basic: no visible global function definition for ‘rbinom’
sim.basic: no visible global function definition for ‘rnorm’
t.test.mult: no visible global function definition for ‘qt’
Undefined global functions or variables:
  abline axis box ecdf gray plot.default points qnorm qt rbinom rnorm
  sd segments
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "box", "plot.default",
             "points", "segments")
  importFrom("stats", "ecdf", "qnorm", "qt", "rbinom", "rnorm", "sd")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Package suggested but not available for checking: ‘ggsubplot’
Package suggested but not available for checking: ‘webfakes’
Running ‘test-async.R’ [12s/12s]
Running the tests in ‘tests/test-async.R’ failed.
Last 13 lines of output:
     vctrs         0.3.7   2021-03-29 [2] CRAN (R 3.6.2)
     waldo         0.2.5   2021-03-08 [2] CRAN (R 3.6.2)
   R webfakes      <NA>    <NA>       [?] <NA>          
     withr         2.4.1   2021-01-26 [2] CRAN (R 3.6.2)
     yaml          2.2.1   2020-02-01 [2] CRAN (R 3.6.0)
  
  [1] /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pkgcache.Rcheck
  [2] /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6
  [3] /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/extralib/3.6
  [4] /Library/Frameworks/R.framework/Versions/3.6/Resources/library
  
   R ── Package was removed from disk.
  Error in loadNamespace(name) : there is no package called 'webfakes'
  Calls: test_dir ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
Package required and available but unsuitable version: ‘pkgcache’

Package suggested but not available for checking: ‘webfakes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
PKmod: no visible global function definition for ‘deriv’
Undefined global functions or variables:
  deriv
Consider adding
  importFrom("stats", "deriv")
to your NAMESPACE file.
PKadjust: no visible binding for global variable ‘jpeg’
PKadjust: no visible binding for global variable ‘bmp’
PKadjust: no visible binding for global variable ‘png’
PKadjust: no visible binding for global variable ‘tiff’
PKadjust: no visible binding for global variable ‘dev.new’
PKadjust: no visible global function definition for ‘dev.off’
PKfigure: no visible global function definition for ‘dev.cur’
PKfigure: no visible global function definition for ‘dev.off’
PKoutput: no visible global function definition for ‘heatmap’
PKoutput: no visible global function definition for
  ‘packageDescription’
PKshow: no visible global function definition for ‘browseURL’
addList1: no visible global function definition for ‘formula’
addList1.old: no visible global function definition for ‘formula’
addList2: no visible global function definition for ‘formula’
generate.plot: no visible global function definition for ‘dev.off’
writeHTML: no visible global function definition for
  ‘packageDescription’
writeLst: no visible global function definition for
  ‘packageDescription’
writeLst.tab: no visible global function definition for
  ‘packageDescription’
writeTable: no visible global function definition for
  ‘packageDescription’
writeTable: no visible global function definition for ‘quantile’
initialize,nonmem: no visible global function definition for
  ‘read.table’
Undefined global functions or variables:
  bmp browseURL dev.cur dev.new dev.off formula heatmap jpeg
  packageDescription png quantile read.table tiff
Consider adding
  importFrom("grDevices", "bmp", "dev.cur", "dev.new", "dev.off", "jpeg",
             "png", "tiff")
  importFrom("stats", "formula", "heatmap", "quantile")
  importFrom("utils", "browseURL", "packageDescription", "read.table")
to your NAMESPACE file.
Package suggested but not available for checking: ‘BiocStyle’
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is 25.4Mb
  sub-directories of 1Mb or more:
    libs  25.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Note: found 150 marked UTF-8 strings
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/PlasmaMutationDetector.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘RColorBrewer’ ‘arm’ ‘epiDisplay’ ‘foreign’ ‘gbm’
  ‘grid’ ‘lattice’ ‘latticeExtra’ ‘lme4’ ‘nnet’ ‘parallel’ ‘splines’
  ‘survey’ ‘twang’ ‘xtable’
  All declared Imports should be used.
No protocol specified
No protocol specified
Namespaces in Imports field not imported from:
  ‘V8’ ‘devtools’ ‘formatR’ ‘gdata’ ‘rhandsontable’ ‘shinybusy’
  ‘shinythemes’ ‘sqldf’ ‘tidyr’
  All declared Imports should be used.
Package required but not available: ‘gWidgets2RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
bwfw.hmm: no visible global function definition for ‘dnorm’
bwfw1.hmm: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘PlackettLuce’ ‘StatRank’ ‘pmr’ ‘prefmod’ ‘rankdist’
  All declared Imports should be used.
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.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   8.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/plot3Drgl.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/plotdap.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘hexbin’ ‘quantreg’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.8Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘patchwork’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
llla.bi: no visible global function definition for ‘as.formula’
llla.bi: no visible global function definition for ‘glm’
llla.bi: no visible global function definition for ‘binomial’
llla.bi: no visible binding for global variable ‘logit’
llla.bi: no visible global function definition for ‘vcov’
llla.bi: no visible global function definition for ‘coef’
llla.mc: no visible global function definition for ‘model.matrix’
llla.mc: no visible global function definition for ‘as.formula’
llla.mc: no visible global function definition for ‘coxph’
llla.mc: no visible global function definition for ‘vcov’
llla.mc: no visible global function definition for ‘coef’
llla.mle: no visible global function definition for ‘as.formula’
llla.mle: no visible global function definition for ‘glm’
llla.mle: no visible global function definition for ‘poisson’
llla.mle: no visible global function definition for ‘coef’
llla.mle: no visible global function definition for ‘vcov’
mclgen: no visible global function definition for ‘reshape’
simRasch.1D: no visible global function definition for ‘rnorm’
simRasch.1D: no visible global function definition for ‘runif’
vcov.sandwich.glm: no visible global function definition for
  ‘model.matrix’
vcov.sandwich.glm: no visible global function definition for ‘weights’
vcov.sandwich.glm: no visible global function definition for
  ‘residuals’
vcov.sandwich.glm: no visible global function definition for ‘vcov’
Undefined global functions or variables:
  as.formula binomial coef coxph glm logit model.matrix poisson reshape
  residuals rnorm runif vcov weights
Consider adding
  importFrom("stats", "as.formula", "binomial", "coef", "glm",
             "model.matrix", "poisson", "reshape", "residuals", "rnorm",
             "runif", "vcov", "weights")
to your NAMESPACE file.
Package suggested but not available for checking: ‘mixOmics’
Running examples in ‘PLSbiplot1-Ex.R’ failed
The error most likely occurred in:

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

Attaching package: ‘pls’

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

    loadings

> X = as.matrix(oliveoil$chemical, ncol=5)
> dimnames(X) = list(paste(c("G1","G2","G3","G4","G5","I1","I2","I3","I4","I5",
+ "S1","S2","S3","S4","S5","S6")),
+ paste(c("Acidity","Peroxide","K232","K270","DK")))
> Y = as.matrix(oliveoil$sensory, ncol=6)
> dimnames(Y) = list(paste(c("G1","G2","G3","G4","G5","I1","I2","I3","I4","I5",
+ "S1","S2","S3","S4","S5","S6")),
+ paste(c("Yellow","Green","Brown","Glossy","Transp","Syrup")))
> Mag.Bmat.plot(X, Y, algorithm=mod.SIMPLS, A=2)
> 
> #nutrimouse data
> if(require(mixOmics))
+ data(nutrimouse, package="mixOmics")
Loading required package: mixOmics
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘mixOmics’
> X1 = as.matrix(nutrimouse$lipid, ncol=21)
Error in as.matrix(nutrimouse$lipid, ncol = 21) : 
  object 'nutrimouse' not found
Execution halted
Package suggested but not available for checking: ‘Rmpi’
Package suggested but not available for checking: ‘Rmpi’
print.densityEHpi: no visible global function definition for ‘str’
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘ssh’
  All declared Imports should be used.
No protocol specified
No protocol specified
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.
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 62 marked UTF-8 strings
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').
Namespaces in Imports field not imported from:
  ‘ggrepel’ ‘gridExtra’
  All declared Imports should be used.
plot_scm: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
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.
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.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘plogr’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘about-podr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 42-64 (about-podr.Rmd) 
Error: processing vignette 'about-podr.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘about-podr.Rmd’

SUMMARY: processing the following file failed:
  ‘about-podr.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘abc’ ‘doParallel’ ‘gdistance’ ‘geosphere’ ‘lhs’ ‘metRology’ ‘raster’
  ‘trend’
  All declared Imports should be used.
Note: found 7256 marked UTF-8 strings
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.
Namespaces in Imports field not imported from:
  ‘car’ ‘lubridate’
  All declared Imports should be used.
Note: found 8 marked UTF-8 strings
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.
Namespaces in Imports field not imported from:
  ‘argonDash’ ‘argonR’ ‘colourpicker’ ‘ggplot2’ ‘grid’ ‘hexSticker’
  ‘png’ ‘shinyWidgets’
  All declared Imports should be used.
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.
Note: found 21 marked UTF-8 strings
Note: found 9 marked UTF-8 strings
Package suggested but not available for checking: ‘pollimetrydata’
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 12.6Mb
  sub-directories of 1Mb or more:
    R      6.9Mb
    data   4.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘polynomials.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'polynomials.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘polynomials.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    1.7Mb
    libs   1.5Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    extdata   4.7Mb
    libs      2.7Mb
Namespace in Imports field not imported from: ‘regtools’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pomp.Rcheck/00install.out’ for details.
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 49.2Mb
  sub-directories of 1Mb or more:
    libs  48.9Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package required but not available: ‘EmpiricalBrownsMethod’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
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.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘ROI.plugin.symphony’
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
Package required but not available: ‘Rsymphony’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘StanHeaders’ ‘dplyr’ ‘ggplot2’ ‘gridExtra’ ‘rstan’ ‘tibble’
  All declared Imports should be used.
Running examples in ‘potential-Ex.R’ failed
The error most likely occurred in:

> ### Name: create_matrix
> ### Title: Create a Distance Matrix Between Two Spatial Objects
> ### Aliases: create_matrix
> 
> ### ** Examples
> 
> g <- create_grid(x = n3_poly, res = 200000)
> mat <- create_matrix(x = n3_pt, y = g)
Warning in CPL_transform(x, crs, aoi, pipeline, reverse, desired_accuracy,  :
  GDAL Error 1: No PROJ.4 translation for source SRS, coordinate transformation initialization has failed.
Error in CPL_transform(x, crs, aoi, pipeline, reverse, desired_accuracy,  : 
  OGRCreateCoordinateTransformation() returned NULL: PROJ available?
Calls: create_matrix ... st_transform.sfc -> st_sfc -> structure -> CPL_transform
Execution halted
Running ‘tinytest.R’ [6s/6s]
Running the tests in ‘tests/tinytest.R’ failed.
Last 13 lines of output:
  Running test_curv.R...................    0 tests    
  Running test_curv.R...................    1 tests [0;32mOK[0m 
  Running test_curv.R...................    2 tests [0;32mOK[0m 
  Running test_curv.R...................    3 tests [0;32mOK[0m 
  Running test_curv.R...................    3 tests [0;32mOK[0m 
  Running test_curv.R...................    4 tests [0;32mOK[0m 
  Running test_curv.R...................    5 tests [0;31m1 fails[0m 
  Running test_curv.R...................    5 tests [0;31m1 fails[0m 
  Running test_curv.R...................    6 tests [0;31m1 fails[0m Error in CPL_transform(x, crs, aoi, pipeline, reverse, desired_accuracy,  : 
    OGRCreateCoordinateTransformation() returned NULL: PROJ available?
  Calls: <Anonymous> ... st_transform.sfc -> st_sfc -> structure -> CPL_transform
  In addition: Warning message:
  In CPL_transform(x, crs, aoi, pipeline, reverse, desired_accuracy,  :
    GDAL Error 1: No PROJ.4 translation for source SRS, coordinate transformation initialization has failed.
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘potential.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Linking to GEOS 3.7.2, GDAL 2.4.2, PROJ 5.2.0
This project is in maintenance mode. 
Core functionalities of `cartography` can be found in `mapsf`.
https://riatelab.github.io/mapsf/
Warning in CPL_transform(x, crs, aoi, pipeline, reverse, desired_accuracy,  :
  GDAL Error 1: No PROJ.4 translation for source SRS, coordinate transformation initialization has failed.
Quitting from lines 214-216 (potential.Rmd) 
Error: processing vignette 'potential.Rmd' failed with diagnostics:
OGRCreateCoordinateTransformation() returned NULL: PROJ available?
--- failed re-building ‘potential.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
'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  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc  12.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘PPQnote.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘PPQnote.Rmd’

--- re-building ‘PPQplan-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="webshot11657509cc45.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot11657509cc45.png': No such file or directory
Quitting from lines 130-131 (PPQplan-vignette.Rmd) 
Error: processing vignette 'PPQplan-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘PPQplan-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Package required and available but unsuitable version: ‘parallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
postppt.plot: no visible global function definition for ‘plot’
priorppt.plot: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Missing link or links in documentation object 'postppt.plot.Rd':
  ‘[base]{plot}’

Missing link or links in documentation object 'priorppt.plot.Rd':
  ‘[base]{plot}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
Malformed Title field: should not end in a period.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Namespaces in Imports field not imported from:
  ‘lmtest’ ‘sandwich’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘class’ ‘forcats’ ‘irr’ ‘lpSolve’ ‘purrr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘shinycssloaders’ ‘shinythemes’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R.cache’ ‘docopt’ ‘here’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/predict3d.Rcheck/00install.out’ for details.
No protocol specified
Namespaces in Imports field not imported from:
  ‘TH.data’ ‘moonBook’
  All declared Imports should be used.
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘predict3d.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: predict3d
No protocol specified
Loading required package: rgl
Quitting from lines 55-58 (predict3d.Rmd) 
Error: processing vignette 'predict3d.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘predict3d.Rmd’

SUMMARY: processing the following file failed:
  ‘predict3d.Rmd’

Error: Vignette re-building failed.
Execution halted
No protocol specified
No protocol specified
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
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.
Namespaces in Imports field not imported from:
  ‘DT’ ‘ROCR’ ‘ada’ ‘colourpicker’ ‘corrplot’ ‘e1071’ ‘flexdashboard’
  ‘glmnet’ ‘kknn’ ‘neuralnet’ ‘plyr’ ‘randomForest’ ‘rattle’ ‘rpart’
  ‘shinyAce’ ‘shinyWidgets’ ‘shinydashboardPlus’ ‘shinyjs’ ‘tidyverse’
  ‘xgboost’ ‘zip’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘here’ ‘tidyr’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘predmixcor/R/firstlib.r’:
  .First.lib calls:
    cat("predmixcor loaded\n", "COPY RIGHT: Longhai Li\n", "http://math.usask.ca/~longhai\n",     "Type ?begin.predmixcor for help\n", sep = "")

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

Predict.mix: no visible global function definition for ‘dbinom’
abs_cor: no visible global function definition for ‘cor’
gen.alpha.IGamma: no visible global function definition for ‘qgamma’
gendata.mix: no visible global function definition for ‘runif’
gendata.mix: no visible global function definition for ‘rbeta’
mh1.unif: no visible global function definition for ‘runif’
train_predict_mix: no visible global function definition for ‘dbinom’
training: no visible global function definition for ‘runif’
training: no visible global function definition for ‘dbinom’
Undefined global functions or variables:
  cor dbinom qgamma rbeta runif
Consider adding
  importFrom("stats", "cor", "dbinom", "qgamma", "rbeta", "runif")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/PReMiuM.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘dplyr’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Note: found 42966 marked UTF-8 strings
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/presser.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘INLA’
No protocol specified
No protocol specified
No protocol specified
No protocol specified
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘lubridate’
  All declared Imports should be used.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/primer.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
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 required but not available: ‘org.Hs.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'gurobi', 'rcbc', 'cplexAPI', 'Rsymphony'
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  10.0Mb
Namespace in Imports field not imported from: ‘exactextractr’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘PRISMA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in getPrisma(studyStatus) :
  prismaFormat is null so attempting to make automatic one from studyStatus
Warning: Factor `Filter` contains implicit NA, consider using `forcats::fct_explicit_na`
Warning in getFormatNode(prismaFormat) :
  fontSize param not passed in prismaFormat
Warning in normalizePath(f2) :
  path[1]="webshot162f53ad3da94.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot162f53ad3da94.png': No such file or directory
Quitting from lines 43-52 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘PRISMA.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘PRISMA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 39-52 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘PRISMA.Rmd’

--- re-building ‘exclusionflowcharts.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 25-31 (exclusionflowcharts.Rmd) 
Error: processing vignette 'exclusionflowcharts.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘exclusionflowcharts.Rmd’

SUMMARY: processing the following files failed:
  ‘PRISMA.Rmd’ ‘exclusionflowcharts.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
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.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/probhat.Rcheck/00install.out’ for details.
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘LaplacesDemon’ ‘epitools’ ‘rpivotTable’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc           8.8Mb
    htmlwidgets   2.5Mb
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/processR.Rcheck/00install.out’ for details.
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.
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 15.4Mb
  sub-directories of 1Mb or more:
    extdata   7.4Mb
    libs      6.9Mb
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
No protocol specified
No protocol specified
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   1.2Mb
    libs      2.5Mb
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  Note: possible error in 'Rprof(prof_output, interval = interval, ': unused argument (filter.callframes = simplify) 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/profvis.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’.
profvis: possible error in Rprof(prof_output, interval = interval,
  line.profiling = TRUE, gc.profiling = TRUE, memory.profiling = TRUE,
  filter.callframes = simplify): unused argument (filter.callframes =
  simplify)
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.
No protocol specified
No protocol specified
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  * _snaps/plots/evd-proj-box-no-outliers.svg
  * _snaps/plots/evd-proj-box-only.svg
  * _snaps/plots/evd-proj-full-red-ribbon-narrow-range.svg
  * _snaps/plots/evd-proj-no-box-custom-lines.svg
  * _snaps/plots/evd-proj-no-ribbon.svg
  * _snaps/plots/evd-proj-red-box.svg
  * _snaps/plots/evd-proj-red-ribbon.svg
  * _snaps/plots/evd-proj-ribbon-only.svg
  * _snaps/plots/evd-proj-with-incidence-incidence-and-custom.svg
  * _snaps/plots/evd-proj-with-incidence-incidence-box-only.svg
  * _snaps/plots/evd-proj-with-incidence-incidence-no-box.svg
  * _snaps/plots/evd-proj-with-incidence-incidence.svg
  * _snaps/plots/evd-proj.svg
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘optimx’ ‘tidyverse’
  All declared Imports should be used.
installed size is 36.5Mb
  sub-directories of 1Mb or more:
    libs  35.9Mb
Namespaces in Imports field not imported from:
  ‘StanHeaders’ ‘methods’ ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Running ‘testthat.R’ [74s/75s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   5.     └─rstan:::.local(object, ...)
   6.       └─sampler$call_sampler(c(args, dotlist))
  ── Error (test_utilities.R:42:3): regressor_coefficients_with_uncertainty ──────
  Error: 'data' must be of a vector type, was 'NULL'
  Backtrace:
      █
   1. ├─base::suppressWarnings(...) test_utilities.R:42:2
   2. │ └─base::withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
   3. └─prophet:::build_model_with_regressors(DATA, mcmc.samples = 100)
   4.   └─prophet::fit.prophet(m, df) test_utilities.R:25:2
   5.     └─base::matrix(m$params[[name]], nrow = n.iteration)
  
  [ FAIL 12 | WARN 1 | SKIP 1 | PASS 309 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: ‘ALDEx2’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   2.2Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
addpi: no visible global function definition for ‘lines’
genPerms: no visible global function definition for ‘combn’
getVar: no visible global function definition for ‘glm’
getVar: no visible global function definition for ‘binomial’
getVar: no visible global function definition for ‘var’
pba: no visible global function definition for ‘glm’
pba: no visible global function definition for ‘binomial’
pba: no visible global function definition for ‘predict’
pba: no visible global function definition for ‘rbinom’
pcr: no visible global function definition for ‘quantile’
plotpi: no visible global function definition for ‘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.
plot.sgpv: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   3.0Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘grDevices’
  All declared Imports should be used.
Package in Depends field not imported from: ‘MASS’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
addIonSatistics: no visible binding for global variable ‘median’
adjustOne: no visible binding for global variable ‘median’
attachModifications: no visible global function definition for
  ‘na.omit’
avrgLoadingCalculation: no visible binding for global variable ‘median’
channelResponses : estimate: no visible binding for global variable
  ‘var’
responseStatisics : func: no visible global function definition for
  ‘aggregate’
testing: no visible global function definition for ‘aov’
testingOneshot: no visible global function definition for ‘anova’
testingTukey: no visible global function definition for ‘TukeyHSD’
Undefined global functions or variables:
  TukeyHSD aggregate anova aov median na.omit var
Consider adding
  importFrom("stats", "TukeyHSD", "aggregate", "anova", "aov", "median",
             "na.omit", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘class’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘class’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
addcircle: no visible global function definition for ‘lines’
addclassifierboundary: no visible global function definition for ‘par’
addclassifierboundary: no visible global function definition for
  ‘contour’
plot.protoclass: no visible global function definition for ‘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.
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  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Packages suggested but not available for checking:
  'Biostrings', 'GOSemSim', 'org.Hs.eg.db'
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.1Mb
Note: found 12717 marked UTF-8 strings
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   2.3Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/prWarp.Rcheck/00install.out’ for details.
Note: found 1 marked UTF-8 string
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.
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   3.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/psfmi.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘forecast’ ‘knitr’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Note: found 26 marked Latin-1 strings
'library' or 'require' call to ‘numDeriv’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
test.problem : g: no visible global function definition for ‘grad’
test.problem: no visible global function definition for ‘new’
psoptim,test.problem-missing-missing-missing-missing: no visible global
  function definition for ‘new’
show,test.result: no visible global function definition for ‘show’
show,test.result: no visible global function definition for ‘sd’
Undefined global functions or variables:
  grad new sd show
Consider adding
  importFrom("methods", "new", "show")
  importFrom("stats", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/psrwe.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 23.8Mb
  sub-directories of 1Mb or more:
    libs  22.9Mb
glm.lambda: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘yaml’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Package required but not available: ‘tweeDEseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘muscle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 28898 marked UTF-8 strings
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc        4.0Mb
    examples   2.6Mb
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
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.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pubh.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
installed size is 40.3Mb
  sub-directories of 1Mb or more:
    libs  39.9Mb
Note: found 35 marked UTF-8 strings
GNU make is a SystemRequirements.
installed size is 36.1Mb
  sub-directories of 1Mb or more:
    libs  35.6Mb
Package suggested but not available for checking: ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pulseTD.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘itsadug’ ‘mgcv’
  All declared Imports should be used.
PurBayes: no visible global function definition for ‘update’
PurBayes: no visible global function definition for ‘sd’
plot.PurBayes: no visible global function definition for ‘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.
Namespaces in Imports field not imported from:
  ‘kableExtra’ ‘readr’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
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.
Error(s) in re-building vignettes:
--- re-building ‘Data_Model.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘Data_Model.Rmd’

--- re-building ‘Example_Save_Data_as_CSV.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘Example_Save_Data_as_CSV.Rmd’

--- re-building ‘Maps_and_Timeseries_Plots.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in monitor_dailyStatistic(PacNW, FUN = mean, minHours = 20) :
  Found 2 timezones. Only 'America/Los_Angeles' will be used
--- finished re-building ‘Maps_and_Timeseries_Plots.Rmd’

--- re-building ‘NowCast.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘NowCast.Rmd’

--- re-building ‘PWFSLSmoke.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 161-162 (PWFSLSmoke.Rmd) 
Error: processing vignette 'PWFSLSmoke.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘PWFSLSmoke.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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').
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
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.
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    gui          1.6Mb
    libs         2.7Mb
    staticdocs   3.3Mb
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rmarkdown’ ‘stats’
  All declared Imports should be used.
sam: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Note: found 76102 marked UTF-8 strings
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.
installed size is 60.4Mb
  sub-directories of 1Mb or more:
    libs  60.2Mb
GNU make is a SystemRequirements.
pcAxisCubeMake: no visible global function definition for ‘aggregate’
pcAxisCubeToCSV: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  aggregate write.csv
Consider adding
  importFrom("stats", "aggregate")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/qpcR.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Note: found 7 marked UTF-8 strings
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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 11.0Mb
  sub-directories of 1Mb or more:
    data  10.8Mb
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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 12.6Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
Malformed Description field: should contain one or more complete sentences.
Note: found 6 marked UTF-8 strings
Found the following executable file:
  src/LICENSES/LZ4_LICENSE.txt
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   9.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/qsub.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘msm’
  All declared Imports should be used.
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
installed size is 37.4Mb
  sub-directories of 1Mb or more:
    extdata   3.3Mb
    libs     32.9Mb
plot_genes : plot_genes_internal: no visible global function definition
  for ‘plot’
plot_onegeno : plot_onegeno_internal: no visible global function
  definition for ‘plot’
plot_peaks : plot_peaks_internal: no visible global function definition
  for ‘plot’
plot_pxg : plot_pxg_internal: no visible global function definition for
  ‘plot’
plot_scan1 : plot_scan1_internal: no visible global function definition
  for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/qtlc.Rcheck/00install.out’ for details.
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 11.3Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.7Mb
    doc       3.0Mb
    libs      1.3Mb
drawcirculargenome: no visible global function definition for ‘plot’
effectplot: no visible global function definition for ‘plot’
mqmplot.circle: no visible global function definition for ‘plot’
mqmplot.cistrans: no visible global function definition for ‘plot’
mqmplot.cofactors: no visible global function definition for ‘plot’
mqmplot.directedqtl: no visible global function definition for ‘plot’
mqmplot.multitrait: no visible global function definition for ‘plot’
mqmplot.singletrait: no visible global function definition for ‘plot’
plot.map: no visible global function definition for ‘plot’
plot.rfmatrix: no visible global function definition for ‘plot’
plot.scanone: no visible global function definition for ‘plot’
plotGeno: no visible global function definition for ‘plot’
plotMap: no visible global function definition for ‘plot’
plotModel: no visible global function definition for ‘plot’
plotPXG: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘MatrixModels’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Qtools.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 124-146 (Qtools.Rmd) 
Error: processing vignette 'Qtools.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘Qtools.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'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').
Namespace in Imports field not imported from: ‘viridis’
  All declared Imports should be used.
quadp: no visible global function definition for ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 83-117 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘wilcox1973.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 92-106 (wilcox1973.Rmd) 
Error: processing vignette 'wilcox1973.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘wilcox1973.Rmd’

SUMMARY: processing the following file failed:
  ‘wilcox1973.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Note: found 4 marked UTF-8 strings
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   6.6Mb
Note: found 35707 marked UTF-8 strings
Namespace in Imports field not imported from: ‘SparseM’
  All declared Imports should be used.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   4.0Mb
Note: found 4145 marked UTF-8 strings
Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 
  > test_check("questionr")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test_weighting.R:42:3): Cross wtd.table is correct ─────────────────
  `tab` not equal to structure(...).
  Attributes: < Component "dim": Mean relative difference: 0.3333333 >
  Numeric: lengths (6, 4) differ
  ── Failure (test_weighting.R:45:3): Cross wtd.table is correct ─────────────────
  `tab` not equal to structure(...).
  Attributes: < Component "dim": Mean relative difference: 0.3333333 >
  Numeric: lengths (6, 4) differ
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 60 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘fastshp’
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘gridExtra’ ‘knitr’
  All declared Imports should be used.
Note: found 12928 marked UTF-8 strings
mutualCoherence : .setOneMutualP: no visible global function definition
  for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Note: found 89912 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘pracma’ ‘zoo’
  All declared Imports should be used.
Package suggested but not available for checking: ‘ReGenesees’
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.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 34 marked UTF-8 strings
'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.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lmerTest’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
'library' or 'require' calls in package code:
  ‘RDCOMClient’ ‘rcom’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: ‘BRugs’
Package unavailable to check Rd xrefs: ‘BRugs’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/R330.Rcheck/00install.out’ for details.
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 11.5Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘r3dmol.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 34-66 (r3dmol.Rmd) 
Error: processing vignette 'r3dmol.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘r3dmol.Rmd’

--- re-building ‘style-functions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 43-49 (style-functions.Rmd) 
Error: processing vignette 'style-functions.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘style-functions.Rmd’

SUMMARY: processing the following files failed:
  ‘r3dmol.Rmd’ ‘style-functions.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Package suggested but not available for checking: ‘batchelor’
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    5.8Mb
    libs   1.2Mb
Namespaces in Imports field not imported from:
  ‘comat’ ‘rgdal’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/racir.Rcheck/00install.out’ for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘car’ ‘dplyr’ ‘grid’ ‘gridExtra’ ‘knitr’ ‘lmerTest’ ‘tidyr’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Note: found 4 marked UTF-8 strings
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
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.
Note: found 3 marked UTF-8 strings
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RadOnc.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
Malformed Description field: should contain one or more complete sentences.
Namespaces in Imports field not imported from:
  ‘qpdf’ ‘utf8’
  All declared Imports should be used.
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.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Namespaces in Imports field not imported from:
  ‘Biobase’ ‘CGHbase’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RAINBOWR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RALSA.Rcheck/00install.out’ for details.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets        9.7Mb
    super-tiny-icons   1.0Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    api           3.1Mb
    htmlwidgets   7.0Mb
Package suggested but not available for checking: ‘Heatplus’
Package unavailable to check Rd xrefs: ‘Heatplus’
Malformed Description field: should contain one or more complete sentences.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.2Mb
    libs   4.6Mb
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
Package unavailable to check Rd xrefs: ‘WGCNA’
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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘randomNames.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-26 (randomNames.Rmd) 
Error: processing vignette 'randomNames.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘randomNames.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘curl’ ‘jsonlite’
  All declared Imports should be used.
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.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rangemap.Rcheck/00install.out’ for details.
Note: found 7734 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘dplyr’ ‘jsonlite’ ‘rgbif’ ‘rgdal’ ‘rgeos’ ‘sp’ ‘spThin’
  ‘spatstat’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
No protocol specified
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.
Namespace in Imports field not imported from: ‘RJDBC’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RapidoPGS.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RAPIDR.Rcheck/00install.out’ for details.
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 15.3Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs   9.7Mb
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rarefy.Rcheck/00install.out’ for details.
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 10.2Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    libs   6.6Mb
No protocol specified
No protocol specified
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
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.
installed size is 60.9Mb
  sub-directories of 1Mb or more:
    libs  60.2Mb
GNU make is a SystemRequirements.
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.
Namespace in Imports field not imported from: ‘hms’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rggobi’
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    etc    1.9Mb
    po     1.2Mb
No protocol specified

(R:23424): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   7.0Mb
sh: sysctl: command not found
sh: sysctl: command not found
sh: sysctl: command not found
sh: sysctl: command not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
sh: sysctl: command not found
sh: sysctl: command not found
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
sh: sysctl: command not found
sh: sysctl: command not found
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
sh: sysctl: command not found
sh: sysctl: command not found
sh: sysctl: command not found
sh: sysctl: command not found
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
sh: sysctl: command not found
sh: sysctl: command not found
sh: sysctl: command not found
sh: sysctl: command not found
sh: sysctl: command not found
sh: sysctl: command not found
sh: sysctl: command not found
sh: sysctl: command not found
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.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RavenR.Rcheck/00install.out’ for details.
.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.
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rayshader.Rcheck/00install.out’ for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   3.2Mb
Note: found 8 marked UTF-8 strings
installed size is 39.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  37.1Mb
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.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rblpapi.Rcheck/00install.out’ for details.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    blp    5.9Mb
    libs   5.2Mb
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Malformed Title field: should not end in a period.
SumTestSens: no visible global function definition for ‘pnorm’
binarysens: no visible global function definition for ‘dbinom’
hlsens: no visible global function definition for ‘wilcox.test’
iv_sens: no visible global function definition for ‘pnorm’
mcontrol: no visible global function definition for ‘pnorm’
psens: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dbinom pnorm wilcox.test
Consider adding
  importFrom("stats", "dbinom", "pnorm", "wilcox.test")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
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.
Note: found 26334 marked UTF-8 strings
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.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    cont  25.8Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
.onAttach: no visible global function definition for
  ‘packageDescription’
rselect.list: no visible global function definition for ‘select.list’
Undefined global functions or variables:
  packageDescription select.list
Consider adding
  importFrom("utils", "packageDescription", "select.list")
to your NAMESPACE file.
Found the following executable file:
  src/vendor/clickhouse-cpp/contrib/lz4/LICENSE
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
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.
Depends: includes the non-default packages:
  'biclust', 'fabia', 'iBBiG', 'superbiclust', 'BcDiag', 'BicARE',
  's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
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.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'library' or 'require' call to ‘FrF2.catlg128’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RcmdrPlugin.EZR.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'library' or 'require' calls in package code:
  ‘abind’ ‘e1071’ ‘qcc’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
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
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
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.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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: ‘ROpenOffice’
Depends: includes the non-default packages:
  'IQCC', 'qcc', 'qicharts2', 'randtests', 'rmarkdown',
  'TeachingDemos', 'tseries'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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  6.4Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   2.3Mb
    po    2.3Mb
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
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.
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  7.6Mb
  sub-directories of 1Mb or more:
    corpora   7.5Mb
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rcplex.Rcheck/00install.out’ for details.
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    include   6.1Mb
    libs      2.2Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RcppClassic.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
installed size is 32.9Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
    libs     24.6Mb
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  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RcppMeCab.Rcheck/00install.out’ for details.
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RcppMLPACK.Rcheck/00install.out’ for details.
installed size is 41.4Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib      27.9Mb
    libs     11.6Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      2.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
GNU make is a SystemRequirements.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    include   6.3Mb
    libs      4.7Mb
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    include        1.7Mb
    jsonexamples   3.8Mb
    libs          12.5Mb
Running ‘tinytest.R’ [19s/19s]
Running the tests in ‘tests/tinytest.R’ failed.
Last 13 lines of output:
  Running test_vectorized_ops.R.........    5 tests [0;32mOK[0m 
  Running test_vectorized_ops.R.........    6 tests [0;32mOK[0m [0;36m14ms[0m
  ----- FAILED[data]: test_deserialization.R<1138--1141>
   call| expect_identical(current = RcppSimdJson:::.deserialize_json(test, 
   call| int64_r_type = int64_opt$integer64), target = target)
   diff| Component "int64": 'is.NA' value mismatch: 1 in current 0 in target
   diff| Component "nested_dfs": Component 1: Component 3: 'current' is not a factor
   diff| Component "nested_dfs": Component 2: Component 3: 'current' is not a factor
  ----- FAILED[data]: test_simdjson_utils.R<63--68>
   call| expect_false(current = any(is_valid_utf8(invalid_utf8)) || any(vapply(invalid_utf8, 
   call| function(.x) is_valid_utf8(charToRaw(.x)), logical(1L))) || 
   call| is_valid_utf8(lapply(invalid_utf8, charToRaw)) || any(validUTF8(invalid_utf8)))
   diff| Expected FALSE, got TRUE
  Error: 2 out of 2969 tests failed
  Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
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.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rcrypt.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘rdf_intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 41-42 (rdf_intro.Rmd) 
Error: processing vignette 'rdf_intro.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘rdf_intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
sumry_categorical: no visible global function definition for ‘freq’
sumry_continous: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  freq quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rdimtools.Rcheck/00install.out’ for details.
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
prepare_Rd: RGL: unable to open X11 display
prepare_Rd: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
Packages suggested but not available for checking:
  'Biostrings', 'GOSemSim', 'org.Hs.eg.db'
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Subdirectory ‘src’ contains:
  CLRApi.hpp CLRFactory.hpp CLRObjectRef.hpp Common.hpp OS.hpp
  RValue.hpp TcpClient.hpp
These are unlikely file names for src files.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
'library' or 'require' call to ‘synchronicity’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Running examples in ‘Rdsm-Ex.R’ failed
The error most likely occurred in:

> ### Name: readsync
> ### Title: Syncing file-backed variables.
> ### Aliases: readsync writesync
> 
> ### ** Examples
> 
> library(parallel)
> c2 <- makeCluster(2)
> mgrinit(c2)
Warning in for (v in val) { :
  closing unused connection 6 (<-localhost:11715)
Warning in for (v in val) { :
  closing unused connection 5 (<-localhost:11715)
[[1]]
[1] 0

[[2]]
[1] 0

> mgrmakevar(c2,"x",1,1,fs=TRUE)
Error in bigmemory::filebacked.big.matrix(nrow = nr, ncol = nc, type = vartype,  : 
  Backing file already exists! Either remove or specify
           different backing file
Calls: mgrmakevar -> <Anonymous>
Execution halted
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.
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  `actual_obj` not equal to `expected_obj`.
  Component 1: Component 1: 'current' is not a factor
  Component 1: Component 2: 'current' is not a factor
  Component 1: Component 3: 'current' is not a factor
  Component 2: Component 1: 'current' is not a factor
  Component 2: Component 2: 'current' is not a factor
  Component 2: Component 3: 'current' is not a factor
  Component 3: Component 1: 'current' is not a factor
  Component 3: Component 2: 'current' is not a factor
  Component 3: Component 3: 'current' is not a factor
  ...
  
  [ FAIL 12 | WARN 0 | SKIP 0 | PASS 241 ]
  Error: Test failures
  Execution halted
Note: found 1 marked Latin-1 string
  Note: found 1 marked UTF-8 string
  Note: found 7 strings marked as "bytes"
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/reasonabletools.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘recexcavAAR-vignette-1.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-17 (recexcavAAR-vignette-1.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-1.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
--- failed re-building ‘recexcavAAR-vignette-1.Rmd’

--- re-building ‘recexcavAAR-vignette-2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-17 (recexcavAAR-vignette-2.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-2.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
--- failed re-building ‘recexcavAAR-vignette-2.Rmd’

--- re-building ‘recexcavAAR-vignette-3.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-17 (recexcavAAR-vignette-3.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-3.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
--- failed re-building ‘recexcavAAR-vignette-3.Rmd’

SUMMARY: processing the following files failed:
  ‘recexcavAAR-vignette-1.Rmd’ ‘recexcavAAR-vignette-2.Rmd’
  ‘recexcavAAR-vignette-3.Rmd’

Error: Vignette re-building failed.
Execution halted
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.
Note: found 1036 marked UTF-8 strings
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘ReDaMoR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 157-163 (ReDaMoR.Rmd) 
Error: processing vignette 'ReDaMoR.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘ReDaMoR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   3.1Mb
Namespaces in Imports field not imported from:
  ‘DBI’ ‘readr’
  All declared Imports should be used.
Package required but not available: ‘maftools’

Packages suggested but not available for checking:
  'BiocStyle', 'TCGAbiolinks'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rmpi’
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
Running examples in ‘redist-Ex.R’ failed
The error most likely occurred in:

> ### Name: compare_plans
> ### Title: Make a comparison between two sets of plans
> ### Aliases: compare_plans
> 
> ### ** Examples
> 
> data(iowa)
> iowa_map = redist_map(iowa, ndists=4, pop_tol=0.05)
OGR: Corrupt data
Error in CPL_crs_parameters(x) : OGR error
Calls: redist_map ... <Anonymous> -> crs_parameters -> CPL_crs_parameters
Execution halted
Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   4.     └─sf:::crs_parameters(crs)
   5.       └─sf:::CPL_crs_parameters(x)
  ── Error (test_smc.R:12:5): County constraint works ────────────────────────────
  Error: OGR error
  Backtrace:
      █
   1. └─redist::redist_map(iowa, ndists = 4, pop_tol = 0.05) test_smc.R:12:4
   2.   ├─base::isTRUE(sf::st_is_longlat(sf::st_geometry(x)))
   3.   └─sf::st_is_longlat(sf::st_geometry(x))
   4.     └─sf:::crs_parameters(crs)
   5.       └─sf:::CPL_crs_parameters(x)
  
  [ FAIL 22 | WARN 1 | SKIP 3 | PASS 44 ]
  Error: Test failures
  Execution halted
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/red.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘pkgload’ ‘processx’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘textshaping’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘glue’ ‘rlang’ ‘testthat’
  All declared Imports should be used.
Note: found 2 marked Latin-1 strings
  Note: found 50022 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘gridExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Deriv’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   3.7Mb
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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 required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rsymphony’

Package which this enhances but not available for checking: ‘Rcplex’
'library' or 'require' call to ‘lars’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘lars’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
relaxo: no visible global function definition for ‘lars’
Undefined global functions or variables:
  lars
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
plot.inference: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Running examples in ‘relevance-Ex.R’ failed
The error most likely occurred in:

> ### Name: relevance-package
> ### Title: Calculate Relevance
> ### Aliases: relevance-package relevance
> ### Keywords: package
> 
> ### ** Examples
> 
>   data(swiss)
>   rr <- lm(Fertility ~ . , data = swiss)
>   termtable(rr)
Error in format.default(lfo[[2]]) : 
  Found no format() method for class "name"
Calls: <Anonymous> ... print.inference -> paste -> format -> format.default
Execution halted
Running ‘relevance-test.R’ [0s/0s]
Running the tests in ‘tests/relevance-test.R’ failed.
Last 13 lines of output:
  > ## install.packages("~/R/regdevelop/pkg/relevance_1.1.tar.gz", repos=NULL, lib="~/local/R_libs")
  > require(relevance)
  Loading required package: relevance
  > 
  > ##
  > d.permeabililty <-
  +   data.frame(perm = c(0.80, 0.83, 1.89, 1.04, 1.45, 1.38, 1.91, 1.64, 0.73, 1.46,
  +                       1.15, 0.88, 0.90, 0.74, 1.21), atterm = rep(1:0, c(10,5))
  +              )
  > rtt <-t.test(perm~atterm, data=d.permeabililty, var.equal=FALSE)
  > rr <-twosamples(perm~atterm, data=d.permeabililty, var.equal=FALSE)
  Error in format.default(substitute(data)) : 
    Found no format() method for class "name"
  Calls: twosamples ... twosamples.formula -> structure -> format -> format.default
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘relevance-descr.Rnw’ using knitr
Quitting from lines 263-274 (relevance-descr.Rnw) 
Error: processing vignette 'relevance-descr.Rnw' failed with diagnostics:
Found no format() method for class "name"
--- failed re-building ‘relevance-descr.Rnw’

SUMMARY: processing the following file failed:
  ‘relevance-descr.Rnw’

Error: Vignette re-building failed.
Execution halted
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.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
Namespace in Imports field not imported from: ‘gWidgets2tcltk’
  All declared Imports should be used.
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.
Packages suggested but not available for checking: 'graph', 'Rgraphviz'
Package suggested but not available for checking: ‘webfakes’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(remotes)
  > 
  > test_check("remotes")
  Error in loadNamespace(name) : there is no package called 'webfakes'
  Calls: test_check ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
  Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    7.0Mb
    libs   2.8Mb
Error(s) in re-building vignettes:
--- re-building ‘getting-started.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'rENA'

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

    show

Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Quitting from lines 107-117 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘getting-started.Rmd’

--- re-building ‘means-rotation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout


Attaching package: 'rENA'

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

    show

--- finished re-building ‘means-rotation.Rmd’

SUMMARY: processing the following file failed:
  ‘getting-started.Rmd’

Error: Vignette re-building failed.
Execution halted
RearrangeData: no visible global function definition for ‘rainbow’
RearrangeData: no visible global function definition for ‘hclust’
RearrangeData: no visible global function definition for
  ‘as.dendrogram’
RearrangeData: no visible global function definition for ‘heatmap’
RearrangeData: no visible global function definition for ‘pdf’
RearrangeData: no visible global function definition for
  ‘colorRampPalette’
RearrangeData: no visible global function definition for ‘legend’
RearrangeData: no visible global function definition for ‘dev.off’
RearrangeJoseph: no visible global function definition for
  ‘write.table’
RearrangeJoseph: no visible global function definition for
  ‘as.dendrogram’
RearrangeJoseph: no visible global function definition for
  ‘order.dendrogram’
colorDendClass : colLab: no visible global function definition for
  ‘is.leaf’
colorDendClass: no visible global function definition for ‘dendrapply’
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.
report.betareg: no visible global function definition for ‘deparse1’
report.brmsfit: no visible global function definition for ‘deparse1’
report.clm: no visible global function definition for ‘deparse1’
report.clmm: no visible global function definition for ‘deparse1’
report.coxph: no visible global function definition for ‘deparse1’
report.default: no visible global function definition for ‘deparse1’
report.glm: no visible global function definition for ‘deparse1’
report.glmerMod: no visible global function definition for ‘deparse1’
report.glmmadmb: no visible global function definition for ‘deparse1’
report.glmnet: no visible global function definition for ‘deparse1’
report.lm: no visible global function definition for ‘deparse1’
report.lqmm: no visible global function definition for ‘deparse1’
report.merModLmerTest: no visible global function definition for
  ‘deparse1’
report.rlm: no visible global function definition for ‘deparse1’
report.rq: no visible global function definition for ‘deparse1’
Undefined global functions or variables:
  deparse1
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/reporter.Rcheck/00install.out’ for details.
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.
Note: found 25 marked UTF-8 strings
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.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rerddapXtracto.Rcheck/00install.out’ for details.
.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').
Plot.TopJournals: no visible global function definition for ‘plot’
Plot.TopPapers: no visible global function definition for ‘plot’
Plot.papertype: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   6.5Mb
Package suggested but not available for checking: ‘rsolr’
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.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    libs      3.2Mb
    swagger   1.4Mb
Namespace in Imports field not imported from: ‘Rserve’
  All declared Imports should be used.
Package suggested but not available for checking: ‘gWidgets2RGtk2’
Namespace in Imports field not imported from: ‘RTriangle’
  All declared Imports should be used.
Running ‘testthat.R’ [10s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Class:   simpleError/error/condition
  Backtrace:
      █
   1. ├─testthat::expect_error(runAllChunks("test-rmarkdown.Rmd"), NA) test-rmarkdown.R:14:4
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat:::.capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. └─retrosheet:::runAllChunks("test-rmarkdown.Rmd")
   7.   └─rmarkdown::render(rmd, output_file = tempR, quiet = TRUE) test-rmarkdown.R:10:8
   8.     └─rmarkdown::pandoc_available(required_pandoc, error = TRUE)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 59 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pkgload’
  All declared Imports should be used.
Note: found 12 marked UTF-8 strings
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.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
installed size is 36.5Mb
  sub-directories of 1Mb or more:
    libs  35.2Mb
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.
Running ‘testthat.R’ [8s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-UtilFuncs-ConvFactor.R:31:5): conv.factor works ───────────────
  all(factorLoc2 == c(TRUE, FALSE, FALSE)) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure (test-UtilFuncs-ConvFactor.R:35:5): conv.factor works ───────────────
  all(factorLoc3 == c(TRUE, FALSE, TRUE)) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 640 ]
  Error: Test failures
  Execution halted
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
fs_author_ids : <anonymous>: no visible global function definition for
  ‘select.list’
fs_download : <anonymous>: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file select.list
Consider adding
  importFrom("utils", "download.file", "select.list")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
License components which are templates and need '+ file LICENSE':
  BSD 3-clause License
Packages in Depends field not imported from:
  ‘XML’ ‘xts’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
quoteFXTsData : function.fx: no visible global function definition for
  ‘xmlValue’
quoteFundTsData : function.fund: no visible global function definition
  for ‘xmlValue’
quoteStockTsData : function.stock: no visible global function
  definition for ‘xmlSize’
quoteStockTsData : function.stock: no visible global function
  definition for ‘xmlValue’
quoteTsData: no visible global function definition for ‘xmlRoot’
quoteTsData: no visible global function definition for ‘htmlTreeParse’
quoteTsData: no visible global function definition for
  ‘xmlErrorCumulator’
quoteTsData: no visible global function definition for ‘xmlSize’
toXts: no visible global function definition for ‘as.xts’
Undefined global functions or variables:
  as.xts htmlTreeParse xmlErrorCumulator xmlRoot xmlSize xmlValue
Package required and available but unsuitable version: ‘arkdb’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
Note: found 5 marked UTF-8 strings
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RFLPtools.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘rfm-customer-level-data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    group_rows

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 231-254 (rfm-customer-level-data.Rmd) 
Error: processing vignette 'rfm-customer-level-data.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘rfm-customer-level-data.Rmd’

--- re-building ‘rfm-transaction-level-data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    group_rows

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 227-251 (rfm-transaction-level-data.Rmd) 
Error: processing vignette 'rfm-transaction-level-data.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘rfm-transaction-level-data.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
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.
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘prob’ ‘titanic’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
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.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data      1.9Mb
    doc       2.2Mb
    extdata   2.7Mb
installed size is 149.4Mb
  sub-directories of 1Mb or more:
    doc         3.4Mb
    libs      142.0Mb
    pictures    1.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rGEDI.Rcheck/00install.out’ for details.
Found the following executable files:
  tests/credentials/GCS_AUTH_FILE.json.gpg
  tests/credentials/cd26ed5dc626f11802a652e81d02762e_data.colec.fbf@gmail.com.gpg
  tests/credentials/credentials.gpg
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
Package required but not available: ‘variancePartition’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
genoud: multiple local function definitions for ‘fn1.bfgs’ with
  different formal arguments
genoud: multiple local function definitions for ‘gr1’ with different
  formal arguments
genoud: multiple local function definitions for ‘hess.fn’ with
  different formal arguments
genoud_transform: multiple local function definitions for ‘fn1.bfgs’
  with different formal arguments
genoud_transform: multiple local function definitions for ‘gr1’ with
  different formal arguments
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rgeoda.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   4.4Mb
    libs      1.7Mb
Namespaces in Imports field not imported from:
  ‘leaflet’ ‘pals’ ‘raster’ ‘sp’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘rgeoprofile.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 141-142 (rgeoprofile.Rmd) 
Error: processing vignette 'rgeoprofile.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘rgeoprofile.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  20.9Mb
Package unavailable to check Rd xrefs: ‘Rsymphony’
Package suggested but not available for checking: ‘webshot2’
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rgl.Rcheck/00install.out’ for details.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    doc     3.6Mb
    fonts   1.5Mb
    libs    4.2Mb
Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.

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.
No protocol specified
No protocol specified
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rglwidget.Rcheck/00install.out’ for details.
installed size is 26.2Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  11.1Mb
    libs   9.6Mb
Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred.
File ‘RGtk2/libs/RGtk2.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_new_custom_connection’,
    ‘Rf_EncodeInteger’, ‘Rf_EncodeLogical’, ‘Rf_EncodeReal’,
    ‘Rf_formatInteger’, ‘Rf_formatLogical’, ‘Rf_formatReal’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 1473 marked UTF-8 strings
GoodmanWeare.rem: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc          10.2Mb
    htmlwidgets   1.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_rhandsontable.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 34-47 (intro_rhandsontable.Rmd) 
Error: processing vignette 'intro_rhandsontable.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘intro_rhandsontable.Rmd’

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

Error: Vignette re-building failed.
Execution halted
.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.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
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').
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rhpc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RHRV.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
RHT.2samp : my.HotellingT2 : my.InvCov2: no visible global function
  definition for ‘cov’
RHT.2samp : get.lambda : get.para: no visible global function
  definition for ‘optimize’
RHT.2samp : get.lambda : gg: no visible global function definition for
  ‘qchisq’
RHT.2samp : get.lambda : ggl: no visible global function definition for
  ‘qnorm’
RHT.2samp : <anonymous>: no visible global function definition for
  ‘cov’
RHT.fun : my.HotellingT : my.InvCov: no visible global function
  definition for ‘cov’
RHT.fun : get.lambda : get.para: no visible global function definition
  for ‘optimize’
RHT.fun : get.lambda : gg: no visible global function definition for
  ‘qchisq’
RHT.fun : get.lambda : ggl: no visible global function definition for
  ‘qnorm’
RHT.fun : <anonymous>: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov optimize qchisq qnorm
Consider adding
  importFrom("stats", "cov", "optimize", "qchisq", "qnorm")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'mimic.demo', 'eicu.demo'
FusedQDA : <anonymous>: no visible global function definition for ‘cov’
RidgeFused: no visible binding for global variable ‘cov2cor’
RidgeFusedCV : <anonymous>: no visible global function definition for
  ‘cov’
SSRidgeFused : <anonymous>: no visible global function definition for
  ‘cov’
Undefined global functions or variables:
  cov cov2cor
Consider adding
  importFrom("stats", "cov", "cov2cor")
to your NAMESPACE file.
ridit.raw: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Riemann.Rcheck/00install.out’ for details.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
prepare_Rd: RGL: unable to open X11 display
prepare_Rd: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Malformed Description field: should contain one or more complete sentences.
R2ngon: no visible global function definition for ‘approx’
plotR2pre: no visible global function definition for ‘plot’
plotR2pre: no visible global function definition for ‘points’
plotR2pre: no visible global function definition for ‘gray’
plotR2pre: no visible global function definition for ‘legend’
plotR2pre: no visible global function definition for ‘rainbow’
Undefined global functions or variables:
  approx gray legend plot points rainbow
Consider adding
  importFrom("grDevices", "gray", "rainbow")
  importFrom("graphics", "legend", "plot", "points")
  importFrom("stats", "approx")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘httr’ ‘remotes’ ‘rmarkdown’ ‘shiny’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘installr’
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RInside.Rcheck/00install.out’ for details.
File ‘RInside/libs/RInside.so’:
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLdo1’, ‘R_ReplDLLinit’,
    ‘R_RunExitFinalizers’, ‘R_SetParams’, ‘R_SignalHandlers’,
    ‘R_TempDir’, ‘Rf_endEmbeddedR’, ‘Rf_initEmbeddedR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘methods’ ‘readr’
  All declared Imports should be used.
Running ‘test-all.R’ [9s/12s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  
      stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, 44: 44:     wrap = wrap, load_package = load_package, parallel = parallel)    wrap = wrap, load_package = load_package, parallel = parallel)test_dir("testthat", package = package, reporter = reporter, test_dir("testthat", package = package, reporter = reporter, 
  
      ..., load_package = "installed")    ..., load_package = "installed")44: 44: 
  
  test_dir("testthat", package = package, reporter = reporter, test_dir("testthat", package = package, reporter = reporter, 45: 45:     ..., load_package = "installed")    ..., load_package = "installed")test_check("rio", reporter = "summary")test_check("rio", reporter = "summary")
  
  
  
  45: 45: An irrecoverable exception occurred. R is aborting now ...
  An irrecoverable exception occurred. R is aborting now ...
  test_check("rio", reporter = "summary")test_check("rio", reporter = "summary")
  
  An irrecoverable exception occurred. R is aborting now ...
  An irrecoverable exception occurred. R is aborting now ...
desmat.sanitize: no visible global function definition for ‘aggregate’
dispdist: no visible global function definition for ‘quantile’
dispdist: no visible global function definition for ‘hist’
dispdist: no visible global function definition for ‘lines’
estate: no visible global function definition for ‘weighted.mean’
estate: no visible global function definition for ‘lm’
genperms: no visible global function definition for ‘combn’
genprobexact: no visible global function definition for ‘ave’
invert.ci: no visible global function definition for ‘quantile’
invert.ci: no visible global function definition for ‘uniroot’
omni.ate: no visible global function definition for ‘hist’
omni.ate: no visible global function definition for ‘lines’
omni.ate: no visible global function definition for ‘quantile’
resresplot: no visible global function definition for ‘lm’
resresplot: no visible global function definition for ‘symbols’
resresplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline aggregate ave combn hist lines lm quantile symbols uniroot
  weighted.mean
Consider adding
  importFrom("graphics", "abline", "hist", "lines", "symbols")
  importFrom("stats", "aggregate", "ave", "lm", "quantile", "uniroot",
             "weighted.mean")
  importFrom("utils", "combn")
to your NAMESPACE file.
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/riskclustr.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  22.2Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
KM.plot: no visible global function definition for ‘plot’
KM.plot: no visible global function definition for ‘lines’
SchoenSmooth: no visible global function definition for ‘lm’
llCoxReg: no visible binding for global variable ‘time’
risksetAUC: no visible global function definition for ‘abline’
risksetROC: no visible global function definition for ‘abline’
weightedKM: no visible binding for global variable ‘time’
Undefined global functions or variables:
  abline lines lm plot time
Consider adding
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "lm", "time")
to your NAMESPACE file.
Alg2: no visible global function definition for ‘uniroot’
Alg3: no visible global function definition for ‘optim’
NVCopula: no visible global function definition for ‘rnorm’
NVCopula: no visible global function definition for ‘rgamma’
NVCopula: no visible global function definition for ‘var’
NVCopula: no visible global function definition for ‘cov’
NVCopula: no visible global function definition for ‘qnorm’
NVCopulaMT: no visible global function definition for ‘rnorm’
NVCopulaMT: no visible global function definition for ‘rgamma’
NVCopulaMT: no visible global function definition for ‘var’
NVCopulaMT: no visible global function definition for ‘cov’
NVCopulaMT: no visible global function definition for ‘qnorm’
R2X: no visible global function definition for ‘write.table’
ReturnCopula: no visible global function definition for ‘qt’
ReturnCopula: no visible global function definition for ‘pt’
SISCopula: no visible global function definition for ‘runif’
SISCopula: no visible global function definition for ‘qnorm’
SISCopula: no visible global function definition for ‘rnorm’
SISCopula: no visible global function definition for ‘qgamma’
SISCopula: no visible global function definition for ‘var’
SISCopula: no visible global function definition for ‘cov’
SISCopulaMT: no visible global function definition for ‘runif’
SISCopulaMT: no visible global function definition for ‘qnorm’
SISCopulaMT: no visible global function definition for ‘rnorm’
SISCopulaMT: no visible global function definition for ‘qgamma’
SISCopulaMT: no visible global function definition for ‘var’
SISCopulaMT: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov optim pt qgamma qnorm qt rgamma rnorm runif uniroot var
  write.table
Consider adding
  importFrom("stats", "cov", "optim", "pt", "qgamma", "qnorm", "qt",
             "rgamma", "rnorm", "runif", "uniroot", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Note: found 14 marked UTF-8 strings
Running examples in ‘RiverLoad-Ex.R’ failed
The error most likely occurred in:

> ### Name: method4
> ### Title: Load estimation with time-weighted concentration method
> ### Aliases: method4
> ### Keywords: univ
> 
> ### ** Examples
> 
> data("flow.data1", "conc.data1")
> union<-db.union(flow.data1, conc.data1)
> met4<-method4(union, 2)
> met4.month<-method4(union, 2, "month")
Error in x[[jj]][iseq] <- vjj : replacement has length zero
Calls: method4 -> [<- -> [<-.data.frame
Execution halted
Packages in Depends field not imported from:
  ‘compiler’ ‘signal’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
NumConv: no visible global function definition for ‘pchip’
NumConv: no visible global function definition for ‘cmpfun’
NumDeconv: no visible global function definition for ‘pchip’
NumDeconv : error_function: no visible global function definition for
  ‘pchip’
NumDeconv: no visible global function definition for ‘cmpfun’
NumDeconv: no visible global function definition for ‘optim’
RivivcA: no visible global function definition for ‘lm’
Undefined global functions or variables:
  cmpfun lm optim pchip
Consider adding
  importFrom("stats", "lm", "optim")
to your NAMESPACE file.
No protocol specified
No protocol specified
Found the following possibly unsafe calls:
File ‘rJava/R/import.R’:
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File ‘rJava/R/jinit.R’:
  unlockBinding(x, .env)
  unlockBinding(x, pe)
GNU make is a SystemRequirements.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile.win
  jri/src/win32/Makefile
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Note: information on .o files is not available
File ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API call to R: ‘R_GlobalContext’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    java   4.4Mb
Namespace in Imports field not imported from: ‘XLConnect’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘coda’
  All declared Imports should be used.
plot_jqpd: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
installed size is  8.5Mb
File
  LICENSE
is not mentioned in the DESCRIPTION file.
'library' or 'require' call to ‘rJava’ which was already attached by Depends.
  Please remove these calls from your code.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    datasets  10.2Mb
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    exe  23.8Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘arules’ ‘pmml’ ‘rJava’
  All declared Imports should be used.
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.9Mb
Packages suggested but not available for checking:
  'Biobase', 'genefilter', 'golubEsets'
cv.coef: no visible global function definition for ‘sd’
normalize.softmax: no visible global function definition for ‘plogis’
plot.rknnBeg: no visible global function definition for ‘plot’
plot.rknnBel: no visible global function definition for ‘plot’
plot.rknnSupport: no visible global function definition for ‘dotchart’
predicted: no visible global function definition for ‘influence’
predicted: no visible global function definition for ‘fitted’
predicted: no visible global function definition for ‘resid’
pressresid: no visible global function definition for ‘influence’
pressresid: no visible global function definition for ‘resid’
Undefined global functions or variables:
  dotchart fitted influence plogis plot resid sd
Consider adding
  importFrom("graphics", "dotchart", "plot")
  importFrom("stats", "fitted", "influence", "plogis", "resid", "sd")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rknots.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
installed size is 26.6Mb
  sub-directories of 1Mb or more:
    extdata  26.3Mb
Malformed Description field: should contain one or more complete sentences.
':::' calls which should be '::':
  ‘stats:::dexp’ ‘stats:::dgamma’ ‘stats:::dweibull’ ‘stats:::pexp’
  ‘stats:::pgamma’ ‘stats:::pweibull’ ‘stats:::qexp’ ‘stats:::qgamma’
  ‘stats:::qweibull’ ‘stats:::rexp’ ‘stats:::rgamma’ ‘stats:::rweibull’
  See the note in ?`:::` about the use of this operator.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 44.4Mb
  sub-directories of 1Mb or more:
    libs  43.8Mb
GNU make is a SystemRequirements.
Packages suggested but not available for checking:
  'org.Hs.eg.db', 'reactome.db'
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Namespace in Imports field not imported from: ‘Hmisc’
  All declared Imports should be used.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RCarb’ ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
Package in Depends field not imported from: ‘msm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘EMSRb_internal’ ‘EM_internal’ ‘PD_internal’
EMSRb_internal: no visible global function definition for ‘qnorm’
EM_internal: no visible global function definition for ‘dnorm’
EM_internal: no visible global function definition for ‘pnorm’
PD_internal: no visible global function definition for ‘qtnorm’
PD_internal: no visible global function definition for ‘sd’
Undefined global functions or variables:
  dnorm pnorm qnorm qtnorm sd
Consider adding
  importFrom("stats", "dnorm", "pnorm", "qnorm", "sd")
to your NAMESPACE file.
ma.filter: no visible global function definition for ‘par’
ma.filter: no visible global function definition for ‘lines’
ma.filter: no visible global function definition for ‘abline’
qn: no visible global function definition for ‘lm’
qn: no visible global function definition for ‘var’
qn: no visible global function definition for ‘resid’
ss.filter: no visible global function definition for ‘smooth.spline’
ss.filter: no visible global function definition for ‘par’
ss.filter: no visible global function definition for ‘lines’
ss.filter: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline lines lm par resid smooth.spline var
Consider adding
  importFrom("graphics", "abline", "lines", "par")
  importFrom("stats", "lm", "resid", "smooth.spline", "var")
to your NAMESPACE file.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Missing or unexported object: ‘tidyr::one_of’
Note: found 31 marked UTF-8 strings
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    rmd   8.2Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RMark.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘magrittr’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rmdcev.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rMEA.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RmecabKo.Rcheck/00install.out’ for details.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   5.7Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs       1.1Mb
    minizinc   3.2Mb
Package required but not available: ‘ROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
CI: no visible global function definition for ‘sd’
CI: no visible global function definition for ‘qt’
L: no visible global function definition for ‘sd’
L: no visible global function definition for ‘residuals’
Qa: no visible global function definition for ‘logLik’
Qb: no visible global function definition for ‘residuals’
Qc: no visible global function definition for ‘residuals’
Qc: no visible global function definition for ‘logLik’
STDERR: no visible global function definition for ‘sd’
group.UCL: no visible global function definition for ‘aggregate’
lr.glover: no visible binding for global variable ‘logLik’
lr.glover: no visible binding for global variable ‘update’
lr.glover : nobs0: no visible binding for global variable ‘nobs’
lr.glover : nobs0 : nobs2: no visible global function definition for
  ‘residuals’
lr.glover : tlab: no visible global function definition for ‘terms’
lr.glover : name: no visible global function definition for ‘formula’
lr.glover : modelUpdate: no visible global function definition for
  ‘as.formula’
lr.glover: no visible global function definition for ‘model.frame’
lr.glover: no visible binding for global variable ‘AIC’
lr.glover: no visible binding for global variable ‘BIC’
summarySE : <anonymous>: no visible global function definition for ‘sd’
summarySE: no visible global function definition for ‘qt’
Undefined global functions or variables:
  AIC BIC aggregate as.formula formula logLik model.frame nobs qt
  residuals sd terms update
Consider adding
  importFrom("stats", "AIC", "BIC", "aggregate", "as.formula", "formula",
             "logLik", "model.frame", "nobs", "qt", "residuals", "sd",
             "terms", "update")
to your NAMESPACE file.
Combi: no visible global function definition for ‘new’
barplotMixCluster: no visible global function definition for ‘is’
barplotMixCluster: no visible global function definition for ‘par’
barplotMixCluster: no visible global function definition for ‘lines’
barplotMixCluster: no visible global function definition for ‘text’
barplotMixCluster: no visible global function definition for ‘title’
barplotMixCluster: no visible global function definition for ‘mtext’
histMixCluster: no visible global function definition for ‘is’
histMixCluster: no visible global function definition for ‘par’
histMixCluster: no visible global function definition for ‘dnorm’
histMixCluster: no visible global function definition for ‘lines’
mixmodEntPlot: no visible global function definition for ‘par’
mixmodEntPlot: no visible global function definition for ‘lines’
mixmodEntPlot: no visible global function definition for ‘axis’
mixmodEntPlot: no visible global function definition for ‘title’
mixmodEntPlot: no visible binding for global variable ‘par’
plot,MixmodCombi: no visible global function definition for ‘par’
plot,MixmodCombi: no visible global function definition for ‘plot.new’
plot,MixmodCombi: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis dnorm is lines mtext new par plot.new text title
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "par", "plot.new",
             "text", "title")
  importFrom("methods", "is", "new")
  importFrom("stats", "dnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rmixmod.Rcheck/00install.out’ for details.
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    libs  28.5Mb
.pLGP_qvec: no visible global function definition for ‘ppois’
.qLGP_pvec: no visible global function definition for ‘qpois’
.rLGP.failsafe: no visible global function definition for ‘runif’
.subdmg: no visible global function definition for ‘dbinom’
dnegbin: no visible global function definition for ‘dnbinom’
pLGP: no visible global function definition for ‘ppois’
qLGP: no visible global function definition for ‘qpois’
rLGP: no visible global function definition for ‘rpois’
rLGP: no visible global function definition for ‘rnorm’
rLGP: no visible global function definition for ‘runif’
rbinegbin: no visible global function definition for ‘rnbinom’
rmanaclash: no visible global function definition for ‘rbinom’
rmanaclash: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dbinom dnbinom ppois qpois rbinom rnbinom rnorm rpois runif
Consider adding
  importFrom("stats", "dbinom", "dnbinom", "ppois", "qpois", "rbinom",
             "rnbinom", "rnorm", "rpois", "runif")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rmpi.Rcheck/00install.out’ for details.
Package required but not available: ‘splineTimeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 52.0Mb
  sub-directories of 1Mb or more:
    libs  51.6Mb
Namespaces in Imports field not imported from:
  ‘RcppParallel’ ‘rstantools’
  All declared Imports should be used.
blrmStats: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
GNU make is a SystemRequirements.
rms.pval: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
No protocol specified
No protocol specified
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
dWishartSpike: no visible global function definition for ‘dnorm’
pWishartSpike: no visible global function definition for ‘pnorm’
qWishartSpike: no visible global function definition for ‘qnorm’
rWishartSpike: no visible global function definition for ‘qnorm’
rmp: no visible global function definition for ‘runif’
rtw: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dnorm pnorm qnorm runif
Consider adding
  importFrom("stats", "dnorm", "pnorm", "qnorm", "runif")
to your NAMESPACE file.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
GNU make is a SystemRequirements.
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Note: found 133 marked Latin-1 strings
Package suggested but not available for checking: ‘rnaturalearthhires’
Note: found 7 marked Latin-1 strings
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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 20.3Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
Namespace in Imports field not imported from: ‘qtl’
  All declared Imports should be used.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Package unavailable to check Rd xrefs: ‘pbdMPI’
well19937.validate: 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  7.0Mb
  sub-directories of 1Mb or more:
    doxygen   1.9Mb
    libs      3.9Mb
installed size is 97.9Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     95.7Mb
Nnls.trimW : fun1: no visible global function definition for ‘runif’
initM: no visible global function definition for ‘runif’
rnmf: no visible global function definition for ‘txtProgressBar’
rnmf: no visible global function definition for ‘setTxtProgressBar’
see: no visible global function definition for ‘heat.colors’
see: no visible global function definition for ‘colorRampPalette’
see: no visible global function definition for ‘grey’
see: no visible global function definition for ‘par’
see: no visible global function definition for ‘image’
see: no visible global function definition for ‘mtext’
simtum: no visible global function definition for ‘runif’
simtum: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  colorRampPalette grey heat.colors image mtext par rnorm runif
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey", "heat.colors")
  importFrom("graphics", "image", "mtext", "par")
  importFrom("stats", "rnorm", "runif")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Found the following executable files:
  inst/extra/CD_BBI_16P02/CD_BBI_16P02-R1/10/fid
  inst/extra/CD_BBI_16P02/CD_BBI_16P02-R2/10/fid
  inst/extra/CD_BBI_16P02/CD_BBI_16P02-R3/10/fid
  inst/extra/CD_BBI_16P02/CD_BBI_16P02-R8/10/fid
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘impute’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rNOMADS.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.7Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R  11.2Mb
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  17.0Mb
'library' or 'require' calls in package code:
  ‘robustbase’ ‘sfsmisc’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.BuildPartial: no visible global function definition for ‘as.formula’
.BuildPartial: no visible global function definition for ‘residuals’
.PairwiseCorrelation : .Standardize : <anonymous>: no visible global
  function definition for ‘na.omit’
.PairwiseCorrelation : .Standardize: no visible binding for global
  variable ‘median’
.PairwiseCorrelation: no visible global function definition for
  ‘complete.cases’
.yw: no visible global function definition for ‘toeplitz’
FastQn: no visible global function definition for ‘median’
FastQn: no visible global function definition for ‘mad’
fqn: no visible global function definition for ‘median’
fqn: no visible global function definition for ‘mad’
psdcor: no visible global function definition for ‘posdefify’
psdcor: no visible global function definition for ‘nearcor’
robar: no visible global function definition for ‘frequency’
robcor: no visible global function definition for ‘covMcd’
s_FastQn: no visible global function definition for ‘median’
Undefined global functions or variables:
  as.formula complete.cases covMcd frequency mad median na.omit nearcor
  posdefify residuals toeplitz
Consider adding
  importFrom("stats", "as.formula", "complete.cases", "frequency", "mad",
             "median", "na.omit", "residuals", "toeplitz")
to your NAMESPACE file.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
Package required but not available: ‘gprege’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs  20.7Mb
Packages suggested but not available for checking:
  'affydata', 'hgu95av2cdf', 'beadarrayExampleData',
  'illuminaHumanv3.db'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RobLoxBioC.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Running ‘testthat.R’ [89s/89s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  x[9]: "Pub. bias       8/12       0.500       0.615    1.596"
  y[9]: "Pub. bias       8/12       0.500       0.615    1.598"
  
  x[13]: "mu              0.533  0.557 0.000 1.341"
  y[13]: "mu              0.537  0.559 0.000 1.333"
  
  x[14]: "tau             0.132  0.000 0.000 0.852"
  y[14]: "tau             0.131  0.000 0.000 0.861"
  
  x[16]: "omega[0.05,0.1] 0.766  0.878 0.139 1.000"
  y[16]: "omega[0.05,0.1] 0.762  0.875 0.130 1.000"
  
  [ FAIL 2 | WARN 0 | SKIP 7 | PASS 3 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
RobRSVD: no visible global function definition for ‘median’
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘DEoptimR’ ‘DT’ ‘PerformanceAnalytics’ ‘ggplot2’ ‘graphics’
  ‘gridExtra’ ‘methods’ ‘shinyjs’ ‘utils’ ‘xts’
  All declared Imports should be used.
Note: found 6 marked UTF-8 strings
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
Packages in Depends field not imported from:
  ‘Rcpp’ ‘RcppArmadillo’ ‘mgcv’ ‘robustbase’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GIC: no visible global function definition for ‘integrate’
QM.poisson: no visible global function definition for ‘ppois’
QM.poisson: no visible global function definition for ‘dpois’
cplot.robustgam: no visible global function definition for ‘plot’
expect.poisson: no visible global function definition for ‘dpois’
expect.poisson: no visible global function definition for ‘ppois’
pred.robustgam: no visible global function definition for
  ‘Predict.matrix’
robust.sigma: no visible global function definition for ‘median’
robustgam: no visible global function definition for ‘s’
robustgam: no visible global function definition for
  ‘smooth.construct.tp.smooth.spec’
robustgam: no visible global function definition for
  ‘smooth.construct.cr.smooth.spec’
robustgam: no visible global function definition for
  ‘smooth.construct.ps.smooth.spec’
robustgam : w.fun: no visible global function definition for ‘covMcd’
robustgam.GIC.optim: no visible global function definition for ‘optim’
robustgam.crossval : w.fun: no visible global function definition for
  ‘covMcd’
robustgam.crossval: no visible global function definition for
  ‘integrate’
smooth.construct.tr.smooth.spec: no visible global function definition
  for ‘quantile’
w.binomial: no visible global function definition for ‘pbinom’
w.poisson: no visible global function definition for ‘ppois’
Undefined global functions or variables:
  Predict.matrix covMcd dpois integrate median optim pbinom plot ppois
  quantile s smooth.construct.cr.smooth.spec
  smooth.construct.ps.smooth.spec smooth.construct.tp.smooth.spec
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dpois", "integrate", "median", "optim", "pbinom",
             "ppois", "quantile")
to your NAMESPACE file.
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    libs  30.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 33.0Mb
  sub-directories of 1Mb or more:
    libs  32.0Mb
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.
aggregateRanks: no visible binding for global variable ‘median’
aggregateRanks: no visible global function definition for ‘pnorm’
betaScores: no visible global function definition for ‘pbeta’
correctBetaPvaluesExact: no visible binding for global variable ‘qbeta’
thresholdBetaScore: no visible global function definition for ‘pbeta’
Undefined global functions or variables:
  median pbeta pnorm qbeta
Consider adding
  importFrom("stats", "median", "pbeta", "pnorm", "qbeta")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RockFab.Rcheck/00install.out’ for details.
Malformed Title field: should not end in a period.
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
Namespace in Imports field not imported from: ‘progress’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ROCS.Rcheck/00install.out’ for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RODBC.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘RODBC’
A package should be listed in only one of these fields.
'library' or 'require' call to ‘RODBC’ which was already attached by Depends.
  Please remove these calls from your code.
Package required but not available: ‘clpAPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcplex’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rsymphony’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
GNU make is a SystemRequirements.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         2.7Mb
    extdata   2.7Mb
Namespace in Imports field not imported from: ‘matrixcalc’
  All declared Imports should be used.
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
sh: cmake: command not found
sh: cmake: command not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
sh: cmake: command not found
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
sh: cmake: command not found
sh: cmake: command not found
sh: cmake: command not found
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: ‘RobLox’
Package unavailable to check Rd xrefs: ‘RobLox’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ROracle.Rcheck/00install.out’ for details.
ROSE.eval: no visible global function definition for ‘methods’
ROSE.eval: no visible binding for global variable ‘model.frame’
ROSE.eval: no visible binding for global variable ‘predict’
adj.formula: no visible global function definition for ‘terms’
adj.formula: no visible global function definition for ‘as.formula’
omnibus.balancing: no visible binding for global variable ‘model.frame’
ou.sampl: no visible global function definition for ‘rbinom’
over.sampl: no visible global function definition for ‘rbinom’
plot.roc.inner: no visible global function definition for ‘plot’
roc.curve: no visible global function definition for ‘lines’
roc.curve: no visible global function definition for ‘abline’
rose.real: no visible binding for global variable ‘sd’
rose.real: no visible global function definition for ‘sd’
rose.real: no visible global function definition for ‘rnorm’
rose.sampl: no visible global function definition for ‘rbinom’
under.sampl: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  abline as.formula lines methods model.frame plot predict rbinom rnorm
  sd terms
Consider adding
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "as.formula", "model.frame", "predict", "rbinom",
             "rnorm", "sd", "terms")
  importFrom("utils", "methods")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘diptest’ ‘methods’ ‘viridis’
  All declared Imports should be used.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.7Mb
    libs   5.3Mb
Running examples in ‘rotations-Ex.R’ failed
The error most likely occurred in:

> ### Name: head
> ### Title: Return the First or Last Parts of an Object
> ### Aliases: head head.SO3 head.Q4
> 
> ### ** Examples
> 
> head(letters)
[1] "a" "b" "c" "d" "e" "f"
> head(letters, n = -6L)
 [1] "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "l" "m" "n" "o" "p" "q" "r" "s"
[20] "t"
> 
> head(freeny.x, n = 10L)
      lag quarterly revenue price index income level market potential
 [1,]               8.79636     4.70997      5.82110          12.9699
 [2,]               8.79236     4.70217      5.82558          12.9733
 [3,]               8.79137     4.68944      5.83112          12.9774
 [4,]               8.81486     4.68558      5.84046          12.9806
 [5,]               8.81301     4.64019      5.85036          12.9831
 [6,]               8.90751     4.62553      5.86464          12.9854
 [7,]               8.93673     4.61991      5.87769          12.9900
 [8,]               8.96161     4.61654      5.89763          12.9943
 [9,]               8.96044     4.61407      5.92574          12.9992
[10,]               9.00868     4.60766      5.94232          13.0033
> head(freeny.y)
[1] 8.79236 8.79137 8.81486 8.81301 8.90751 8.93673
> 
> head(iris3)
[1] 5.1 4.9 4.7 4.6 5.0 5.4
> head(iris3, c(6L, 2L))
Error in head.default(iris3, c(6L, 2L)) : length(n) == 1L is not TRUE
Calls: head -> head.default -> stopifnot
Execution halted
bestFM: no visible global function definition for ‘data’
gaRoth: no visible global function definition for ‘data’
ros: no visible global function definition for ‘na.omit’
rosunc: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  data na.omit rnorm
Consider adding
  importFrom("stats", "na.omit", "rnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
.computeValueReduct: no visible global function definition for ‘combn’
.findAllReductsFromCore: no visible global function definition for
  ‘combn’
.findFirstReductsFromCore: no visible global function definition for
  ‘combn’
.findSmallestReductFamilyFromCore: no visible global function
  definition for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘geometry’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘httpuv’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
royston.test: no visible global function definition for ‘shapiro.test’
royston.test: no visible global function definition for ‘cor’
royston.test: no visible global function definition for ‘qnorm’
royston.test: no visible global function definition for ‘pnorm’
royston.test: no visible global function definition for ‘cov’
royston.test: no visible global function definition for ‘mahalanobis’
royston.test: no visible global function definition for ‘qqplot’
royston.test: no visible global function definition for ‘qchisq’
royston.test: no visible global function definition for ‘ppoints’
royston.test: no visible global function definition for ‘abline’
royston.test: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  abline cor cov mahalanobis pchisq pnorm ppoints qchisq qnorm qqplot
  shapiro.test
Consider adding
  importFrom("graphics", "abline")
  importFrom("stats", "cor", "cov", "mahalanobis", "pchisq", "pnorm",
             "ppoints", "qchisq", "qnorm", "qqplot", "shapiro.test")
to your NAMESPACE file.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R       3.3Mb
    libs    2.4Mb
    tests   1.8Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rpanel.Rcheck/00install.out’ for details.
License components which are templates and need '+ file LICENSE':
  MIT
Package in Depends field not imported from: ‘hash’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
P: no visible global function definition for ‘has.key’
get_rand_int: no visible global function definition for ‘runif’
last: no visible global function definition for ‘tail’
rand_partitions: no visible global function definition for ‘hash’
Undefined global functions or variables:
  has.key hash runif tail
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "tail")
to your NAMESPACE file.
evalMedian: no visible global function definition for ‘xtabs’
evalMode: no visible global function definition for ‘xtabs’
rpartScore: no visible global function definition for ‘model.extract’
rpartScore: no visible global function definition for ‘var’
rpartScore: no visible binding for global variable ‘var’
splitAbs: no visible global function definition for ‘xtabs’
Undefined global functions or variables:
  model.extract var xtabs
Consider adding
  importFrom("stats", "model.extract", "var", "xtabs")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
'library' or 'require' call to ‘RODBC’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
rpart.rules.push: no visible global function definition for ‘sqlSave’
rpart.rules.table : <anonymous>: no visible global function definition
  for ‘setNames’
rpart.subrules.table : <anonymous>: no visible global function
  definition for ‘setNames’
Undefined global functions or variables:
  setNames sqlSave
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘survival’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘MASS’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GenerateData: no visible global function definition for ‘mvrnorm’
GetVarImp : FitPenalizedModel: no visible global function definition
  for ‘clogit’
Undefined global functions or variables:
  clogit mvrnorm
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rpdb.Rcheck/00install.out’ for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  20.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘NEWS.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘NEWS.Rmd’

--- re-building ‘rpivotTableIntroduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 51-53 (rpivotTableIntroduction.Rmd) 
Error: processing vignette 'rpivotTableIntroduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘rpivotTableIntroduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rpolyhedra.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘testthat’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rpoppler.Rcheck/00install.out’ for details.
Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/libpq/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RPPASPACE.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘rpredictit-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 54-56 (rpredictit-vignette.Rmd) 
Error: processing vignette 'rpredictit-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘rpredictit-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'graph', 'Rgraphviz'
GNU make is a SystemRequirements.
installed size is 32.2Mb
  sub-directories of 1Mb or more:
    libs  30.4Mb
Namespaces in Imports field not imported from:
  ‘ape’ ‘igraph’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
installed size is 90.4Mb
  sub-directories of 1Mb or more:
    libs  89.8Mb
Namespace in Imports field not imported from: ‘NatureSounds’
  All declared Imports should be used.
Missing link or links in documentation object 'exp_est.Rd':
  ‘[warbleR]{resample_est_waves}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Rraven.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: tuneR
Loading required package: seewave
Loading required package: NatureSounds
Loading required package: knitr

NOTE: functions are being renamed (run 'print(new_function_names)' to see new names). Both old and new names are available in this version 
 Please see citation('warbleR') for use in publication
Quitting from lines 232-246 (Rraven.Rmd) 
Error: processing vignette 'Rraven.Rmd' failed with diagnostics:
could not find function "spectro_analysis"
--- failed re-building ‘Rraven.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rrd.Rcheck/00install.out’ for details.
Packages in Depends field not imported from:
  ‘glasso’ ‘matrixcalc’ ‘mvoutlier’ ‘pcaPP’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
rrest: no visible binding for global variable ‘glasso’
rrest: no visible global function definition for ‘pcout’
rrest: no visible global function definition for ‘var’
rrest: no visible global function definition for ‘mahalanobis’
rrlda : centerObservations: no visible global function definition for
  ‘l1median_NLM’
rrlda : df.L2glasso: no visible global function definition for
  ‘duplication.matrix’
rrlda : alt.df.L2glasso: no visible global function definition for
  ‘lower.triangle’
Undefined global functions or variables:
  duplication.matrix glasso l1median_NLM lower.triangle mahalanobis
  pcout var
Consider adding
  importFrom("stats", "mahalanobis", "var")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
No protocol specified
No protocol specified
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘robustbase’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.computekappa: no visible global function definition for ‘pnorm’
.computekappa: no visible global function definition for ‘dnorm’
.initmethod : <anonymous>: no visible global function definition for
  ‘median’
.initmethod: no visible global function definition for ‘model.matrix’
.mspe: no visible global function definition for ‘rnorm’
.mspe : <anonymous>: no visible global function definition for ‘rnorm’
makedata: no visible global function definition for ‘rnorm’
makedata : addraneff: no visible global function definition for ‘rnorm’
plot.meanssaemodel: no visible global function definition for ‘par’
plot.meanssaemodel: no visible global function definition for ‘plot’
plot.meanssaemodel: no visible global function definition for ‘lines’
plot.meanssaemodel: no visible global function definition for ‘axis’
plot.meanssaemodel: no visible global function definition for ‘grid’
plot.meanssaemodel: no visible global function definition for ‘box’
plot.meanssaemodel: no visible global function definition for ‘legend’
plot.meanssaemodel: no visible global function definition for ‘arrows’
saemodel: no visible global function definition for ‘model.frame’
saemodel: no visible global function definition for ‘model.response’
saemodel: no visible global function definition for ‘model.matrix’
summary.fitsaemodel: no visible global function definition for ‘pt’
summary.fitsaemodel: no visible global function definition for
  ‘printCoefmat’
Undefined global functions or variables:
  arrows axis box dnorm grid legend lines median model.frame
  model.matrix model.response par plot pnorm printCoefmat pt rnorm
Consider adding
  importFrom("graphics", "arrows", "axis", "box", "grid", "legend",
             "lines", "par", "plot")
  importFrom("stats", "dnorm", "median", "model.frame", "model.matrix",
             "model.response", "pnorm", "printCoefmat", "pt", "rnorm")
to your NAMESPACE file.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
stripslash: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lubridate’ ‘reshape2’ ‘tidyr’
  All declared Imports should be used.
Package required but not available: ‘gWidgets2RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    dependencies  20.2Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘labelled’
  All declared Imports should be used.
convexhull: no visible global function definition for ‘chull’
convexhull: no visible global function definition for ‘rnorm’
drawcompletegraph: no visible global function definition for ‘plot’
drawcompletegraph: no visible global function definition for ‘segments’
getbag: no visible global function definition for ‘plot’
getbag: no visible global function definition for ‘chull’
getbag: no visible global function definition for ‘polygon’
getbag: no visible global function definition for ‘points’
inflate: no visible global function definition for ‘rnorm’
rsmed: no visible global function definition for ‘runif’
rsplot: no visible global function definition for ‘plot’
rsplot: no visible global function definition for ‘chull’
rsplot: no visible global function definition for ‘polygon’
rsplot: no visible global function definition for ‘points’
rsrings: no visible global function definition for ‘plot’
rsrings: no visible global function definition for ‘chull’
rsrings: no visible global function definition for ‘polygon’
rsrings: no visible global function definition for ‘points’
rstinterval: no visible global function definition for ‘plot’
rstinterval: no visible global function definition for ‘runif’
rstinterval: no visible global function definition for ‘rnorm’
rstinterval: no visible global function definition for ‘chull’
rstinterval: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  chull plot points polygon rnorm runif segments
Consider adding
  importFrom("grDevices", "chull")
  importFrom("graphics", "plot", "points", "polygon", "segments")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Found the following executable file:
  data/GH.RData
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘Rcompression’
Namespaces in Imports field not imported from:
  ‘binman’ ‘httr’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Note: information on .o files is not available
File ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
addNoisyCopies: no visible global function definition for ‘rnorm’
eta: no visible global function definition for ‘var’
gaussClassifier: no visible global function definition for ‘runif’
getSigma: no visible global function definition for ‘sd’
getSigma: no visible binding for global variable ‘sd’
sfaClassify: no visible global function definition for ‘rainbow’
sfaClassify: no visible global function definition for ‘par’
sfaClassify: no visible global function definition for ‘plot’
sfaClassify: no visible global function definition for ‘points’
sfaClassify: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines par plot points rainbow rnorm runif sd var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "lines", "par", "plot", "points")
  importFrom("stats", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
installed size is 27.4Mb
  sub-directories of 1Mb or more:
    libs  25.5Mb
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
Note: found 467 marked UTF-8 strings
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Running ‘rsolr_unit_tests.R’ [8s/11s]
Running the tests in ‘tests/rsolr_unit_tests.R’ failed.
Last 13 lines of output:
  100   180  100   180    0     0    166      0  0:00:01  0:00:01 --:--:--   166
  
  100   645  100   645    0     0    451      0  0:00:01  0:00:01 --:--:--   451
  
    1  144M    1 2177k    0     0  1107k      0  0:02:13  0:00:01  0:02:12 1107k
   15  144M   15 22.8M    0     0  7885k      0  0:00:18  0:00:02  0:00:16 20.7M
   30  144M   30 44.4M    0     0  11.2M      0  0:00:12  0:00:03  0:00:09 21.1M
   46  144M   46 67.0M    0     0  13.5M      0  0:00:10  0:00:04  0:00:06 21.6M
   62  144M   62 90.4M    0     0  15.1M      0  0:00:09  0:00:05  0:00:04 22.0M
   79  144M   79  114M    0     0  16.4M      0  0:00:08  0:00:06  0:00:02 22.4M
   96  144M   96  139M    0     0  17.4M      0  0:00:08  0:00:07  0:00:01 23.2M
  100  144M  100  144M    0     0  17.6M      0  0:00:08  0:00:08 --:--:-- 23.7M
  Error in unzip(file, exdir = exdir) : 'exdir' does not exist
  Calls: <Anonymous> ... runSolr -> maybeInstallSolr -> installSolr -> unpack -> unzip
  Execution halted
Errors in running code in vignettes:
when running code in ‘intro.Rnw’
  ...

 18  144M   18 27.1M    0     0  21.8M      0  0:00:06  0:00:01  0:00:05 21.8M
 40  144M   40 58.8M    0     0  26.1M      0  0:00:05  0:00:02  0:00:03 31.6M
 62  144M   62 90.8M    0     0  27.9M      0  0:00:05  0:00:03  0:00:02 31.8M
 84  144M   84  122M    0     0  28.8M      0  0:00:05  0:00:04  0:00:01 31.8M
100  144M  100  144M    0     0  29.3M      0  0:00:04  0:00:04 --:--:-- 31.8M

  When sourcing ‘intro.R’:
Error: 'exdir' does not exist
Execution halted

  ‘intro.Rnw’... failed
Namespace in Imports field not imported from: ‘h2o’
  All declared Imports should be used.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
Package suggested but not available for checking: ‘INLA’
installed size is 46.4Mb
  sub-directories of 1Mb or more:
    libs  45.8Mb
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
negbin.pow : negbin.disp: no visible global function definition for
  ‘rpois’
negbin.pow : negbin.disp: no visible global function definition for
  ‘rnbinom’
negbin.pow : inner.fcn: no visible global function definition for
  ‘na.omit’
negbin.pow : inner.fcn: no visible global function definition for
  ‘quantile’
negbin.pow: no visible global function definition for ‘txtProgressBar’
negbin.pow: no visible global function definition for
  ‘setTxtProgressBar’
poiss.pow : inner.fcn: no visible global function definition for
  ‘rpois’
poiss.pow : inner.fcn: no visible global function definition for
  ‘quantile’
poiss.pow: no visible global function definition for ‘txtProgressBar’
poiss.pow: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  na.omit quantile rnbinom rpois setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit", "quantile", "rnbinom", "rpois")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘knitr’
  All declared Imports should be used.
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Error: 'nchar()' requires a character vector
  Backtrace:
      █
   1. └─rsql$gen_update("mtcars", values = update_values, where_values = where_values_df) test_sql_lib.R:138:4
   2.   └─RSQL:::sql_gen_update(...)
   3.     └─RSQL::stuff_df_quoted(text.df = values.df)
   4.       └─base::sapply(text.df[i, ], FUN = rm_quotes)
   5.         └─base::lapply(X = X, FUN = FUN, ...)
   6.           └─RSQL:::FUN(X[[i]], ...)
   7.             └─base::substr(text, nchar(text), nchar(text))
  
  [ FAIL 1 | WARN 7 | SKIP 0 | PASS 20 ]
  Finalizing object and disconnecting
  Error: Test failures
  Execution halted
Package required but not available: ‘GMMAT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
installed size is 177.2Mb
  sub-directories of 1Mb or more:
    R       1.5Mb
    doc     4.5Mb
    libs  170.6Mb
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Running examples in ‘rstanarm-Ex.R’ failed
The error most likely occurred in:

> ### Name: example_jm
> ### Title: Example joint longitudinal and time-to-event model
> ### Aliases: example_jm
> 
> ### ** Examples
> 
>   # set.seed(123)
>   if (.Platform$OS.type != "windows" || .Platform$r_arch !="i386")
+   example_jm <- 
+      stan_jm(formulaLong = logBili ~ year + (1 | id), 
+              dataLong = pbcLong[1:101,],
+              formulaEvent = survival::Surv(futimeYears, death) ~ sex + trt, 
+              dataEvent = pbcSurv[1:15,],
+              time_var = "year",
+              # this next line is only to keep the example small in size!
+              chains = 1, seed = 12345, iter = 100, refresh = 0)
Loading required namespace: data.table
Fitting a univariate joint model.

Please note the warmup may be much slower than later iterations!
[1] "Error in sampler$call_sampler(args_list[[i]]) : "             
[2] "  empty_nested() must be true before calling recover_memory()"
error occurred during calling the sampler; sampling not done
Error in check_stanfit(stanfit) : 
  Invalid stanfit object produced please report bug
Calls: stan_jm -> stan_jm.fit -> check_stanfit
Execution halted
Running ‘testthat.R’ [12s/52s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
            ^
  /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/StanHeaders/include/stan/math/rev/mat/fun/squared_distance.hpp:64:11: warning: unused type alias 'idx_t' [-Wunused-local-typedef]
      using idx_t = typename index_type<matrix_d>::type;
            ^
  make: *** [fileff283e609676.o] Interrupt: 2
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_stan_functions.R:70:1): (code run outside of `test_that()`) ─────
  Error: $ operator is invalid for atomic vectors
  Backtrace:
      █
   1. └─rstan::expose_stan_functions(stanc_ret, rebuild = TRUE, verbose = TRUE) test_stan_functions.R:70:0
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 1 ]
  Error: Test failures
  Execution halted
installed size is 35.0Mb
  sub-directories of 1Mb or more:
    libs  34.5Mb
GNU make is a SystemRequirements.
installed size is 260.3Mb
  sub-directories of 1Mb or more:
    lib    29.0Mb
    libs  228.6Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘RcppParallel’
  All declared Imports should be used.
installed size is 69.5Mb
  sub-directories of 1Mb or more:
    libs  68.3Mb
Namespace in Imports field not imported from: ‘loo’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Note: found 117 marked UTF-8 strings
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    libs  16.0Mb
Namespace in Imports field not imported from: ‘mc2d’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
Malformed Title field: should not end in a period.
installed size is 94.0Mb
  sub-directories of 1Mb or more:
    libs  93.6Mb
Note: found 18627 marked UTF-8 strings
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rsymphony.Rcheck/00install.out’ for details.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    Lib  11.6Mb
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Math.Sym: no visible binding for global variable ‘transtab’
jythonStart: no visible global function definition for ‘.jinit’
jythonStart: no visible global function definition for ‘.jnew’
jythonStart: no visible binding for global variable ‘.Jython’
sympy: no visible binding for global variable ‘.Jython’
sympy: no visible global function definition for ‘.jstrVal’
sympyStart: no visible binding for global variable ‘.Jython’
Undefined global functions or variables:
  .Jython .jinit .jnew .jstrVal transtab
Error(s) in re-building vignettes:
  ...
--- re-building ‘rsyncrosim_tutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 15-19 (rsyncrosim_tutorial.Rmd) 
Error: processing vignette 'rsyncrosim_tutorial.Rmd' failed with diagnostics:
object 'params' not found
--- failed re-building ‘rsyncrosim_tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R           1.0Mb
    bootstrap   1.6Mb
    data        2.2Mb
Malformed Title field: should not end in a period.
barplot.rtconnect: no visible global function definition for ‘rainbow’
barplot.rtconnect: no visible global function definition for ‘text’
plot.rtconnect: no visible global function definition for ‘par’
plot.rtconnect: no visible global function definition for ‘plot’
plot.rtconnect: no visible global function definition for ‘axis.Date’
rtconnect: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  axis.Date par plot rainbow read.table text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis.Date", "par", "plot", "text")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘stats’
  All declared Imports should be used.
Note: found 2 marked UTF-8 strings
Malformed Description field: should contain one or more complete sentences.
plotGLCM: no visible global function definition for ‘plot’
plotGLCM: no visible global function definition for ‘points’
Undefined global functions or variables:
  plot points
Consider adding
  importFrom("graphics", "plot", "points")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘httr’ ‘logger’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘stringr’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘MASS’ ‘gridExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.9Mb
    projects   2.7Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RTL.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘memoise’ ‘tidyr’
  All declared Imports should be used.
Note: found 37 marked UTF-8 strings
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is 29.4Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  20.7Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘DT’ ‘rmarkdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Note: found 113868 marked UTF-8 strings
GNU make is a SystemRequirements.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   2.7Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   6.5Mb
Packages required and available but unsuitable versions: 'stats', 'utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘urltools’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
Packages required but not available:
  'GSVAdata', 'clusterProfiler', 'org.Hs.eg.db', 'rWikiPathways'

Packages required and available but unsuitable versions:
  'edgeR', 'ComplexHeatmap', 'GSEABase'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 41.2Mb
  sub-directories of 1Mb or more:
    libs  40.5Mb
Package suggested but not available for checking: ‘webfakes’
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [4s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Error: there is no package called 'webfakes'
  Backtrace:
      █
   1. └─webfakes::local_app_process test-session.R:89:2
   2.   └─base::getExportedValue(pkg, name)
   3.     └─base::asNamespace(ns)
   4.       └─base::getNamespace(ns)
   5.         └─base::loadNamespace(name)
   6.           └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   7.             └─base:::withOneRestart(expr, restarts[[1L]])
   8.               └─base:::doWithOneRestart(return(expr), restart)
  
  [ FAIL 2 | WARN 0 | SKIP 26 | PASS 90 ]
  Error: Test failures
  Execution halted
Malformed Title field: should not end in a period.
HapMendlianCheck: no visible global function definition for
  ‘write.table’
rvPDT.test.sub: no visible global function definition for ‘pnorm’
whap.prehap: no visible global function definition for ‘write.table’
whap.prehap: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  pnorm read.table write.table
Consider adding
  importFrom("stats", "pnorm")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Package required but not available: ‘rpanel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gpuR’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
installed size is 63.3Mb
  sub-directories of 1Mb or more:
    include   3.9Mb
    libs     59.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RVowpalWabbit.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
lc_TDT: no visible global function definition for ‘pchisq’
rvTDT: no visible global function definition for ‘dbeta’
Undefined global functions or variables:
  dbeta pchisq
Consider adding
  importFrom("stats", "dbeta", "pchisq")
to your NAMESPACE file.
LASSO: no visible global function definition for ‘lm’
LASSO: no visible global function definition for ‘anova’
LASSO: no visible global function definition for ‘glm’
LASSO: no visible global function definition for ‘pchisq’
LASSO : <anonymous>: no visible global function definition for
  ‘extractAIC’
PCR : <anonymous>: no visible global function definition for ‘cor’
PLS : <anonymous>: no visible global function definition for ‘cor’
RR : RRscore: no visible binding for global variable ‘sd’
SPLS: no visible global function definition for ‘lm’
SPLS: no visible global function definition for ‘anova’
SPLS : <anonymous>: no visible global function definition for
  ‘extractAIC’
VTWOD : getScores: no visible global function definition for ‘sd’
VTWOD : getScores: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  anova cor extractAIC glm lm pchisq pnorm sd
Consider adding
  importFrom("stats", "anova", "cor", "extractAIC", "glm", "lm",
             "pchisq", "pnorm", "sd")
to your NAMESPACE file.
check_ISO_code: no visible binding for global variable ‘NoAm_country’
check_ISO_code: no visible binding for global variable ‘SoAm_country’
check_ISO_code: no visible binding for global variable ‘Oceana_country’
check_ISO_code: no visible binding for global variable ‘Africa_country’
check_ISO_code: no visible binding for global variable ‘Asia_country’
check_ISO_code: no visible binding for global variable ‘Eur_country’
climate_map: no visible binding for global variable ‘data’
date_correct: no visible global function definition for ‘tail’
Undefined global functions or variables:
  Africa_country Asia_country Eur_country NoAm_country Oceana_country
  SoAm_country data tail
Consider adding
  importFrom("utils", "data", "tail")
to your NAMESPACE file.
RWBP.default: no visible global function definition for ‘na.omit’
RWBP.default: no visible global function definition for ‘kmeans’
RWBP.formula: no visible global function definition for ‘model.extract’
plot.RWBP: no visible global function definition for ‘plot’
predict.RWBP: no visible global function definition for ‘head’
Undefined global functions or variables:
  head kmeans model.extract na.omit plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "kmeans", "model.extract", "na.omit")
  importFrom("utils", "head")
to your NAMESPACE file.
weblogo: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
Note: found 4250 marked UTF-8 strings
Note: found 6 marked UTF-8 strings
File
  LICENSE
is not mentioned in the DESCRIPTION file.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Note: found 2016 marked UTF-8 strings
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Malformed Title field: should not end in a period.
Note: found 426306 marked UTF-8 strings
.dwt: no visible global function definition for ‘median’
.udwt: no visible global function definition for ‘median’
plotSignalTransformation: no visible global function definition for
  ‘plot’
plotSignalTransformation: no visible global function definition for
  ‘box’
plotSignalTransformation: no visible global function definition for
  ‘axis’
plotSignalTransformation: no visible global function definition for
  ‘lines’
plotSignalTransformation: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  axis box legend lines median plot
Consider adding
  importFrom("graphics", "axis", "box", "legend", "lines", "plot")
  importFrom("stats", "median")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RxODE.Rcheck/00install.out’ for details.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs    8.5Mb
    yacas   1.3Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs    9.2Mb
    yacas   1.3Mb
Malformed Title field: should not end in a period.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
installed size is 31.7Mb
  sub-directories of 1Mb or more:
    include   2.4Mb
    libs     28.3Mb
Namespace in Imports field not imported from: ‘spanel’
  All declared Imports should be used.
calculate.summary: no visible global function definition for ‘sd’
detect.saccades: no visible global function definition for ‘median’
diagnostic.plot: no visible global function definition for ‘dev.new’
diagnostic.plot: no visible global function definition for ‘par’
diagnostic.plot: no visible global function definition for ‘recordPlot’
diagnostic.plot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.new dev.off median par recordPlot sd
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "recordPlot")
  importFrom("graphics", "par")
  importFrom("stats", "median", "sd")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘R6’ ‘mgcv’
  All declared Imports should be used.
Graf.Diagnostic: no visible global function definition for ‘plot’
Plot.ll: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
fit.saery.AR1: no visible global function definition for ‘qnorm’
fit.saery.MA1: no visible global function definition for ‘qnorm’
fit.saery.indep: no visible global function definition for ‘qnorm’
mse.saery.boot.AR1.typeI: no visible global function definition for
  ‘rnorm’
mse.saery.boot.AR1.typeI: no visible global function definition for
  ‘write.table’
mse.saery.boot.AR1.typeII: no visible global function definition for
  ‘rnorm’
mse.saery.boot.AR1.typeII: no visible global function definition for
  ‘write.table’
mse.saery.boot.MA1.typeI: no visible global function definition for
  ‘rnorm’
mse.saery.boot.MA1.typeI: no visible global function definition for
  ‘write.table’
mse.saery.boot.MA1.typeII: no visible global function definition for
  ‘rnorm’
mse.saery.boot.MA1.typeII: no visible global function definition for
  ‘write.table’
plot.saery: no visible global function definition for ‘devAskNewPage’
plot.saery: no visible global function definition for ‘par’
plot.saery: no visible global function definition for ‘plot’
plot.saery: no visible global function definition for ‘abline’
plot.saery: no visible global function definition for ‘title’
plot.saery: no visible global function definition for ‘axis’
plot.saery: no visible global function definition for ‘lines’
plot.saery: no visible global function definition for ‘legend’
pvalue: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline axis devAskNewPage legend lines par plot pnorm qnorm rnorm
  title write.table
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "title")
  importFrom("stats", "pnorm", "qnorm", "rnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
rc.plot: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Package in Depends field not imported from: ‘lpSolveAPI’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
glm: no visible binding for global variable ‘gaussian’
glm: no visible global function definition for ‘glm.control’
glm: no visible global function definition for ‘model.response’
glm: no visible global function definition for ‘is.empty.model’
glm: no visible global function definition for ‘model.matrix’
glm: no visible global function definition for ‘model.weights’
glm: no visible global function definition for ‘model.offset’
glm: no visible global function definition for ‘model.extract’
glm: no visible global function definition for ‘glm.fit’
glm: no visible global function definition for ‘.getXlevels’
separator: no visible global function definition for ‘make.lp’
separator: no visible global function definition for ‘set.column’
separator: no visible global function definition for ‘set.rhs’
separator: no visible global function definition for ‘set.constr.type’
separator: no visible global function definition for ‘set.objfn’
separator: no visible global function definition for ‘set.bounds’
separator: no visible global function definition for ‘lp.control’
separator: no visible global function definition for ‘get.variables’
separator: no visible global function definition for ‘set.basis’
separator: no visible global function definition for
  ‘get.dual.solution’
Undefined global functions or variables:
  .getXlevels gaussian get.dual.solution get.variables glm.control
  glm.fit is.empty.model lp.control make.lp model.extract model.matrix
  model.offset model.response model.weights set.basis set.bounds
  set.column set.constr.type set.objfn set.rhs
Consider adding
  importFrom("stats", ".getXlevels", "gaussian", "glm.control",
             "glm.fit", "is.empty.model", "model.extract",
             "model.matrix", "model.offset", "model.response",
             "model.weights")
to your NAMESPACE file.
Note: found 3 marked Latin-1 strings
Namespace in Imports field not imported from: ‘shinybusy’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   9.9Mb
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
propdiff.acc: no visible global function definition for ‘rbeta’
propdiff.acc: no visible global function definition for ‘rbinom’
propdiff.acc: no visible global function definition for ‘pbeta’
propdiff.alc: no visible global function definition for ‘rbeta’
propdiff.alc: no visible global function definition for ‘rbinom’
propdiff.alc: no visible global function definition for ‘qbeta’
propdiff.freq: no visible global function definition for ‘qnorm’
propdiff.mblacc: no visible global function definition for ‘rbeta’
propdiff.mblacc: no visible global function definition for ‘rbinom’
propdiff.mblacc: no visible global function definition for ‘pbeta’
propdiff.mblalc: no visible global function definition for ‘rbeta’
propdiff.mblalc: no visible global function definition for ‘rbinom’
propdiff.mblalc: no visible global function definition for ‘qbeta’
propdiff.mblmodwoc: no visible global function definition for ‘qchisq’
propdiff.mblmodwoc: no visible global function definition for ‘pbeta’
propdiff.mblwoc: no visible global function definition for ‘pbeta’
propdiff.modwoc: no visible global function definition for ‘qchisq’
propdiff.modwoc: no visible global function definition for ‘pbeta’
propdiff.woc: no visible global function definition for ‘pbeta’
Undefined global functions or variables:
  pbeta qbeta qchisq qnorm rbeta rbinom
Consider adding
  importFrom("stats", "pbeta", "qbeta", "qchisq", "qnorm", "rbeta",
             "rbinom")
to your NAMESPACE file.
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  22.2Mb
installed size is 41.7Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  39.1Mb
GraphBinaryForestPlot: no visible global function definition for
  ‘abline’
GraphBinaryForestPlot: no visible global function definition for ‘text’
GraphContinuousForestPlot: no visible global function definition for
  ‘abline’
GraphContinuousForestPlot: no visible global function definition for
  ‘text’
ImputeBinaryEvents: no visible global function definition for ‘rbinom’
ImputeSMD: no visible global function definition for ‘rnorm’
funnelplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline rbinom rnorm text
Consider adding
  importFrom("graphics", "abline", "text")
  importFrom("stats", "rbinom", "rnorm")
to your NAMESPACE file.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   3.4Mb
generate.sample.core: no visible global function definition for
  ‘predict’
mdh: no visible global function definition for ‘model.frame’
mdh: no visible binding for global variable ‘na.fail’
mdh: no visible global function definition for ‘.getXlevels’
mdh: no visible global function definition for ‘quantile’
mdh: no visible global function definition for ‘hist’
predict.mdh: no visible global function definition for ‘model.frame’
samur: no visible global function definition for ‘predict’
Undefined global functions or variables:
  .getXlevels hist model.frame na.fail predict quantile
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", ".getXlevels", "model.frame", "na.fail", "predict",
             "quantile")
to your NAMESPACE file.
Packages suggested but not available for checking: 'GO.db', 'org.Sc.sgd.db'
Note: found 6 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs  22.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘sankeywheel.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 43-44 (sankeywheel.Rmd) 
Error: processing vignette 'sankeywheel.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘sankeywheel.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
Running examples in ‘sara4r-Ex.R’ failed
The error most likely occurred in:

> ### Name: sara4r
> ### Title: An R-GUI for Spatial Analysis of Surface Runoff using the
> ###   NRCS-CN Method
> ### Aliases: sara4r
> 
> ### ** Examples
> 
> sara4r()

(R:68100): GLib-GObject-WARNING **: invalid (NULL) pointer instance

(R:68100): GLib-GObject-CRITICAL **: g_signal_connect_data: assertion `G_TYPE_CHECK_INSTANCE (instance)' failed

(R:68100): Gtk-WARNING **: Screen for GtkWindow not set; you must always set
a screen for a GtkWindow before using the window

(R:68100): Gdk-CRITICAL **: gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed

(R:68100): Gdk-CRITICAL **: gdk_colormap_get_visual: assertion `GDK_IS_COLORMAP (colormap)' failed

(R:68100): Gdk-CRITICAL **: gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed

(R:68100): Gdk-CRITICAL **: gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed

(R:68100): Gdk-CRITICAL **: gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed

(R:68100): Gdk-CRITICAL **: gdk_window_new: assertion `GDK_IS_WINDOW (parent)' failed

 *** caught segfault ***
address 0x18, cause 'memory not mapped'

Traceback:
 1: .RGtkCall("S_gtk_widget_show_all", object, PACKAGE = "RGtk2")
 2: method(obj, ...)
 3: INIRENA$showAll()
 4: sara4r()
An irrecoverable exception occurred. R is aborting now ...
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    bin   4.4Mb
download.sas7bdat.sources : <anonymous>: no visible global function
  definition for ‘download.file’
generate.sas7bdat.source: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
parse.SAScii: no visible binding for global variable ‘end’
parse.SAScii: no visible binding for global variable ‘start’
read.SAScii: no visible global function definition for ‘download.file’
read.SAScii: no visible global function definition for ‘unzip’
read.SAScii: no visible global function definition for ‘read.fwf’
read.SAScii: no visible global function definition for ‘capture.output’
Undefined global functions or variables:
  capture.output download.file end read.fwf start unzip
Consider adding
  importFrom("stats", "end", "start")
  importFrom("utils", "capture.output", "download.file", "read.fwf",
             "unzip")
to your NAMESPACE file.
Missing or unexported object: ‘base::plot’
Running examples in ‘sasfunclust-Ex.R’ failed
The error most likely occurred in:

> ### Name: sasfclust
> ### Title: Sparse and Smooth Functional Data Clustering
> ### Aliases: sasfclust
> 
> ### ** Examples
> 
> library(sasfunclust)
> train<-simulate_data("Scenario I",n_i=20,var_e = 1,var_b = 0.5^2)
> mod<-sasfclust(X=train$X,grid=train$grid,lambda_s = 10^-6,lambda_l =10,G = 2,maxit = 5,q=10)
> plot(mod)
Error in get(name, envir = ns, inherits = FALSE) : 
  object 'plot' not found
Calls: plot -> plot.sasfclust -> :: -> getExportedValue -> get
Execution halted
Running ‘testthat.R’ [70s/70s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   7.     └─base::getExportedValue(pkg, name)
   8.       └─base::get(name, envir = ns, inherits = FALSE)
  ── Error (test-sasfunclust_functions.R:7:1): (code run outside of `test_that()`) ──
  Error: object 'plot' not found
  Backtrace:
      █
   1. ├─graphics::plot(mod_cv) test-sasfunclust_functions.R:7:0
   2. └─sasfunclust:::plot.sasfclust_cv(mod_cv)
   3.   └─base::plot
   4.     └─base::getExportedValue(pkg, name)
   5.       └─base::get(name, envir = ns, inherits = FALSE)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 6 ]
  Error: Test failures
  Execution halted
pB: no visible global function definition for ‘plot’
pD: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
SASPECT: no visible global function definition for ‘dbinom’
my.SOnePro: missing arguments not allowed in calls to ‘c’
my.ttest: no visible global function definition for ‘var’
Undefined global functions or variables:
  dbinom var
Consider adding
  importFrom("stats", "dbinom", "var")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Packages required but not available: 'libr', 'reporter'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘maptools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
loads: no visible global function definition for ‘untar’
saves: no visible global function definition for ‘tar’
Undefined global functions or variables:
  tar untar
Consider adding
  importFrom("utils", "tar", "untar")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
K: no visible global function definition for ‘dnorm’
sBF: no visible global function definition for ‘density’
sBF: no visible global function definition for ‘txtProgressBar’
sBF: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  density dnorm setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "density", "dnorm")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘network’
  All declared Imports should be used.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    libs   3.3Mb
plot.word_coverage: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
Malformed Description field: should contain one or more complete sentences.
fitSBSA: no visible binding for global variable ‘var’
fitSBSA: no visible global function definition for ‘var’
fitSBSA: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm var
Consider adding
  importFrom("stats", "qnorm", "var")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘pvclust’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘methods’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
'library' or 'require' call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.scair: no visible global function definition for ‘par’
plot.scair: no visible global function definition for ‘plot’
plot.scair: no visible global function definition for ‘points’
plot.scar: no visible global function definition for ‘par’
plot.scar: no visible global function definition for ‘plot’
plot.scar: no visible global function definition for ‘points’
predict.scair: no visible global function definition for ‘approx’
predict.scar: no visible global function definition for ‘approx’
scair: no visible global function definition for ‘gaussian’
scair: no visible global function definition for ‘runif’
scair: no visible global function definition for ‘rnorm’
scar: no visible global function definition for ‘gaussian’
scar: no visible global function definition for ‘glm.fit’
scar: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx gaussian glm.fit par plot points rnorm runif
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "approx", "gaussian", "glm.fit", "rnorm", "runif")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘R6’ ‘cowplot’ ‘ggplot2’ ‘ggridges’ ‘ggstance’ ‘jmvcore’
  All declared Imports should be used.
Packages suggested but not available for checking: 'pcalg', 'Rgraphviz'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
prime.factor: no visible global function definition for ‘data’
prime.factor: no visible binding for global variable ‘primlist’
Undefined global functions or variables:
  data primlist
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘stringi’ ‘stringr’ ‘tibble’ ‘tidyr’ ‘tidytext’
  All declared Imports should be used.
Note: found 464 marked UTF-8 strings
Error(s) in re-building vignettes:
  ...
--- re-building ‘scipub_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 172-173 (scipub_vignette.Rmd) 
Error: processing vignette 'scipub_vignette.Rmd' failed with diagnostics:
Can't convert from <character> to <factor<ee706>> due to loss of generality.
* Locations: 1
--- failed re-building ‘scipub_vignette.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
score.GGUM: no visible global function definition for ‘dnorm’
score.GGUM: no visible global function definition for ‘hist’
score.GGUM: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  dnorm hist write.table
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "dnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
CreatePssm: no visible binding for global variable ‘training’
Undefined global functions or variables:
  training
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘gettingstarted.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘gettingstarted.Rmd’

--- re-building ‘article.Rnw’ using knitr
Error: processing vignette 'article.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'article.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘article.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pracma’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/scpm.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
License components which are templates and need '+ file LICENSE':
  MIT License
Note: found 1 marked UTF-8 string
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls to packages already attached by Depends:
  ‘RCurl’ ‘XML’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RCurl’ ‘XML’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
scrape: no visible global function definition for ‘getURLAsynchronous’
scrape: no visible global function definition for ‘runif’
scrape: no visible global function definition for ‘capture.output’
scrape: no visible binding for global variable ‘xmlParse’
scrape: no visible binding for global variable ‘htmlParse’
Undefined global functions or variables:
  capture.output getURLAsynchronous htmlParse runif xmlParse
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Package suggested but not available for checking: ‘oligoClasses’
Found the following significant warnings:
  Note: possible error in 'getSelectedNodes(node.suids = TRUE)': unused argument (node.suids = TRUE) 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ScriptMapR.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’.
scriptmapr: possible error in getSelectedNodes(node.suids = TRUE):
  unused argument (node.suids = TRUE)
Packages required but not available: 'ALL', 'ConsensusClusterPlus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 57 marked UTF-8 strings
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘methods’ ‘pbapply’ ‘utils’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘glmGamPoi’
lahiri.design: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
No protocol specified
No protocol specified
Namespace in Imports field not imported from: ‘spatstat’
  All declared Imports should be used.
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   3.7Mb
Namespace in Imports field not imported from: 'lpSolveAPI'
  All declared Imports should be used.
estimateTimeToComputeTargetDefinition: no visible global function
  definition for ‘flush.console’
estimateTimeToComputeTargetDefinition: no visible global function
  definition for ‘combn’
initialize,sdcTargetDefinitionClass: no visible global function
  definition for ‘flush.console’
initialize,sdcTargetDefinitionClass: no visible global function
  definition for ‘combn’
initialize,sdcTargetDefinitionClass: no visible global function
  definition for ‘quantile’
initialize,sdcTargetMatrixClass: no visible global function definition
  for ‘flush.console’
Undefined global functions or variables:
  combn flush.console quantile
Consider adding
  importFrom("stats", "quantile")
  importFrom("utils", "combn", "flush.console")
to your NAMESPACE file.
Package required but not available: ‘rpanel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
Namespaces in Imports field not imported from:
  ‘CENFA’ ‘DT’ ‘SSDM’ ‘biomod2’ ‘blockCV’ ‘data.table’ ‘dismo’
  ‘ggcorrplot’ ‘haven’ ‘kernlab’ ‘rJava’ ‘randomForest’ ‘readxl’
  ‘rgeos’ ‘rhandsontable’ ‘shinyBS’ ‘shinyFiles’ ‘sp’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gbm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
Found the following executable file:
  inst/external/env/bio14.bil
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘covr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘rgeos’ ‘tidyr’
  All declared Imports should be used.
Package in Depends field not imported from: ‘lars’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
sealasso: no visible global function definition for ‘lars’
weight.calc: no visible global function definition for ‘lars’
Undefined global functions or variables:
  lars
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R   7.2Mb
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.
adx: no visible global function definition for ‘abline’
adx: no visible global function definition for ‘legend’
dx: no visible global function definition for ‘abline’
dx: no visible global function definition for ‘legend’
maxd: no visible global function definition for ‘abline’
maxd: no visible global function definition for ‘legend’
pc: no visible global function definition for ‘rainbow’
pc: no visible global function definition for ‘plot’
pc: no visible global function definition for ‘abline’
pc: no visible global function definition for ‘legend’
pc: no visible global function definition for ‘points’
pcu: no visible global function definition for ‘rainbow’
pcu: no visible global function definition for ‘plot’
pcu: no visible global function definition for ‘abline’
pcu: no visible global function definition for ‘legend’
pcu: no visible global function definition for ‘points’
rmsd: no visible global function definition for ‘abline’
rmsd: no visible global function definition for ‘legend’
rsd: no visible global function definition for ‘abline’
rsd: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline legend plot points rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "legend", "plot", "points")
to your NAMESPACE file.
Note: found 3 marked UTF-8 strings
Package in Depends field not imported from: ‘JM’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SEchart: no visible global function definition for ‘plot’
SEchart: no visible global function definition for ‘rect’
SEchart: no visible global function definition for ‘par’
SEchart: no visible global function definition for ‘grid’
SEchart: no visible global function definition for ‘axis’
SEchart: no visible global function definition for ‘text’
SEchart: no visible global function definition for ‘lines’
SEchart: no visible global function definition for ‘heat.colors’
SEchart: no visible global function definition for ‘topo.colors’
SEchart: no visible global function definition for ‘cm.colors’
SEchart: no visible global function definition for ‘terrain.colors’
SEchart: no visible global function definition for ‘gray.colors’
SEchart: no visible global function definition for ‘rainbow’
SEchart: no visible global function definition for ‘points’
SEchart: no visible global function definition for ‘legend’
Undefined global functions or variables:
  axis cm.colors gray.colors grid heat.colors legend lines par plot
  points rainbow rect terrain.colors text topo.colors
Consider adding
  importFrom("grDevices", "cm.colors", "gray.colors", "heat.colors",
             "rainbow", "terrain.colors", "topo.colors")
  importFrom("graphics", "axis", "grid", "legend", "lines", "par",
             "plot", "points", "rect", "text")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
fdc2s: no visible global function definition for ‘lm’
fdc3s: no visible global function definition for ‘lm’
fds2s: no visible global function definition for ‘lm’
fds3s: no visible global function definition for ‘lm’
Undefined global functions or variables:
  lm
Consider adding
  importFrom("stats", "lm")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs  14.0Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘fansi’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/seedr.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘rsbml’
Package required but not available: ‘rpanel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SEERaBomb.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rpanel’
Package required and available but unsuitable version: ‘OasisR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'flowMerge', 'flowClust', 'flowCore'
Packages unavailable to check Rd xrefs: ‘flowClust’, ‘flowMerge’
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
plot.SEIRfansy: no visible global function definition for ‘plot’
plot.SEIRfansyPredict: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
get.infectiousness: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  qchisq
Consider adding
  importFrom("stats", "qchisq")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘cluster’ ‘factoextra’ ‘tidyr’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘FD’
  All declared Imports should be used.
get_statistics_from_file: no visible global function definition for
  ‘read.csv’
glm_anova: no visible global function definition for ‘aov’
glm_anova: no visible global function definition for ‘glm’
glm_anova: no visible global function definition for ‘gaussian’
glm_anova: no visible global function definition for ‘anova’
glm_anova: no visible global function definition for ‘quasipoisson’
glm_anova: no visible global function definition for ‘sd’
glm_anova: no visible global function definition for ‘p.adjust’
ttest_cohens_d: no visible global function definition for ‘t.test’
ttest_cohens_d: no visible global function definition for ‘sd’
Undefined global functions or variables:
  anova aov gaussian glm p.adjust quasipoisson read.csv sd t.test
Consider adding
  importFrom("stats", "anova", "aov", "gaussian", "glm", "p.adjust",
             "quasipoisson", "sd", "t.test")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
predict.SEL: warning in splineDesign(newdata, knots = knts, ord =
  object$nord, deriv = rep(deriv, length(newdata)), outer.ok = TRUE):
  partial argument match of 'deriv' to 'derivs'
getbinPost: no visible binding for global variable ‘dbeta’
getbinPost: no visible binding for global variable ‘pbeta’
getbinPost : fu: no visible global function definition for ‘dbinom’
getbinPost : fu: no visible global function definition for ‘predict’
getbinPost: no visible global function definition for ‘integrate’
getbinPost: no visible global function definition for ‘splinefun’
int.funct: no visible global function definition for ‘integrate’
int.funct2: no visible global function definition for ‘integrate’
min.abs: no visible global function definition for ‘uniroot’
plot.SEL: no visible global function definition for ‘plot’
print.SEL: no visible global function definition for ‘integrate’
print.summary.SEL : foo1: no visible global function definition for
  ‘predict’
print.summary.SEL : foo2: no visible global function definition for
  ‘predict’
print.summary.SEL: no visible global function definition for
  ‘integrate’
quantSEL: no visible global function definition for ‘predict’
quantSEL: no visible global function definition for ‘splinefun’
rvSEL: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dbeta dbinom integrate pbeta plot predict runif splinefun uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dbeta", "dbinom", "integrate", "pbeta", "predict",
             "runif", "splinefun", "uniroot")
to your NAMESPACE file.
Package in Depends field not imported from: ‘sem’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lavaan’ ‘psych’ ‘semPlot’ ‘semTools’ ‘shinyAce’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘SemiCompRisks.ltx’ using tex
Error: processing vignette 'SemiCompRisks.ltx' failed with diagnostics:
Running 'texi2dvi' on 'SemiCompRisks.ltx' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm8): Font bbm8 at 600 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘SemiCompRisks.ltx’

SUMMARY: processing the following file failed:
  ‘SemiCompRisks.ltx’

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ChiSquaredLRTest: no visible global function definition for ‘na.omit’
ChiSquaredLRTest: no visible global function definition for ‘cov’
ChiSquaredLRTest: no visible global function definition for ‘dmvnorm’
ChiSquaredLRTest: no visible global function definition for ‘pchisq’
NormalTheoryLRTest: no visible global function definition for ‘na.omit’
NormalTheoryLRTest: no visible global function definition for ‘cov’
NormalTheoryLRTest: no visible global function definition for ‘dmvnorm’
NormalTheoryLRTest: no visible global function definition for ‘sd’
NormalTheoryLRTest: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  cov dmvnorm na.omit pchisq pnorm sd
Consider adding
  importFrom("stats", "cov", "na.omit", "pchisq", "pnorm", "sd")
to your NAMESPACE file.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘grid’ ‘purrr’
  All declared Imports should be used.
'library' or 'require' calls in package code:
  ‘XML’ ‘boot’ ‘sem’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  ‘boot:::const’ ‘stats:::AIC.logLik’ ‘stats:::BIC.logLik’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘addPath.plsm’ ‘endogenous’ ‘predecessors’ ‘qSquared’ ‘reorder’
  ‘resempls’ ‘residuals.sempls’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SEMsens.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘expm’ ‘matrixStats’ ‘matrixcalc’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
.plot_attachment: no visible global function definition for ‘dev.off’
.update_list: no visible global function definition for ‘modifyList’
mime_part.data.frame: no visible global function definition for
  ‘write.table’
mime_part.ggplot: no visible binding for global variable ‘pdf’
mime_part.matrix: no visible global function definition for
  ‘write.table’
mime_part.trellis: no visible binding for global variable ‘pdf’
Undefined global functions or variables:
  dev.off modifyList pdf write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "modifyList", "write.table")
to your NAMESPACE file.
gconv: no visible global function definition for ‘convolve’
sens.analysis.aberrant.rank: no visible global function definition for
  ‘pnorm’
sens.analysis.mh: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  convolve pnorm
Consider adding
  importFrom("stats", "convolve", "pnorm")
to your NAMESPACE file.
mscorev: no visible global function definition for ‘quantile’
senmwCI : funcCI: no visible global function definition for ‘qnorm’
senmwCI : funcCI2: no visible global function definition for ‘qnorm’
separable1k: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm quantile
Consider adding
  importFrom("stats", "pnorm", "qnorm", "quantile")
to your NAMESPACE file.
plot.sensitivity.2.0d: no visible global function definition for ‘gray’
sensitivitySGD: no visible global function definition for ‘tail’
sensitivitySGL: no visible global function definition for ‘tail’
Undefined global functions or variables:
  gray tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("utils", "tail")
to your NAMESPACE file.
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    libs    16.7Mb
    models   1.3Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.2Mb
Note: found 4436 marked UTF-8 strings
GNU make is a SystemRequirements.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Found the following significant warnings:
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SeqFeatR.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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: ‘airway’
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs   8.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Package suggested but not available for checking: ‘muscle’
Found the following executable files:
  inst/vcf/all.anno.filtered.extract.headerFixed.bcf.gz.scIdx
  inst/vcf/all.anno.filtered.extract.vcf.gz.scIdx
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    libs  21.7Mb
GNU make is a SystemRequirements.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
plotenz : addmark: no visible global function definition for ‘par’
plotenz : addmark: no visible global function definition for ‘plot’
plotenz : addmark: no visible global function definition for ‘text’
plotenz : addmark: no visible global function definition for ‘segments’
plotenz : addband: no visible global function definition for ‘segments’
plotenz : addband: no visible global function definition for ‘text’
plotenz: no visible global function definition for ‘layout’
plotenz: no visible global function definition for ‘text’
plotenz: no visible global function definition for ‘dev.new’
Undefined global functions or variables:
  dev.new layout par plot segments text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "layout", "par", "plot", "segments", "text")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/sequenza.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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 17.2Mb
  sub-directories of 1Mb or more:
    libs  16.0Mb
Malformed Title field: should not end in a period.
capture: no visible binding for global variable ‘resultText’
restore.session: no visible binding for global variable
  ‘.save.session.packages’
restore.session: no visible binding for global variable
  ‘.save.session.search’
save.session: no visible global function definition for ‘dev.list’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.search’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.packages’
Undefined global functions or variables:
  .save.session.packages .save.session.search dev.list resultText
Consider adding
  importFrom("grDevices", "dev.list")
to your NAMESPACE file.
setpath: no visible global function definition for ‘cov’
setpath: no visible global function definition for ‘median’
setpath: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  cov median pchisq
Consider adding
  importFrom("stats", "cov", "median", "pchisq")
to your NAMESPACE file.
random.number.test: no visible global function definition for ‘runif’
random.number.test: no visible global function definition for ‘rnorm’
setRNG: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'SingleCellExperiment', 'MAST', 'monocle'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Seurat.Rcheck/00install.out’ for details.
'library' or 'require' call to ‘graphics’ which was already attached by Depends.
  Please remove these calls from your code.
severity: no visible global function definition for ‘qnorm’
severity: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
L_exp: no visible global function definition for ‘pnorm’
L_hNV: no visible global function definition for ‘pnorm’
L_trunc: no visible global function definition for ‘pnorm’
L_trunc_mufest: no visible global function definition for ‘pnorm’
dgp: no visible global function definition for ‘runif’
dgp: no visible global function definition for ‘rnorm’
eff.sfa: no visible global function definition for ‘predict’
fitted.sfa: no visible global function definition for ‘predict’
predict.sfa: no visible global function definition for ‘coef’
print.sfa: no visible global function definition for ‘coef’
residuals.sfa: no visible global function definition for ‘fitted’
sfa: no visible global function definition for ‘model.frame’
sfa: no visible global function definition for ‘model.response’
sfa.fit: no visible global function definition for ‘lm’
sfa.fit: no visible global function definition for ‘resid’
sfa.fit: no visible global function definition for ‘var’
sfa.fit: no visible global function definition for ‘optim’
summary.sfa: no visible global function definition for ‘logLik’
summary.sfa: no visible global function definition for ‘pchisq’
te.eff.sfa: no visible global function definition for ‘residuals’
te.eff.sfa: no visible global function definition for ‘pnorm’
u.sfa: no visible global function definition for ‘residuals’
u.sfa: no visible global function definition for ‘dnorm’
u.sfa: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  coef dnorm fitted lm logLik model.frame model.response optim pchisq
  pnorm predict resid residuals rnorm runif var
Consider adding
  importFrom("stats", "coef", "dnorm", "fitted", "lm", "logLik",
             "model.frame", "model.response", "optim", "pchisq", "pnorm",
             "predict", "resid", "residuals", "rnorm", "runif", "var")
to your NAMESPACE file.
sfcr_set:
  function(..., exclude)
sfcr_set.formula:
  function(..., exclude)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Namespace in Imports field not imported from: ‘geometries’
  All declared Imports should be used.
Running ‘testthat.R’ [8s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  sf_poly[2, ]$prop[[1]][[1]] not equal to letters[10:13].
  'current' is not a factor
  ── Failure (test-sf_polygon.R:224:3): polygons are closed and list-column properties follow the same structure as geometires, and first row is repeated where closed ──
  sf_multi[1, ]$prop[[1]][[1]][[1]] not equal to c(letters[1:4], letters[1]).
  'current' is not a factor
  ── Failure (test-sf_polygon.R:225:3): polygons are closed and list-column properties follow the same structure as geometires, and first row is repeated where closed ──
  sf_multi[1, ]$prop[[1]][[1]][[2]] not equal to letters[5:9].
  'current' is not a factor
  ── Failure (test-sf_polygon.R:226:3): polygons are closed and list-column properties follow the same structure as geometires, and first row is repeated where closed ──
  sf_multi[1, ]$prop[[1]][[2]][[1]] not equal to c(letters[10:13], letters[10]).
  'current' is not a factor
  
  [ FAIL 9 | WARN 0 | SKIP 0 | PASS 1662 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘v1_intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘v1_intro.Rmd’

--- re-building ‘v3_analyzing_landing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

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: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 61-70 (v3_analyzing_landing.Rmd) 
Error: processing vignette 'v3_analyzing_landing.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘v3_analyzing_landing.Rmd’

SUMMARY: processing the following file failed:
  ‘v3_analyzing_landing.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 179.7Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    libs    172.2Mb
    sqlite    1.5Mb
Error(s) in re-building vignettes:
--- re-building ‘sf1.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘sf1.Rmd’

--- re-building ‘sf2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘sf2.Rmd’

--- re-building ‘sf3.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘sf3.Rmd’

--- re-building ‘sf4.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘sf4.Rmd’

--- re-building ‘sf5.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 213-215 (sf5.Rmd) 
Error: processing vignette 'sf5.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘sf5.Rmd’

--- re-building ‘sf6.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘sf6.Rmd’

--- re-building ‘sf7.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘sf7.Rmd’

SUMMARY: processing the following file failed:
  ‘sf5.Rmd’

Error: Vignette re-building failed.
Execution halted
No protocol specified
No protocol specified
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
Malformed Description field: should contain one or more complete sentences.
.computePStar: no visible global function definition for ‘uniroot’
plotBoundary: no visible global function definition for
  ‘scale_y_continuous’
Undefined global functions or variables:
  scale_y_continuous uniroot
Consider adding
  importFrom("stats", "uniroot")
to your NAMESPACE file.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘SGPdata.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-28 (SGPdata.Rmd) 
Error: processing vignette 'SGPdata.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGPdata.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: package ‘mixOmics’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/sgPLS.Rcheck/00install.out’ for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.4Mb
Error(s) in re-building vignettes:
--- re-building ‘SGP.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-29 (SGP.Rmd) 
Error: processing vignette 'SGP.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGP.Rmd’

--- re-building ‘SGP_Data_Analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-29 (SGP_Data_Analysis.Rmd) 
Error: processing vignette 'SGP_Data_Analysis.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGP_Data_Analysis.Rmd’

--- re-building ‘SGP_Data_Preparation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-29 (SGP_Data_Preparation.Rmd) 
Error: processing vignette 'SGP_Data_Preparation.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGP_Data_Preparation.Rmd’

SUMMARY: processing the following files failed:
  ‘SGP.Rmd’ ‘SGP_Data_Analysis.Rmd’ ‘SGP_Data_Preparation.Rmd’

Error: Vignette re-building failed.
Execution halted
amse: no visible global function definition for ‘na.omit’
arb: no visible global function definition for ‘na.omit’
rdatagen: no visible global function definition for ‘qnorm’
rdatagen: no visible global function definition for ‘pbinom’
rdatagen: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  na.omit pbinom pnorm qnorm
Consider adding
  importFrom("stats", "na.omit", "pbinom", "pnorm", "qnorm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘foreign’ which was already attached by Depends.
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/shapes.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘hydromad’
Namespaces in Imports field not imported from:
  ‘rpart’ ‘testthat’ ‘tree’
  All declared Imports should be used.
chernoff_bound: no visible global function definition for ‘plot’
confidence_interval: no visible global function definition for ‘plot’
shattering_simulations: no visible global function definition for
  ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
popify: no visible global function definition for ‘runif’
tipify: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    www   9.4Mb
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shinydashboard’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reactable’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘DT’ ‘VGAM’ ‘data.table’ ‘ggdendro’ ‘gridExtra’ ‘knitr’
  ‘latticeExtra’ ‘msm’ ‘plotly’ ‘purrr’ ‘shinyBS’ ‘shinydashboard’
  ‘xtable’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘KGode’ ‘XML’ ‘ggplot2’ ‘gridExtra’ ‘mvtnorm’ ‘reshape2’ ‘shinyjs’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘scales’ ‘websocket’
  All declared Imports should be used.
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    shinyApp  21.0Mb
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘shiny’ ‘shinyjs’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    R     1.6Mb
    www   8.8Mb
Namespaces in Imports field not imported from:
  ‘CARE1’ ‘LCMCR’ ‘coda’ ‘conting’ ‘dga’ ‘future’ ‘ggplot2’ ‘ipc’
  ‘promises’ ‘reshape’ ‘shinycssloaders’ ‘testthat’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/shinyRGL.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    help   2.5Mb
    www    8.0Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘shiny’
  All declared Imports should be used.
shrink.estim: no visible global function definition for ‘cov’
shrink.estim: no visible global function definition for ‘cor’
shrink.estim: no visible global function definition for ‘cov2cor’
targetCor: no visible global function definition for ‘cor.test’
targetCor: no visible global function definition for ‘cor’
targetCor: no visible global function definition for ‘sd’
targetCor: no visible global function definition for ‘cov’
targetD: no visible binding for global variable ‘var’
targetF: no visible global function definition for ‘cov’
targetF: no visible global function definition for ‘cor’
targetG: no visible global function definition for ‘cor’
targetG: no visible global function definition for ‘sd’
targetG: no visible global function definition for ‘cov’
targetGpos: no visible global function definition for ‘cor’
targetGpos: no visible global function definition for ‘sd’
targetGpos: no visible global function definition for ‘cov’
targetGstar: no visible global function definition for ‘cor’
targetGstar: no visible global function definition for ‘sd’
targetGstar: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cor cor.test cov cov2cor sd var
Consider adding
  importFrom("stats", "cor", "cor.test", "cov", "cov2cor", "sd", "var")
to your NAMESPACE file.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Depends: includes the non-default packages:
  'hdrcde', 'coda', 'MASS', 'bayesm', 'mnormt', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  ‘MASS’ ‘bayesm’ ‘coda’ ‘hdrcde’ ‘mnormt’ ‘spatstat’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: ‘edgeR’
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘ade4’ ‘corpcor’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
filter.PCA.default: no visible global function definition for
  ‘princomp’
filter.mRMR.default: no visible global function definition for
  ‘discretize’
gaussian.default: no visible global function definition for ‘cov’
gaussian.default: no visible global function definition for
  ‘cov.shrink’
plot.verify.cv: no visible global function definition for ‘plot’
plot.verify.cv: no visible global function definition for ‘points’
plot.verify.ho: no visible global function definition for ‘plot’
plot.verify.ho: no visible global function definition for ‘points’
plot.verify.loo: no visible global function definition for ‘plot’
plot.verify.loo: no visible global function definition for ‘points’
predict.dpa1: no visible global function definition for ‘cor’
predict.filter.PCA: no visible global function definition for ‘predict’
predict.filter.RegressionTreeFilter: no visible global function
  definition for ‘is.struct’
predict.filter.RegressionTreeFilter: no visible global function
  definition for ‘var’
simulator.Simple1: no visible global function definition for ‘rnorm’
verify.ho.default: no visible global function definition for ‘predict’
verify.loo.default: no visible global function definition for ‘predict’
Undefined global functions or variables:
  cor cov cov.shrink discretize is.struct plot points predict princomp
  rnorm var
Consider adding
  importFrom("graphics", "plot", "points")
  importFrom("stats", "cor", "cov", "predict", "princomp", "rnorm",
             "var")
to your NAMESPACE file.
dSepAdji: no visible global function definition for ‘as’
dag2cpdagAdj: no visible global function definition for ‘as’
randomDAG: no visible global function definition for ‘rbinom’
structIntervDist: no visible global function definition for ‘as’
Undefined global functions or variables:
  as rbinom
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "rbinom")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.cluster: no visible global function definition for ‘kmeans’
.plot.sigclust: no visible global function definition for ‘par’
.plot.sigclust: no visible global function definition for ‘density’
.plot.sigclust: no visible global function definition for ‘runif’
.plot.sigclust: no visible global function definition for ‘dnorm’
.plot.sigclust: no visible global function definition for ‘lines’
.plot.sigclust: no visible global function definition for ‘points’
.plot.sigclust: no visible global function definition for ‘title’
.plot.sigclust: no visible global function definition for ‘text’
.plot.sigclust: no visible global function definition for ‘qnorm’
.plot.sigclust: no visible global function definition for ‘abline’
.plot.sigclust: no visible global function definition for ‘quantile’
.plot.sigclust: no visible global function definition for ‘legend’
.simnull: no visible global function definition for ‘rnorm’
.vareigen: no visible global function definition for ‘mad’
.vareigen: no visible global function definition for ‘cov’
sigclust: no visible global function definition for ‘sd’
sigclust: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline cov density dnorm kmeans legend lines mad par pnorm points
  qnorm quantile rnorm runif sd text title
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "points",
             "text", "title")
  importFrom("stats", "cov", "density", "dnorm", "kmeans", "mad",
             "pnorm", "qnorm", "quantile", "rnorm", "runif", "sd")
to your NAMESPACE file.
Note: found 28 marked UTF-8 strings
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting-started.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 89-90 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘getting-started.Rmd’

SUMMARY: processing the following file failed:
  ‘getting-started.Rmd’

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

Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  'ggbio', 'biovizBase', 'AnnotationFilter'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
signmedian.test: no visible global function definition for ‘median’
signmedian.test: no visible global function definition for ‘binom.test’
signmedian.test: no visible global function definition for ‘pbinom’
signmedian.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  binom.test median pbinom pnorm
Consider adding
  importFrom("stats", "binom.test", "median", "pbinom", "pnorm")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.2Mb
Namespaces in Imports field not imported from:
  ‘KernSmooth’ ‘MASS’ ‘class’ ‘cluster’ ‘lattice’ ‘nnet’
  All declared Imports should be used.
'library' or 'require' calls in package code:
  ‘gdata’ ‘splines’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.SII: no visible global function definition for ‘plot’
plot.SII: no visible global function definition for ‘lines’
plot.SII: no visible global function definition for ‘abline’
plot.SII: no visible global function definition for ‘legend’
sii : approx.l: no visible global function definition for ‘approx’
sii.excel: no visible global function definition for ‘predict’
sii.excel : approx.l: no visible global function definition for
  ‘approx’
Undefined global functions or variables:
  abline approx legend lines plot predict
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "plot")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘car’ ‘ggplot2’ ‘magrittr’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘grid’
  All declared Imports should be used.
Package suggested but not available for checking: ‘doMPI’
No protocol specified
No protocol specified
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SimEUCartelLaw.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘RcppSimdJson’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘digest’
  All declared Imports should be used.
getFormula: no visible global function definition for ‘as.formula’
internalSimXyplot : f: no visible global function definition for
  ‘median’
runSimulation: no visible global function definition for ‘runif’
setup: no visible global function definition for ‘runif’
clusterSetup,ANY-data.frame-SampleControl: no visible binding for
  global variable ‘cnam’
clusterSetup,ANY-data.frame-TwoStageControl: no visible binding for
  global variable ‘cnam’
initialize,DCARContControl: no visible binding for global variable
  ‘rnorm’
initialize,DataControl: no visible binding for global variable ‘rnorm’
Undefined global functions or variables:
  as.formula cnam median rnorm runif
Consider adding
  importFrom("stats", "as.formula", "median", "rnorm", "runif")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘future’ ‘magrittr’ ‘purrr’ ‘rlang’ ‘utils’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
GNU make is a SystemRequirements.
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  11.5Mb
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’
cumallcausehr: no visible global function definition for ‘integrate’
plotbe: no visible global function definition for ‘plot’
plotbe: no visible global function definition for ‘lines’
plotbe: no visible global function definition for ‘legend’
plotcph: no visible global function definition for ‘confint’
plotcph: no visible global function definition for ‘plot’
plotcph: no visible global function definition for ‘abline’
plotcph: no visible global function definition for ‘axis’
plotcph: no visible global function definition for ‘polygon’
plotcph: no visible global function definition for ‘lines’
plotnae: no visible global function definition for ‘plot’
simCR: no visible global function definition for ‘rnorm’
simEBMT: no visible global function definition for ‘model.matrix’
simexit: no visible global function definition for ‘runif’
simexitinner: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  abline axis confint integrate legend lines model.matrix plot polygon
  rnorm runif uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "plot",
             "polygon")
  importFrom("stats", "confint", "integrate", "model.matrix", "rnorm",
             "runif", "uniroot")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Package suggested but not available for checking: ‘topologyGSA’
Error(s) in re-building vignettes:
  ...
--- re-building ‘simPATHy.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 252-258 (simPATHy.Rmd) 
Error: processing vignette 'simPATHy.Rmd' failed with diagnostics:
there is no package called 'topologyGSA'
--- failed re-building ‘simPATHy.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Namespaces in Imports field not imported from:
  ‘DT’ ‘jsonlite’ ‘readr’ ‘rmarkdown’ ‘shinycssloaders’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Error(s) in re-building vignettes:
--- re-building ‘simplevis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

`summarise()` has grouped output by 'cut'. You can override using the `.groups` argument.
`summarise()` has grouped output by 'cut'. You can override using the `.groups` argument.
`summarise()` has grouped output by 'cut', 'clarity'. You can override using the `.groups` argument.
Quitting from lines 170-179 (simplevis.Rmd) 
Error: processing vignette 'simplevis.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘simplevis.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.3Mb
Package in Depends field not imported from: ‘mclust’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Simpsons: no visible global function definition for ‘Mclust’
Simpsons: no visible global function definition for ‘lm’
Simpsons: no visible global function definition for ‘plot’
Simpsons: no visible global function definition for ‘abline’
Simpsons: no visible global function definition for ‘par’
Simpsons: no visible global function definition for ‘legend’
Simpsons: no visible global function definition for ‘txtProgressBar’
Simpsons: no visible global function definition for ‘setTxtProgressBar’
Simpsons: no visible global function definition for ‘quantile’
plot.Simpson: no visible global function definition for ‘plot’
plot.Simpson: no visible global function definition for ‘lm’
plot.Simpson: no visible global function definition for ‘abline’
plot.Simpson: no visible global function definition for ‘par’
plot.Simpson: no visible global function definition for ‘legend’
Undefined global functions or variables:
  Mclust abline legend lm par plot quantile setTxtProgressBar
  txtProgressBar
Consider adding
  importFrom("graphics", "abline", "legend", "par", "plot")
  importFrom("stats", "lm", "quantile")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SimRAD.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘simrec-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 155-198 (simrec-vignette.Rmd) 
Error: processing vignette 'simrec-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘simrec-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
Package unavailable to check Rd xrefs: ‘Rmpi’
Running ‘testthat.R’ [9s/90s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > test_check("sims")
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  ● only test getwd at console (1)
  ● only visually test add progress bar at console (1)
  ● only visually test sims progress bar at console (1)
  
  [ FAIL 0 | WARN 0 | SKIP 3 | PASS 215 ]
  > 
  > proc.time()
     user  system elapsed 
    7.977   0.868  89.256 
  
   *** caught bus error ***
  address 0x7f82eb023ee0, cause 'non-existent physical address'
  An irrecoverable exception occurred. R is aborting now ...
Found the following hidden files and directories:
  vignettes/.Rhistory
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘abind’ ‘svUnit’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
simSummary: no visible global function definition for ‘abind’
simSummary_unitTests: no visible global function definition for
  ‘clearLog’
simSummary_unitTests: no visible global function definition for
  ‘runTest’
simSummary_unitTests: no visible global function definition for
  ‘svSuite’
simSummary_unitTests: no visible global function definition for ‘Log’
simSummary_unitTests: no visible global function definition for ‘stats’
simSummary_unitTests: no visible global function definition for
  ‘metadata’
simSummary_unitTests: no visible global function definition for
  ‘errorLog’
Undefined global functions or variables:
  Log abind clearLog errorLog metadata runTest stats svSuite
Package suggested but not available for checking: ‘INLA’
Namespaces in Imports field not imported from:
  ‘rgeos’ ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘metafor’
  All declared Imports should be used.
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  18.2Mb
Namespaces in Imports field not imported from:
  ‘crqa’ ‘plot3D’
  All declared Imports should be used.
Package suggested but not available for checking: ‘SingleCellExperiment’
Namespace in Imports field not imported from: ‘pracma’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’ ‘psych’ ‘stringr’
  All declared Imports should be used.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   5.9Mb
No protocol specified
No protocol specified
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
No protocol specified
No protocol specified
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lubridate’ ‘rmarkdown’ ‘yaml’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
plot.classify: no visible global function definition for ‘plot’
plot.gonadMat: no visible global function definition for ‘plot’
plot.morphMat: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cvskda: no visible global function definition for ‘detectCores’
cvskda: no visible global function definition for ‘makeCluster’
cvskda: no visible global function definition for ‘clusterApplyLB’
cvskda: no visible global function definition for ‘mclapply’
cvskda: no visible global function definition for ‘stopCluster’
Undefined global functions or variables:
  clusterApplyLB detectCores makeCluster mclapply stopCluster
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/skedastic.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘methods’
  All declared Imports should be used.
Packages required and available but unsuitable versions:
  'parallel', 'methods', 'grDevices', 'graphics', 'utils'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
dskt: no visible global function definition for ‘dt’
pskt: no visible global function definition for ‘pt’
qskt: no visible global function definition for ‘qt’
rskt: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dt pt qt runif
Consider adding
  importFrom("stats", "dt", "pt", "qt", "runif")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘kmndirs’
Unavailable namespace imported from by a ':::' call: ‘kmndirs’
  See the note in ?`:::` about the use of this operator.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.5Mb
GNU make is a SystemRequirements.
installed size is 31.8Mb
  sub-directories of 1Mb or more:
    libs  30.2Mb
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘maps’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘methods’ ‘xtable’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SLBDD.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Note: found 23 marked UTF-8 strings
slcestimates: no visible global function definition for ‘par’
slcestimates: no visible global function definition for ‘plot’
slcestimates: no visible global function definition for ‘abline’
slcestimates: no visible global function definition for ‘lines’
slcestimates: no visible global function definition for ‘axis’
slcestimates: no visible global function definition for ‘points’
slcestimates: no visible global function definition for ‘title’
Undefined global functions or variables:
  abline axis lines par plot points title
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "par", "plot",
             "points", "title")
to your NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
Namespace in Imports field not imported from: ‘viridisLite’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SlidingWindows.Rcheck/00install.out’ for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Note: found 2 marked Latin-1 strings
Note: found 15 marked Latin-1 strings
  Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘spatstat’
  All declared Imports should be used.
Running ‘testthat.R’ [7s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Component "publish": Component "region": target is character, current is factor
  Component "publish": Component "hovedint": Modes: character, numeric
  Component "publish": Component "hovedint": Attributes: < target is NULL, current is list >
  Component "publish": Component "hovedint": target is character, current is factor
  Component "publish": Component "mnd": Modes: character, numeric
  Component "publish": Component "mnd": Attributes: < target is NULL, current is list >
  Component "publish": Component "mnd": target is character, current is factor
  Backtrace:
      █
   1. └─SmallCountRounding:::PLStest(...) test-PLSrounding.R:148:2
   2.   └─testthat::expect_identical(a, b) test-PLSrounding.R:137:2
  
  [ FAIL 3 | WARN 0 | SKIP 1 | PASS 42 ]
  Error: Test failures
  Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
GNU make is a SystemRequirements.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SMARTbayesR.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘qpdf’
  All declared Imports should be used.
Note: found 1122 marked UTF-8 strings
Namespace in Imports field not imported from: ‘covr’
  All declared Imports should be used.
Package required but not available: ‘gWidgets2RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: package ‘BiocParallel’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SmartSVA.Rcheck/00install.out’ for details.
File ‘smco/R/smco.R’:
  .onAttach calls:
    cat(paste("This is smco package", version, "\n"))

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

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

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

.MHUpdateFuncGen.PF : MHUpdateFunc: no visible global function
  definition for ‘runif’
MarkovSwitchingFuncGenerator : generateNextStreamsFunc: no visible
  global function definition for ‘runif’
MarkovSwitchingFuncGenerator: no visible global function definition for
  ‘rnorm’
MarkovSwitchingFuncGenerator: no visible global function definition for
  ‘runif’
MarkovSwitchingFuncGenerator : logObsDensFunc: no visible global
  function definition for ‘dnorm’
MarkovSwitchingFuncGenerator : propagateFunc: no visible global
  function definition for ‘dnorm’
MarkovSwitchingFuncGenerator : propagateFunc: no visible global
  function definition for ‘runif’
Undefined global functions or variables:
  dnorm rnorm runif
Consider adding
  importFrom("stats", "dnorm", "rnorm", "runif")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
em: no visible global function definition for ‘coxph’
em: no visible global function definition for ‘optim’
plotpredictsmcure: no visible global function definition for ‘plot’
plotpredictsmcure: no visible global function definition for ‘matplot’
plotpredictsmcure: no visible global function definition for ‘lines’
smcure: no visible binding for global variable ‘na.omit’
smcure: no visible global function definition for ‘model.frame’
smcure: no visible global function definition for ‘model.extract’
smcure: no visible global function definition for ‘model.matrix’
smcure: no visible global function definition for ‘coxph’
smcure: no visible global function definition for ‘survreg’
smcure: no visible binding for global variable ‘var’
smcure: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  coxph lines matplot model.extract model.frame model.matrix na.omit
  optim plot pnorm survreg var
Consider adding
  importFrom("graphics", "lines", "matplot", "plot")
  importFrom("stats", "model.extract", "model.frame", "model.matrix",
             "na.omit", "optim", "pnorm", "var")
to your NAMESPACE file.
Package required but not available: ‘maftools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Grad.sph: no visible global function definition for ‘dist’
IMDS: no visible global function definition for ‘cmdscale’
IMDS: no visible global function definition for ‘as.dist’
IMDS: no visible global function definition for ‘runif’
IMDS: no visible global function definition for ‘optim’
idistSph: no visible global function definition for ‘dist’
obj.sph: no visible global function definition for ‘dist’
plot.imds: no visible binding for global variable ‘lines’
plot.imds: no visible global function definition for ‘plot’
plot.imds: no visible global function definition for ‘text’
plot.imds: no visible global function definition for ‘rect’
Undefined global functions or variables:
  as.dist cmdscale dist lines optim plot rect runif text
Consider adding
  importFrom("graphics", "lines", "plot", "rect", "text")
  importFrom("stats", "as.dist", "cmdscale", "dist", "optim", "runif")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘ggplot2’ ‘reshape’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘corpcor’ ‘ggplot2’ ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Malformed Description field: should contain one or more complete sentences.
lines.SmithWilsonYieldCurve: no visible global function definition for
  ‘lines’
plot.SmithWilsonYieldCurve: no visible global function definition for
  ‘plot’
points.SmithWilsonYieldCurve: no visible global function definition for
  ‘points’
Undefined global functions or variables:
  lines plot points
Consider adding
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SMLE.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘smm.Rnw’ using Sweave
Error: processing vignette 'smm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'smm.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘smm.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Malformed Description field: should contain one or more complete sentences.
colour.key: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘rmarkdown’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/smoothAPC.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘compiler’ ‘lmtest’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Fourier2d: no visible global function definition for ‘fft’
kernel2dsmooth: no visible global function definition for ‘fft’
Undefined global functions or variables:
  fft
Consider adding
  importFrom("stats", "fft")
to your NAMESPACE file.
'library' or 'require' call to ‘MASS’ which was already attached by Depends.
  Please remove these calls from your code.
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    3.6Mb
    libs   9.5Mb
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
Package required but not available: ‘rpanel’

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

> ### Name: sm.surface3d
> ### Title: Adding a regression surface to an rgl plot.
> ### Aliases: sm.surface3d
> ### Keywords: nonparametric regression smooth
> 
> ### ** Examples
> 
> with(trawl, {
+    Zone93    <- (Year == 1 & Zone == 1)
+    Position  <- cbind(Longitude - 143, Latitude)
+    model1 <- sm.regression(Position[Zone93,], Score1[Zone93],
+         h= c(0.1, 0.1), display = "rgl", xlab="Longitude - 143")
+    model2 <- sm.regression(Position[Zone93,], Score1[Zone93],
+         h= c(0.2, 0.2), display = "none")
+    sm.surface3d(model2$eval.points, model2$est, model1$scaling, col = "red")
+ })
Error in sm.surface3d(model2$eval.points, model2$est, model1$scaling,  : 
  a scaling must be specified.
Calls: with -> with.default -> eval -> eval -> sm.surface3d
Execution halted
Malformed Description field: should contain one or more complete sentences.
dNMR: no visible global function definition for ‘pnorm’
dNMR: no visible global function definition for ‘dnorm’
pNMR: no visible global function definition for ‘pnorm’
pNMR: no visible global function definition for ‘dnorm’
rMR: no visible global function definition for ‘rnorm’
rMR: no visible global function definition for ‘rchisq’
Undefined global functions or variables:
  dnorm pnorm rchisq rnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm", "rchisq", "rnorm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
SMVar.paired : <anonymous>: no visible global function definition for
  ‘var’
SMVar.paired: no visible global function definition for ‘var’
SMVar.paired: no visible global function definition for ‘pt’
SMVar.paired: no visible global function definition for ‘p.adjust’
SMVar.paired: no visible global function definition for ‘write.table’
SMVar.unpaired : <anonymous>: no visible global function definition for
  ‘var’
SMVar.unpaired: no visible global function definition for ‘var’
SMVar.unpaired: no visible global function definition for ‘pt’
SMVar.unpaired: no visible global function definition for ‘p.adjust’
SMVar.unpaired: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  p.adjust pt var write.table
Consider adding
  importFrom("stats", "p.adjust", "pt", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
No protocol specified
No protocol specified
Malformed Description field: should contain one or more complete sentences.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘ggplot2’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rmpi’
Malformed Title field: should not end in a period.
Package in Depends field not imported from: ‘snow’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: ‘Rmpi’
Package suggested but not available for checking: ‘Rmpi’
KS.test: no visible global function definition for ‘quantile’
KS.test : Fgaus: no visible global function definition for ‘pnorm’
KS.test: no visible global function definition for ‘setNames’
cs.test: no visible global function definition for ‘pbinom’
cs.test: no visible global function definition for ‘pnorm’
cs.test: no visible global function definition for ‘setNames’
kde: no visible global function definition for ‘quantile’
kde : Fgaus: no visible global function definition for ‘pnorm’
kde: no visible global function definition for ‘par’
kre: no visible global function definition for ‘quantile’
kre: no visible global function definition for ‘lines’
ns.test: no visible global function definition for ‘complete.cases’
ns.test: no visible global function definition for ‘qnorm’
ns.test: no visible global function definition for ‘pnorm’
ns.test: no visible global function definition for ‘pchisq’
ns.test: no visible global function definition for ‘setNames’
ns.test: no visible global function definition for ‘qt’
quant.test: no visible global function definition for ‘complete.cases’
quant.test: no visible global function definition for ‘pbinom’
quant.test: no visible global function definition for ‘pnorm’
quant.test: no visible global function definition for ‘setNames’
quant.test: no visible global function definition for ‘quantile’
quant.test: no visible global function definition for ‘phyper’
runs.test: no visible global function definition for ‘median’
runs.test: no visible global function definition for ‘setNames’
runs.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  complete.cases lines median par pbinom pchisq phyper pnorm qnorm qt
  quantile setNames
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "complete.cases", "median", "pbinom", "pchisq",
             "phyper", "pnorm", "qnorm", "qt", "quantile", "setNames")
to your NAMESPACE file.
Package required but not available: ‘BiocStyle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.5Mb
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘mvtnorm’ ‘combinat’
A package should be listed in only one of these fields.
chisq.test.a: no visible global function definition for ‘chisq.test’
maxsel: no visible global function definition for ‘complete.cases’
maxsel.asymp.test: no visible global function definition for
  ‘complete.cases’
Undefined global functions or variables:
  chisq.test complete.cases
Consider adding
  importFrom("stats", "chisq.test", "complete.cases")
to your NAMESPACE file.
Package in Depends field not imported from: ‘grid’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/snpReady.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages in Depends field not imported from:
  ‘colorspace’ ‘snpStats’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
check.args: no visible global function definition for ‘is’
write.sbams: no visible global function definition for ‘as’
write.sbams: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  as is write.table
Consider adding
  importFrom("methods", "as", "is")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Namespaces in Imports field not imported from:
  ‘devtools’ ‘raster’ ‘rlang’ ‘sp’ ‘usethis’
  All declared Imports should be used.
Note: found 833 marked UTF-8 strings
Malformed Title field: should not end in a period.
calculate.areas: no visible global function definition for ‘runif’
calculate.gradedareas: no visible global function definition for
  ‘rnorm’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Ssimpute.als: no visible global function definition for ‘rnorm’
Ssvd.als: no visible global function definition for ‘rnorm’
cs.default: no visible binding for global variable ‘weighted.mean’
simpute.als: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm weighted.mean
Consider adding
  importFrom("stats", "rnorm", "weighted.mean")
to your NAMESPACE file.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
Note: found 145 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lattice’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SoilHyP.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘rpanel’
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
Running examples in ‘soilphysics-Ex.R’ failed
The error most likely occurred in:

> ### Name: fitsoilwater
> ### Title: Interactive Estimation of van Genuchten's (1980) Model
> ###   Parameters
> ### Aliases: fitsoilwater
> 
> ### ** Examples
> 
> # Liu et al. (2011)
> h <- c(0.001, 50.65, 293.77, 790.14, 992.74, 5065, 10130, 15195)
> w <- c(0.5650, 0.4013, 0.2502, 0.2324, 0.2307, 0.1926, 0.1812, 0.1730)
> fitsoilwater(w, h)
Error in fitsoilwater(w, h) : package rpanel is required
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
No protocol specified
No protocol specified
Warning in fun(libname, pkgname) : couldn't connect to display ":0"
Quitting from lines 136-139 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
package rpanel is required
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘AGread’ ‘caret’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘lgr’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
plot.soma: no visible global function definition for ‘plot’
soma: no visible global function definition for ‘runif’
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.
bm: no visible global function definition for ‘rnorm’
bm: no visible global function definition for ‘ts’
fbm: no visible global function definition for ‘fft’
fbm: no visible global function definition for ‘rnorm’
fbm: no visible global function definition for ‘ts’
gbm: no visible global function definition for ‘rnorm’
gbm: no visible global function definition for ‘ts’
Undefined global functions or variables:
  fft rnorm ts
Consider adding
  importFrom("stats", "fft", "rnorm", "ts")
to your NAMESPACE file.
getAlpha: no visible global function definition for ‘pbinom’
kfweOrd: no visible global function definition for ‘qnbinom’
Undefined global functions or variables:
  pbinom qnbinom
Consider adding
  importFrom("stats", "pbinom", "qnbinom")
to your NAMESPACE file.
draw: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘rlist’
  All declared Imports should be used.
Hexagons: no visible global function definition for ‘plot’
UmatGraph: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    2.2Mb
    libs   6.8Mb
'library' or 'require' call to ‘hexbin’ which was already attached by Depends.
  Please remove these calls from your code.
hexbinpie: no visible global function definition for ‘quantile’
hexbinpie: no visible global function definition for ‘polygon’
hexbinpie: no visible global function definition for ‘text’
makehexbinplot: no visible global function definition for ‘rainbow’
makehexbinplot: no visible global function definition for ‘col2rgb’
makehexbinplot: no visible global function definition for ‘edit’
makehexbinplot: no visible global function definition for ‘dev.new’
makehexbinplot: no visible global function definition for ‘plot.new’
makehexbinplot: no visible global function definition for ‘plot.window’
makehexbinplot: no visible global function definition for ‘box’
makehexbinplot: no visible global function definition for ‘axis’
makehexbinplot: no visible global function definition for ‘legend’
som.plot: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  axis box col2rgb dev.new edit legend plot.new plot.window polygon
  quantile rainbow read.table text
Consider adding
  importFrom("grDevices", "col2rgb", "dev.new", "rainbow")
  importFrom("graphics", "axis", "box", "legend", "plot.new",
             "plot.window", "polygon", "text")
  importFrom("stats", "quantile")
  importFrom("utils", "edit", "read.table")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
No protocol specified
Found the following hidden files and directories:
  .gitignore
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Malformed Title field: should not end in a period.
License components which are templates and need '+ file LICENSE':
  MIT
Error(s) in re-building vignettes:
--- re-building ‘built_in.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘built_in.Rmd’

--- re-building ‘cloning.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘cloning.Rmd’

--- re-building ‘novel_solutions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘novel_solutions.Rmd’

--- re-building ‘understanding_sortable_js.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshot1658776514481.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot1658776514481.png': No such file or directory
Quitting from lines 85-86 (understanding_sortable_js.Rmd) 
Error: processing vignette 'understanding_sortable_js.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘understanding_sortable_js.Rmd’

--- re-building ‘using_custom_css.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘using_custom_css.Rmd’

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

Error: Vignette re-building failed.
Execution halted
convert_municipality_names: no visible global function definition for
  ‘read.csv’
regression_plot: no visible binding for global variable ‘loess’
regression_plot: no visible global function definition for
  ‘colorRampPalette’
regression_plot: no visible global function definition for
  ‘loess.control’
regression_plot: no visible global function definition for ‘predict’
regression_plot : <anonymous>: no visible global function definition
  for ‘quantile’
regression_plot : <anonymous>: no visible global function definition
  for ‘pnorm’
regression_plot: no visible global function definition for
  ‘flush.console’
regression_plot: no visible global function definition for ‘density’
Undefined global functions or variables:
  colorRampPalette density flush.console loess loess.control pnorm
  predict quantile read.csv
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "density", "loess", "loess.control", "pnorm",
             "predict", "quantile")
  importFrom("utils", "flush.console", "read.csv")
to your NAMESPACE file.
Package suggested but not available for checking: ‘SciencesPo’
Found the following significant warnings:
  Note: possible error in 'approx(x = 1:lc, y = cnt, ': unused argument (na.rm = FALSE) 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/soundgen.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’.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
plotSpec: possible error in approx(x = 1:lc, y = cnt, xout = seq(1, lc,
  length.out = length(X)), na.rm = FALSE): unused argument (na.rm =
  FALSE)
Note: found 15 marked UTF-8 strings
Error(s) in re-building vignettes:
  ...
--- re-building ‘acoustic_analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 206-207 (acoustic_analysis.Rmd) 
Error: processing vignette 'acoustic_analysis.Rmd' failed with diagnostics:
Failed to analyze any input
--- failed re-building ‘acoustic_analysis.Rmd’

--- re-building ‘sound_generation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘sound_generation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘DropletUtils’
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data   9.8Mb
    doc    1.1Mb
License components which are templates and need '+ file LICENSE':
  MIT
Namespaces in Imports field not imported from:
  ‘gtools’ ‘reshape2’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'r2cytoscape', 'BiocStyle', 'hgu95av2.db', 'ALL', 'org.Hs.eg.db'
Package unavailable to check Rd xrefs: ‘ALL’
Error(s) in re-building vignettes:
--- re-building ‘SourceSet.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

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

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

    IQR, mad, sd, var, xtabs

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

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

Identifing all possible orderings..
Total run time: 1.46 secs
Identifing all possible orderings..
Total run time: 0.79 secs
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshot1036025ae8906.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot1036025ae8906.png': No such file or directory
Quitting from lines 346-347 (SourceSet.Rmd) 
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘SourceSet.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
analyzeSP23Design: no visible global function definition for ‘plot’
exploreSP23Design: no visible global function definition for
  ‘txtProgressBar’
exploreSP23Design: no visible global function definition for
  ‘setTxtProgressBar’
generateClinicalTrialData : <anonymous>: no visible global function
  definition for ‘runif’
generateClinicalTrialData: no visible global function definition for
  ‘rbinom’
generateClinicalTrialData: no visible global function definition for
  ‘rexp’
mHP.b : crossingProbDiff: no visible global function definition for
  ‘pnorm’
mHP.b : crossingProbDiff: no visible global function definition for
  ‘Miwa’
mHP.b: no visible global function definition for ‘qnorm’
mHP.b: no visible global function definition for ‘uniroot’
mHP.c : crossingProbDiff: no visible global function definition for
  ‘Miwa’
mHP.c: no visible global function definition for ‘uniroot’
mHP.c: no visible global function definition for ‘qnorm’
performInterimLook: no visible global function definition for ‘optim’
performInterimLook: no visible global function definition for
  ‘constrOptim’
performInterimLook: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  Miwa constrOptim optim plot pnorm qnorm rbinom rexp runif
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "constrOptim", "optim", "pnorm", "qnorm", "rbinom",
             "rexp", "runif", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    include   2.1Mb
    libs      3.3Mb
No protocol specified
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Namespaces in Imports field not imported from:
  ‘devtools’ ‘rstudioapi’
  All declared Imports should be used.
No protocol specified
No protocol specified
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is 37.8Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs  34.9Mb
hausman: no visible global function definition for ‘pchisq’
span.formula: no visible global function definition for ‘model.frame’
span.formula: no visible global function definition for ‘model.matrix’
span.formula: no visible global function definition for
  ‘model.response’
spbe: no visible global function definition for ‘cor’
spbe: no visible global function definition for ‘pt’
spfe: no visible global function definition for ‘cor’
spfe: no visible global function definition for ‘pt’
sprandom: no visible global function definition for ‘cor’
sprandom: no visible global function definition for ‘pt’
summary.span: no visible global function definition for ‘printCoefmat’
Undefined global functions or variables:
  cor model.frame model.matrix model.response pchisq printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.frame", "model.matrix",
             "model.response", "pchisq", "printCoefmat", "pt")
to your NAMESPACE file.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
svs_1h_brain_analysis: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_sparkline.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshot4c28b900111.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot4c28b900111.png': No such file or directory
Quitting from lines 20-30 (intro_sparkline.Rmd) 
Error: processing vignette 'intro_sparkline.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘intro_sparkline.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    java   3.0Mb
Namespace in Imports field not imported from: ‘lifecycle’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘RCurl’ ‘XML’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SPARQL : <anonymous>: no visible global function definition for
  ‘URLencode’
SPARQL: no visible binding for global variable ‘getURL’
SPARQL: no visible global function definition for ‘URLencode’
SPARQL: no visible binding for global variable ‘xmlParse’
SPARQL: no visible global function definition for ‘getNodeSet’
SPARQL: no visible global function definition for ‘xpathApply’
SPARQL: no visible binding for global variable ‘postForm’
get_attr: no visible global function definition for ‘getNodeSet’
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for ‘getNodeSet’
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for ‘xmlDoc’
get_value: no visible global function definition for ‘xmlDoc’
get_value: no visible global function definition for ‘xpathSApply’
get_value: no visible binding for global variable ‘xmlValue’
get_value: no visible global function definition for ‘xpathApply’
get_value: no visible binding for global variable ‘xmlGetAttr’
readCSVstring: no visible global function definition for ‘read.csv’
readTSVstring: no visible global function definition for ‘read.delim’
Undefined global functions or variables:
  URLencode getNodeSet getURL postForm read.csv read.delim xmlDoc
  xmlGetAttr xmlParse xmlValue xpathApply xpathSApply
Consider adding
  importFrom("utils", "URLencode", "read.csv", "read.delim")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
f.I2.cont: no visible global function definition for ‘combn’
f.I2.dich: no visible global function definition for ‘combn’
f.pstar.cont: no visible global function definition for ‘combn’
f.pstar.dich: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘gtable’ ‘rlang’ ‘testthat’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    libs  16.5Mb
Namespaces in Imports field not imported from:
  ‘future’ ‘geosphere’ ‘lubridate’ ‘tidyverse’ ‘viridis’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    libs  29.8Mb
Namespace in Imports field not imported from: ‘spatstat.linnet’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘irlba’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/spatialEco.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘INLA’
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘SpatialEpi’ ‘dplyr’ ‘dygraphs’ ‘ggplot2’
  ‘htmlwidgets’ ‘knitr’ ‘leaflet’ ‘mapproj’ ‘maptools’ ‘rgdal’ ‘rgeos’
  ‘rmarkdown’ ‘shinyjs’ ‘spdep’ ‘xts’
  All declared Imports should be used.
Package suggested but not available for checking: ‘INLA’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SpatialKWD.Rcheck/00install.out’ for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    libs   1.1Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Note: found 25 marked Latin-1 strings
  Note: found 335 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  13.2Mb
Running examples in ‘spatsoc-Ex.R’ failed
The error most likely occurred in:

> ### Name: build_lines
> ### Title: Build Lines
> ### Aliases: build_lines
> 
> ### ** Examples
> 
> # Load data.table
> library(data.table)
> 
> # Read example data
> DT <- fread(system.file("extdata", "DT.csv", package = "spatsoc"))
> 
> # Cast the character column to POSIXct
> DT[, datetime := as.POSIXct(datetime, tz = 'UTC')]
> 
> # EPSG code for example data
> utm <- 'EPSG:32736'
> 
> # Build lines for each individual
> lines <- build_lines(DT, projection = utm, id = 'ID', coords = c('X', 'Y'),
+             sortBy = 'datetime')
Error in sp::CRS(projection) : no arguments in initialization list
Calls: build_lines -> <Anonymous>
Execution halted
Running ‘testthat.R’ [36s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    3. │ │ └─base::force(code)
    4. │ ├─base::withCallingHandlers(...)
    5. │ └─base::withVisible(code)
    6. └─spatsoc::group_polys(...)
    7.   └─spatsoc::build_polys(...)
    8.     ├─sp::SpatialPointsDataFrame(...)
    9.     │ └─sp::SpatialPoints(coords, proj4string = proj4string, bbox = bbox)
   10.     │   └─methods::new("SpatialPoints", coords = coords, bbox = bbox, proj4string = proj4string)
   11.     │     ├─methods::initialize(value, ...)
   12.     │     └─methods::initialize(value, ...)
   13.     └─sp::CRS(projection)
  
  [ FAIL 26 | WARN 0 | SKIP 0 | PASS 225 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘using-edge-and-dyad.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘using-edge-and-dyad.Rmd’

--- re-building ‘faq.Rmd’ using knitr
--- finished re-building ‘faq.Rmd’

--- re-building ‘intro-spatsoc.Rmd’ using knitr
Quitting from lines 138-149 (intro-spatsoc.Rmd) 
Error: processing vignette 'intro-spatsoc.Rmd' failed with diagnostics:
no arguments in initialization list
--- failed re-building ‘intro-spatsoc.Rmd’

--- re-building ‘using-in-sna.Rmd’ using knitr
--- finished re-building ‘using-in-sna.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      3.1Mb
    help   3.1Mb
No protocol specified
No protocol specified
No protocol specified
No protocol specified
Package required but not available: ‘rpanel’

Depends: includes the non-default packages:
  'spatstat.geom', 'spatstat.core', 'spatstat.linnet', 'spatstat.data',
  'rpanel', 'tcltk'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘spatstat’
  All declared Imports should be used.
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs  19.3Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
    libs   9.1Mb
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
GenerateCliquesCovariance: no visible global function definition for
  ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Package suggested but not available for checking: ‘spDataLarge’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.2Mb
Note: found 56 marked UTF-8 strings
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    help   1.5Mb
Note: found 34 marked UTF-8 strings
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   6.0Mb
    etc   1.3Mb
Namespaces in Imports field not imported from:
  ‘readr’ ‘tidyverse’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
bartlett: no visible global function definition for ‘pchisq’
local.rbfdot: no visible binding for global variable ‘sd’
local.rbfdot: no visible global function definition for ‘dist’
local.rbfdot : <anonymous>: no visible global function definition for
  ‘median’
speccalt: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  dist kmeans median pchisq sd
Consider adding
  importFrom("stats", "dist", "kmeans", "median", "pchisq", "sd")
to your NAMESPACE file.
ChaoBunge: no visible global function definition for ‘qnorm’
ChaoLee1992: no visible global function definition for ‘qnorm’
Pmix: no visible global function definition for ‘dpois’
PmixSCon: no visible global function definition for ‘dbeta’
bootPCG: no visible global function definition for ‘flush.console’
bootPCG: no visible global function definition for ‘quantile’
bootPnpmle: no visible global function definition for ‘flush.console’
bootPnpmle: no visible global function definition for ‘quantile’
bootUnpmle: no visible global function definition for ‘flush.console’
bootUnpmle: no visible global function definition for ‘quantile’
chao1984: no visible global function definition for ‘qnorm’
jackknife: no visible global function definition for ‘dbinom’
jackknife: no visible global function definition for ‘qnorm’
pcg: no visible global function definition for ‘flush.console’
unpmle: no visible global function definition for ‘flush.console’
untrunPmix: no visible global function definition for ‘dpois’
Undefined global functions or variables:
  dbeta dbinom dpois flush.console qnorm quantile
Consider adding
  importFrom("stats", "dbeta", "dbinom", "dpois", "qnorm", "quantile")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/specmine.datasets.Rcheck/00install.out’ for details.
Package required but not available: ‘specmine.datasets’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   3.2Mb
Note: found 5 marked Latin-1 strings
Namespace in Imports field not imported from: ‘pdftools’
  All declared Imports should be used.
'library' or 'require' call to ‘leaps’ which was already attached by Depends.
  Please remove these calls from your code.
modSearch: no visible global function definition for ‘glm’
modSearch: no visible binding for global variable ‘binomial’
modSearch: no visible global function definition for ‘na.omit’
modSearch: no visible global function definition for ‘as.formula’
speff: no visible binding for global variable ‘na.pass’
speff: no visible global function definition for ‘model.matrix’
speff: no visible global function definition for ‘terms’
speff: no visible global function definition for ‘model.response’
speff: no visible global function definition for ‘as.formula’
speff: no visible global function definition for ‘predict’
speff: no visible global function definition for ‘na.omit’
speff: no visible global function definition for ‘glm’
speff: no visible binding for global variable ‘na.omit’
speffSurv: no visible global function definition for ‘model.matrix’
speffSurv: no visible global function definition for ‘terms’
speffSurv: no visible global function definition for ‘model.response’
speffSurv: no visible global function definition for ‘as.formula’
speffSurv: no visible global function definition for ‘uniroot’
summary.speff: no visible global function definition for ‘qnorm’
summary.speff: no visible global function definition for ‘pnorm’
summary.speffSurv: no visible global function definition for ‘qnorm’
summary.speffSurv: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as.formula binomial glm model.matrix model.response na.omit na.pass
  pnorm predict qnorm terms uniroot
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "model.matrix",
             "model.response", "na.omit", "na.pass", "pnorm", "predict",
             "qnorm", "terms", "uniroot")
to your NAMESPACE file.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nr' to 'nrow'
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nc' to 'ncol'
spe: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘mathjaxr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘class’ ‘mlbench’
  All declared Imports should be used.
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    libs  24.4Mb
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/spherepc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/sphereplot.Rcheck/00install.out’ for details.
Package in Depends field not imported from: ‘rgl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pointsphere: no visible global function definition for ‘runif’
rgl.sphMW: no visible global function definition for ‘plot3d’
rgl.sphcirc: no visible global function definition for ‘rotate3d’
rgl.sphcirc: no visible global function definition for ‘lines3d’
rgl.sphgrid: no visible global function definition for ‘open3d’
rgl.sphgrid: no visible global function definition for ‘plot3d’
rgl.sphgrid: no visible global function definition for ‘lines3d’
rgl.sphgrid: no visible global function definition for ‘text3d’
rgl.sphpoints: no visible global function definition for ‘points3d’
rgl.sphsun: no visible global function definition for ‘plot3d’
rgl.sphtext: no visible global function definition for ‘text3d’
Undefined global functions or variables:
  lines3d open3d plot3d points3d rotate3d runif text3d
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SphericalCubature.Rcheck/00install.out’ for details.
Packages in Depends field not imported from:
  ‘lars’ ‘parallel’ ‘randomForest’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
'library' or 'require' call to ‘quadprog’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘quadprog’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SPIn: no visible global function definition for ‘density’
SPIn: no visible global function definition for ‘quantile’
SPIn: no visible global function definition for ‘solve.QP’
bootSPIn: no visible global function definition for ‘runif’
plot.SPIn: no visible global function definition for ‘hist’
plot.SPIn: no visible global function definition for ‘lines’
plot.SPIn: no visible global function definition for ‘text’
plot.SPIn: no visible global function definition for ‘quantile’
plot.SPIn: no visible global function definition for ‘legend’
Undefined global functions or variables:
  density hist legend lines quantile runif solve.QP text
Consider adding
  importFrom("graphics", "hist", "legend", "lines", "text")
  importFrom("stats", "density", "quantile", "runif")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespace in Imports field not imported from: ‘biomod2’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    extdata   5.6Mb
    libs      3.6Mb
Running ‘testthat.R’ [157s/153s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  `obs_value` not equal to `real_value`.
  1/1 mismatches
  [1] 0.00192 - 0.00384 == -0.00192
  ── Failure (test_kernels.R:95:3): Testing the discontinuous kernel with a simple case ──
  `obs_value` not equal to `real_value`.
  1/1 mismatches
  [1] Inf - 0.00128 == Inf
  ── Failure (test_kernels.R:144:3): Testing the continuous kernel with a simple case ──
  `obs_value` not equal to `real_value`.
  1/1 mismatches
  [1] 0 - 0.12 == -0.12
  
  [ FAIL 3 | WARN 6 | SKIP 0 | PASS 1 ]
  Error: Test failures
  Execution halted
Malformed Description field: should contain one or more complete sentences.
R2.global: no visible global function definition for ‘var’
calculer.var.exp: no visible global function definition for ‘var’
creer.noeud: no visible global function definition for ‘var’
ponderer.classe: no visible global function definition for ‘var’
ponderer.classe: no visible global function definition for ‘cov’
spodt: no visible global function definition for ‘model.frame’
spodt.tree: no visible global function definition for ‘plot.new’
spodt.tree: no visible global function definition for ‘par’
spodt.tree: no visible global function definition for ‘plot.window’
spodt.tree: no visible global function definition for ‘text’
spodt.tree: no visible global function definition for ‘segments’
test.spodt: no visible global function definition for ‘model.frame’
test.spodt: no visible global function definition for ‘hist’
test.spodt: no visible global function definition for ‘abline’
tracer.noeud: no visible global function definition for ‘text’
tracer.noeud: no visible global function definition for ‘segments’
Undefined global functions or variables:
  abline cov hist model.frame par plot.new plot.window segments text
  var
Consider adding
  importFrom("graphics", "abline", "hist", "par", "plot.new",
             "plot.window", "segments", "text")
  importFrom("stats", "cov", "model.frame", "var")
to your NAMESPACE file.
plotor: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Note: found 7587 marked UTF-8 strings
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fetch_NBAPlayerStatistics: no visible global function definition for
  ‘read.table’
Undefined global functions or variables:
  read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
Note: found 8 marked Latin-1 strings
  Note: found 83 marked UTF-8 strings
sportscausal: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘batchtools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sampling’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘ggplot2’
  All declared Imports should be used.
plot.SPRT: no visible global function definition for ‘par’
plot.SPRT: no visible global function definition for ‘plot’
plot.SPRT: no visible global function definition for ‘abline’
print.SPRT: no visible global function definition for ‘head’
Undefined global functions or variables:
  abline head par plot
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("utils", "head")
to your NAMESPACE file.
Package required but not available: ‘spsUtil’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘car’ ‘knitr’ ‘lmtest’ ‘rmarkdown’
  All declared Imports should be used.
installed size is 43.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  41.8Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/spsUtil.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘matrixcalc’ ‘mvtnorm’ ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘spatstat’ ‘spatstat.data’ ‘spatstat.linnet’ ‘spatstat.sparse’
  ‘spatstat.utils’ ‘testthat’
  All declared Imports should be used.
sGda : <anonymous>: no visible global function definition for ‘cov’
sortgene: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  cov model.matrix
Consider adding
  importFrom("stats", "cov", "model.matrix")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
'library' or 'require' calls in package code:
  ‘RJDBC’ ‘RMySQL’ ‘RODBC’ ‘RPostgreSQL’ ‘RSQLite’ ‘tcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
cacheQuery: no visible global function definition for ‘read.csv’
cacheQuery: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  read.csv write.csv
Consider adding
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
SQN: no visible binding for global variable ‘median’
SQN: no visible global function definition for ‘quantile’
SQN.demo.data: no visible global function definition for ‘rnorm’
mix.qn: no visible global function definition for ‘ecdf’
mix.qn: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  ecdf median quantile rnorm
Consider adding
  importFrom("stats", "ecdf", "median", "quantile", "rnorm")
to your NAMESPACE file.
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    libs  25.7Mb
GNU make is a SystemRequirements.
File ‘sqp/libs/sqp.so’:
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)
    Object: ‘solver_dense.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.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/squashinformr.Rcheck/00install.out’ for details.
Found the following hidden files and directories:
  .Rapp.history
  inst/script/.Rapp.history
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
File ‘sROC/R/onload.R’:
  .onLoad calls:
    packageStartupMessage("sROC 0.1-2 loaded")

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

AUC : TrapezInt: no visible global function definition for ‘approx’
AUC : SimpsonInt: no visible global function definition for ‘approx’
CI.CDF: no visible global function definition for ‘qnorm’
bw.CDF: no visible global function definition for ‘sd’
bw.CDF: no visible global function definition for ‘IQR’
bw.CDF.pi: no visible global function definition for ‘sd’
bw.CDF.pi: no visible global function definition for ‘bw.nrd0’
bw.CDF.pi: no visible global function definition for ‘bw.nrd’
bw.CDF.pi: no visible global function definition for ‘bw.ucv’
bw.CDF.pi: no visible global function definition for ‘bw.bcv’
bw.CDF.pi: no visible global function definition for ‘bw.SJ’
bw.CDF.pi: no visible global function definition for ‘IQR’
plot.CDF: no visible global function definition for ‘plot.default’
plot.CDF: no visible global function definition for ‘lines’
plot.CDF: no visible global function definition for ‘polygon’
plot.ROC: no visible global function definition for ‘plot.default’
plot.ROC: no visible global function definition for ‘abline’
Undefined global functions or variables:
  IQR abline approx bw.SJ bw.bcv bw.nrd bw.nrd0 bw.ucv lines
  plot.default polygon qnorm sd
Consider adding
  importFrom("graphics", "abline", "lines", "plot.default", "polygon")
  importFrom("stats", "IQR", "approx", "bw.SJ", "bw.bcv", "bw.nrd",
             "bw.nrd0", "bw.ucv", "qnorm", "sd")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘shinyFiles’
  All declared Imports should be used.
ssd : correction_method_D: no visible global function definition for
  ‘rnorm’
ssd : generate_bootstrap: no visible global function definition for
  ‘rmultinom’
ssd : bootstrap_method: no visible global function definition for
  ‘median’
ssd : bootstrap_method: no visible global function definition for
  ‘quantile’
ssd : unbalanced_generate_bootstrap: no visible global function
  definition for ‘rmultinom’
ssd : unbalanced_bootstrap_method: no visible global function
  definition for ‘median’
ssd : unbalanced_bootstrap_method: no visible global function
  definition for ‘quantile’
ssd: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  median qchisq quantile rmultinom rnorm
Consider adding
  importFrom("stats", "median", "qchisq", "quantile", "rmultinom",
             "rnorm")
to your NAMESPACE file.
L_hNV: no visible global function definition for ‘pnorm’
L_hNV_rho: no visible global function definition for ‘pnorm’
eff.ssfa: no visible global function definition for ‘pnorm’
plot_fitted: no visible global function definition for ‘lines’
plot_moran: no visible global function definition for ‘residuals’
print.summary.ssfa: no visible global function definition for
  ‘printCoefmat’
ssfa: no visible global function definition for ‘model.frame’
ssfa: no visible global function definition for ‘model.response’
ssfa.fit: no visible global function definition for ‘lm’
ssfa.fit: no visible global function definition for ‘var’
ssfa.fit: no visible global function definition for ‘logLik’
summary.ssfa: no visible global function definition for ‘pnorm’
summary.ssfa: no visible global function definition for ‘logLik’
summary.ssfa: no visible global function definition for ‘pchisq’
summary.ssfa: no visible binding for global variable ‘df’
u.ssfa: no visible global function definition for ‘dnorm’
u.ssfa: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  df dnorm lines lm logLik model.frame model.response pchisq pnorm
  printCoefmat residuals var
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "df", "dnorm", "lm", "logLik", "model.frame",
             "model.response", "pchisq", "pnorm", "printCoefmat",
             "residuals", "var")
to your NAMESPACE file.
Package in Depends field not imported from: ‘survey’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fit.model: no visible global function definition for ‘hadamard’
Undefined global functions or variables:
  hadamard
Namespace in Imports field not imported from: ‘sessioninfo’
  All declared Imports should be used.
plot.sshaped: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
mem.usage: no visible global function definition for ‘read.delim’
Undefined global functions or variables:
  read.delim
Consider adding
  importFrom("utils", "read.delim")
to your NAMESPACE file.
installed size is 57.7Mb
  sub-directories of 1Mb or more:
    libs  57.4Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
map.world: no visible global function definition for ‘par’
map.world: no visible global function definition for ‘plot.new’
map.world: no visible global function definition for ‘plot.window’
map.world: no visible global function definition for ‘lines’
map.world: no visible global function definition for ‘title’
map.world: no visible global function definition for ‘axis’
map.world: no visible global function definition for ‘box’
plot.smooth.sspline: no visible global function definition for
  ‘predict’
plot.smooth.sspline: no visible global function definition for
  ‘filled.contour’
plot.smooth.sspline: no visible binding for global variable
  ‘terrain.colors’
plot.smooth.sspline: no visible global function definition for ‘title’
plot.smooth.sspline: no visible global function definition for ‘axis’
station: no visible binding for global variable ‘WTdiff’
station: no visible global function definition for ‘points’
Undefined global functions or variables:
  WTdiff axis box filled.contour lines par plot.new plot.window points
  predict terrain.colors title
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "axis", "box", "filled.contour", "lines", "par",
             "plot.new", "plot.window", "points", "title")
  importFrom("stats", "predict")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shinydashboard’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
error.est : <anonymous>: no visible global function definition for
  ‘median’
holm.robust: no visible global function definition for ‘pnorm’
holm.robust: no visible global function definition for ‘median’
holm.robust: no visible global function definition for ‘mad’
huberize: no visible global function definition for ‘quantile’
ssvd.initial: no visible global function definition for ‘mad’
ssvd.iter.thresh: no visible global function definition for ‘mad’
Undefined global functions or variables:
  mad median pnorm quantile
Consider adding
  importFrom("stats", "mad", "median", "pnorm", "quantile")
to your NAMESPACE file.
Note: found 123 marked UTF-8 strings
Error(s) in re-building vignettes:
  ...
--- re-building ‘forests.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 124-128 (forests.Rmd) 
Error: processing vignette 'forests.Rmd' failed with diagnostics:
object 'credit_risk' not found
--- failed re-building ‘forests.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘stabledist’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘yardstick’
  All declared Imports should be used.
genericPlot: no visible global function definition for ‘dev.new’
genericPlot: no visible global function definition for ‘par’
genericPlot: no visible global function definition for ‘rainbow’
genericPlot: no visible global function definition for ‘plot’
genericPlot: no visible global function definition for ‘lines’
genericPlot: no visible global function definition for ‘legend’
genericPlot: no visible global function definition for ‘dev.copy2pdf’
genericPlot: no visible global function definition for ‘dev.copy2eps’
genericPlot: no visible global function definition for ‘dev.print’
genericPlot: no visible binding for global variable ‘png’
genericPlot: no visible binding for global variable ‘tiff’
plotStrains: no visible global function definition for ‘rainbow’
plotStrains: no visible global function definition for ‘dev.new’
plotStrains: no visible global function definition for ‘par’
plotStrains: no visible global function definition for ‘plot’
plotStrains: no visible global function definition for ‘lines’
plotStrains: no visible global function definition for ‘legend’
plotStrains: no visible global function definition for ‘dev.copy2pdf’
plotStrains: no visible global function definition for ‘dev.copy2eps’
plotStrains: no visible global function definition for ‘dev.print’
plotStrains: no visible binding for global variable ‘png’
plotStrains: no visible binding for global variable ‘tiff’
Undefined global functions or variables:
  dev.copy2eps dev.copy2pdf dev.new dev.print legend lines par plot png
  rainbow tiff
Consider adding
  importFrom("grDevices", "dev.copy2eps", "dev.copy2pdf", "dev.new",
             "dev.print", "png", "rainbow", "tiff")
  importFrom("graphics", "legend", "lines", "par", "plot")
to your NAMESPACE file.
File
  LICENCE
is not mentioned in the DESCRIPTION file.
'library' or 'require' calls to packages already attached by Depends:
  ‘np’ ‘sp’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘np’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
stkde: no visible global function definition for ‘npudensbw’
stkde: no visible global function definition for ‘npudens’
stkde: no visible global function definition for ‘quantile’
stkde: no visible global function definition for ‘heat.colors’
stkde: no visible global function definition for ‘par’
stkde: no visible global function definition for ‘image’
stkde: no visible global function definition for ‘contour’
stkde.base: no visible global function definition for ‘npudensbw’
stkde.base: no visible global function definition for ‘npudens’
stkde.sig: no visible global function definition for ‘SpatialPoints’
stkde.sig: no visible global function definition for ‘spsample’
stkde.sig: no visible global function definition for ‘bbox’
stkde.sig: no visible global function definition for ‘quantile’
stkde.sig: no visible global function definition for ‘heat.colors’
stkde.sig: no visible global function definition for ‘par’
stkde.sig: no visible global function definition for ‘image’
stkde.sig: no visible global function definition for ‘contour’
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.
find.names: no visible global function definition for ‘na.omit’
generate.names: no visible global function definition for ‘na.omit’
standardize.countrynames: no visible global function definition for
  ‘data’
standardize.names: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    include  10.2Mb
    lib       1.9Mb
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘iterators’ ‘methods’ ‘rgdal’
  All declared Imports should be used.
Packages required and available but unsuitable versions:
  'parallel', 'graphics'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘mnlogit’
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
'library' or 'require' call to ‘codetools’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘codetools’ ‘gss’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Namespaces in Imports field not imported from:
  ‘pander’ ‘readr’ ‘tidyselect’
  All declared Imports should be used.
Package suggested but not available for checking: ‘starsdata’
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc   2.4Mb
    nc    4.5Mb
No protocol specified
No protocol specified
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/starvars.Rcheck/00install.out’ for details.
Note: found 14 marked UTF-8 strings
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/STAT2.Rcheck/00install.out’ for details.
Package required but not available: ‘gWidgets2RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StatDA.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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:
    libs   5.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘differences-gw-cow.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘differences-gw-cow.Rmd’

--- re-building ‘statelists.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 28-30 (statelists.Rmd) 
Error: processing vignette 'statelists.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘statelists.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   5.2Mb
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
Package suggested but not available for checking: ‘asreml’
Namespace in Imports field not imported from: ‘mapproj’
  All declared Imports should be used.
actvspred: no visible global function definition for ‘quantile’
actvspred: no visible global function definition for ‘aggregate’
actvspred: no visible global function definition for ‘par’
actvspred: no visible global function definition for ‘plot’
actvspred: no visible global function definition for ‘lines’
auc: no visible global function definition for ‘par’
auc: no visible global function definition for ‘plot’
decile: no visible global function definition for ‘quantile’
dqcontinuous : numoutliers: no visible global function definition for
  ‘quantile’
dqcontinuous : <anonymous>: no visible global function definition for
  ‘sd’
dqcontinuous : <anonymous>: no visible global function definition for
  ‘quantile’
gini: no visible global function definition for ‘par’
gini: no visible global function definition for ‘plot’
gini: no visible global function definition for ‘abline’
iv: no visible global function definition for ‘quantile’
iv: no visible global function definition for ‘aggregate’
ks: no visible global function definition for ‘aggregate’
ks: no visible global function definition for ‘par’
ks: no visible global function definition for ‘plot’
ks: no visible global function definition for ‘lines’
outliers: no visible global function definition for ‘quantile’
outliers: no visible global function definition for ‘na.omit’
pentile: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline aggregate lines na.omit par plot quantile sd
Consider adding
  importFrom("graphics", "abline", "lines", "par", "plot")
  importFrom("stats", "aggregate", "na.omit", "quantile", "sd")
to your NAMESPACE file.
Note: found 49 marked UTF-8 strings
inspect: no visible global function definition for ‘par’
inspect: no visible global function definition for ‘abline’
inspect: no visible global function definition for ‘lines’
inspect: no visible global function definition for ‘points’
plotfit: no visible global function definition for ‘dev.off’
plotfit: no visible global function definition for ‘par’
plotfit: no visible global function definition for ‘lines’
plotfit: no visible global function definition for ‘points’
plotfit: no visible global function definition for ‘legend’
plothill: no visible global function definition for ‘par’
plothill: no visible global function definition for ‘abline’
plothill: no visible global function definition for ‘points’
plotmultifit: no visible global function definition for ‘par’
plotmultifit: no visible global function definition for ‘lines’
plotmultifit: no visible global function definition for ‘points’
plotmultifit: no visible global function definition for ‘pexp’
plotmultifit: no visible global function definition for ‘plnorm’
plotmultifit: no visible global function definition for ‘ppois’
plotmultifit: no visible global function definition for ‘legend’
plotols: no visible global function definition for ‘dev.off’
plotols: no visible global function definition for ‘lm’
plotols: no visible global function definition for ‘par’
plotols: no visible global function definition for ‘abline’
plotols: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline dev.off legend lines lm par pexp plnorm points ppois
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("graphics", "abline", "legend", "lines", "par", "points")
  importFrom("stats", "lm", "pexp", "plnorm", "ppois")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘corrgram’ ‘datasets’ ‘dplyr’ ‘psych’ ‘psycho’ ‘rpivotTable’
  ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gbm’ ‘ggfortify’ ‘tibble’ ‘tidyverse’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.7Mb
getStp: no visible global function definition for ‘lm’
plot.steeptest: no visible global function definition for ‘plot’
plot.steeptest: no visible global function definition for ‘axis’
plot.steeptest: no visible global function definition for ‘box’
plot.steeptest: no visible global function definition for ‘lm’
plot.steeptest: no visible global function definition for ‘abline’
plot.steeptest: no visible global function definition for ‘legend’
plot.steeptest: no visible global function definition for
  ‘as.graphicsAnnot’
steeptest: no visible global function definition for ‘lm’
summary.steeptest: no visible global function definition for ‘var’
summary.steeptest: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline as.graphicsAnnot axis box legend lm plot quantile var
Consider adding
  importFrom("grDevices", "as.graphicsAnnot")
  importFrom("graphics", "abline", "axis", "box", "legend", "plot")
  importFrom("stats", "lm", "quantile", "var")
to your NAMESPACE file.
'library' or 'require' call to ‘MASS’ which was already attached by Depends.
  Please remove these calls from your code.
Stem.Bootstrap: no visible global function definition for ‘runif’
filtering: no visible global function definition for ‘is.ts’
filtering: no visible global function definition for ‘ts’
filtering: no visible global function definition for ‘start’
filtering: no visible global function definition for ‘end’
filtering: no visible global function definition for ‘frequency’
kalman: no visible global function definition for ‘ts’
smoothing: no visible global function definition for ‘is.ts’
smoothing: no visible global function definition for ‘ts’
smoothing: no visible global function definition for ‘start’
smoothing: no visible global function definition for ‘end’
smoothing: no visible global function definition for ‘frequency’
Undefined global functions or variables:
  end frequency is.ts runif start ts
Consider adding
  importFrom("stats", "end", "frequency", "is.ts", "runif", "start",
             "ts")
to your NAMESPACE file.
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
       █
    1. ├─testthat::expect_error(...) test-types.R:43:2
    2. │ └─testthat:::quasi_capture(...)
    3. │   ├─testthat:::.capture(...)
    4. │   │ └─base::withCallingHandlers(...)
    5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    6. ├─stencilaschema::Datatable(...)
    7. │ └─stencilaschema:::check_property(...)
    8. │   └─stencilaschema:::as_type(value, type)
    9. └─stencilaschema::DatatableColumn(name = "A", values = matrix())
   10.   └─stencilaschema:::check_property(...)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 73 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Getting_Started.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 161-163 (Getting_Started.Rmd) 
Error: processing vignette 'Getting_Started.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘Getting_Started.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Note: found 42 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘tm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘huge’ ‘readr’ ‘scales’ ‘shinyjs’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   2.4Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   6.0Mb
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    libs  25.7Mb
Note: found 22474 marked UTF-8 strings
Malformed Title field: should not end in a period.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R          2.1Mb
    datasets   2.6Mb
Note: found 327 marked UTF-8 strings
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.8Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Package required but not available: ‘rpanel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/str2str.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘Rsymphony’
Note: found 1 marked UTF-8 string
StratPhyloCongruence: no visible global function definition for ‘runif’
StratPhyloCongruence: no visible global function definition for
  ‘txtProgressBar’
StratPhyloCongruence: no visible global function definition for
  ‘setTxtProgressBar’
StratPhyloCongruence: no visible global function definition for ‘pnorm’
StratPhyloCongruence: no visible global function definition for ‘sd’
geoscalePhylo: no visible global function definition for ‘data’
geoscalePhylo: no visible global function definition for ‘par’
geoscalePhylo: no visible global function definition for ‘text’
geoscalePhylo: no visible global function definition for ‘segments’
geoscalePhylo: no visible global function definition for ‘rect’
geoscalePhylo: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  data par pnorm rect rgb runif sd segments setTxtProgressBar text
  txtProgressBar
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "par", "rect", "segments", "text")
  importFrom("stats", "pnorm", "runif", "sd")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Package suggested but not available for checking: ‘StrathE2E2examples’
Namespace in Imports field not imported from: ‘bnlearn’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/StratigrapheR.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘ks’
  All declared Imports should be used.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs  10.1Mb
Namespace in Imports field not imported from: ‘dbscan’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
GNU make is a SystemRequirements.
installed size is 33.3Mb
  sub-directories of 1Mb or more:
    libs  32.5Mb
Note: found 3 marked UTF-8 strings
Package suggested but not available for checking: ‘STRaitRazoR’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/STRMPS.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘broom’ ‘car’ ‘lmerTest’ ‘pbkrtest’
  All declared Imports should be used.
Package suggested but not available for checking: ‘seasonal’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/stR.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘stRvignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-17 (stRvignette.Rmd) 
Error: processing vignette 'stRvignette.Rmd' failed with diagnostics:
there is no package called 'seasonal'
--- failed re-building ‘stRvignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
Namespaces in Imports field not imported from:
  ‘pls’ ‘tibble’
  All declared Imports should be used.
Package required but not available: ‘EmiStatR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 2 marked UTF-8 strings
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘UpSetR’ ‘alluvial’ ‘gridBase’
  All declared Imports should be used.
identifyGraph: no visible global function definition for ‘phyper’
mytriangle: no visible global function definition for ‘symbols’
plotGraph: no visible global function definition for ‘par’
plotGraph: no visible global function definition for ‘plot’
updateOrgEnvir: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  par phyper plot read.table symbols
Consider adding
  importFrom("graphics", "par", "plot", "symbols")
  importFrom("stats", "phyper")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘DT’ ‘bsplus’ ‘colourpicker’ ‘grDevices’ ‘graphics’ ‘jsonlite’
  ‘purrr’ ‘shinyWidgets’ ‘shinyjs’
  All declared Imports should be used.
Package required but not available: ‘ChemmineR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘ROCR’ ‘penalized’
  Please remove these calls from your code.
ELF: no visible global function definition for ‘pt’
ELF: no visible global function definition for ‘qnorm’
ELF: no visible global function definition for ‘lm’
ELF: no visible global function definition for ‘lowess’
ELF: no visible global function definition for ‘dnorm’
ELF: no visible global function definition for ‘approx’
subtype: no visible global function definition for ‘runif’
subtype: no visible global function definition for ‘hclust’
subtype: no visible global function definition for ‘dist’
subtype: no visible global function definition for ‘cutree’
subtype: no visible global function definition for ‘pt’
subtype: no visible global function definition for ‘heatmap’
test_subtype_only: no visible global function definition for ‘pt’
test_subtype_only: no visible global function definition for ‘survdiff’
test_subtype_only: no visible global function definition for ‘survfit’
test_subtype_only: no visible global function definition for ‘title’
ufun: no visible global function definition for ‘dnorm’
ufun: no visible global function definition for ‘lowess’
Undefined global functions or variables:
  approx cutree dist dnorm hclust heatmap lm lowess pt qnorm runif
  survdiff survfit title
Consider adding
  importFrom("graphics", "title")
  importFrom("stats", "approx", "cutree", "dist", "dnorm", "hclust",
             "heatmap", "lm", "lowess", "pt", "qnorm", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SubVis.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘shinygains.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘shinygains.Rmd’

--- re-building ‘suddengains-tutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 472-479 (suddengains-tutorial.Rmd) 
Error: processing vignette 'suddengains-tutorial.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘suddengains-tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘suddengains-tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
'library' or 'require' call to ‘tkrplot’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
playSudoku : replot: no visible global function definition for ‘par’
playSudoku : replot: no visible global function definition for ‘plot’
playSudoku : replot: no visible global function definition for
  ‘segments’
playSudoku : replot: no visible global function definition for ‘text’
playSudoku: no visible global function definition for ‘tktoplevel’
playSudoku: no visible global function definition for ‘tkwm.title’
playSudoku: no visible global function definition for ‘tkrplot’
playSudoku: no visible global function definition for ‘tktext’
playSudoku: no visible global function definition for ‘tkscrollbar’
playSudoku : <anonymous>: no visible global function definition for
  ‘tkyview’
playSudoku: no visible global function definition for ‘tkconfigure’
playSudoku : <anonymous>: no visible global function definition for
  ‘tkset’
playSudoku: no visible global function definition for ‘tkpack’
playSudoku: no visible global function definition for ‘tcl’
playSudoku: no visible global function definition for ‘tkcget’
playSudoku : showz: no visible global function definition for
  ‘tkrreplot’
playSudoku : type: no visible global function definition for ‘tkinsert’
playSudoku : type: no visible global function definition for ‘tksee’
playSudoku : kb: no visible global function definition for ‘tkdestroy’
playSudoku: no visible global function definition for
  ‘getGraphicsEvent’
playSudoku: no visible global function definition for ‘tkbind’
playSudoku: no visible global function definition for ‘tkwait.window’
Undefined global functions or variables:
  getGraphicsEvent par plot segments tcl text tkbind tkcget tkconfigure
  tkdestroy tkinsert tkpack tkrplot tkrreplot tkscrollbar tksee tkset
  tktext tktoplevel tkwait.window tkwm.title tkyview
Consider adding
  importFrom("grDevices", "getGraphicsEvent")
  importFrom("graphics", "par", "plot", "segments", "text")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
SUE.fitted.values: no visible global function definition for
  ‘model.frame’
SUE.lm: no visible global function definition for ‘model.frame’
SUE.lm: no visible global function definition for ‘lm’
SUE.lm: no visible global function definition for ‘anova’
SUE.plot: no visible global function definition for ‘plot’
SUE.residuals: no visible global function definition for ‘model.frame’
parameters : para2: no visible global function definition for ‘uniroot’
parameters: no visible global function definition for ‘optimize’
parameters: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  anova lm model.frame optimize plot uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "anova", "lm", "model.frame", "optimize",
             "uniroot")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘lwgeom’ ‘utf8’
  All declared Imports should be used.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
Note: found 78 marked UTF-8 strings
Package suggested but not available for checking: ‘INLA’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.7Mb
Malformed Description field: should contain one or more complete sentences.
MCMCCV: no visible global function definition for ‘rnorm’
MLCVGauss: no visible global function definition for ‘runif’
MLCVGauss: no visible global function definition for ‘optim’
SimSunderData: no visible global function definition for ‘runif’
SimSunderData: no visible global function definition for ‘dist’
SimSunderData: no visible global function definition for ‘rnorm’
SimSunderData: no visible global function definition for ‘qgamma’
SimSunderData: no visible global function definition for ‘pnorm’
SimSunderData: no visible global function definition for ‘rmultinom’
Undefined global functions or variables:
  dist optim pnorm qgamma rmultinom rnorm runif
Consider adding
  importFrom("stats", "dist", "optim", "pnorm", "qgamma", "rmultinom",
             "rnorm", "runif")
to your NAMESPACE file.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.1Mb
Malformed Description field: should contain one or more complete sentences.
sunter: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
supcluster : itgamma: no visible global function definition for
  ‘rgamma’
supcluster : itgamma: no visible global function definition for
  ‘dgamma’
supcluster : itgamma: no visible global function definition for ‘runif’
supcluster : itbeta: no visible global function definition for ‘rnorm’
supcluster : itbeta: no visible global function definition for ‘runif’
supcluster : itj: no visible global function definition for ‘dmultinom’
supcluster: no visible global function definition for ‘kmeans’
tab1: no visible global function definition for ‘image’
tab1: no visible global function definition for ‘gray’
tab1: no visible global function definition for ‘var’
Undefined global functions or variables:
  dgamma dmultinom gray image kmeans rgamma rnorm runif var
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "image")
  importFrom("stats", "dgamma", "dmultinom", "kmeans", "rgamma", "rnorm",
             "runif", "var")
to your NAMESPACE file.
plot.pelora: no visible global function definition for ‘plot’
plot.wilma: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
HCLtree: no visible global function definition for ‘hclust’
HCLtree: no visible global function definition for ‘as.dist’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘matplot’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘matlines’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘axis’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘box’
plotProfilesWithinBicluster: no visible global function definition for
  ‘matplot’
plotProfilesWithinBicluster: no visible global function definition for
  ‘title’
plotProfilesWithinBicluster: no visible global function definition for
  ‘axis’
plotProfilesWithinBicluster: no visible global function definition for
  ‘par’
plotProfilesWithinBicluster: no visible global function definition for
  ‘box’
plotProfilesWithinBicluster: no visible global function definition for
  ‘matlines’
plotProfilesWithinBicluster: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  as.dist axis box hclust legend matlines matplot par title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "matlines", "matplot",
             "par", "title")
  importFrom("stats", "as.dist", "hclust")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘ggsci’ ‘matrixcalc’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
'library' or 'require' call to ‘gam’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
TrainSuperMDS: no visible global function definition for ‘rnorm’
TrainSuperMDSOnce: no visible global function definition for ‘cmdscale’
TrainSuperMDSOnce: no visible global function definition for ‘quantile’
distmat: no visible global function definition for ‘dist’
Undefined global functions or variables:
  cmdscale dist quantile rnorm
Consider adding
  importFrom("stats", "cmdscale", "dist", "quantile", "rnorm")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘R.matlab’ ‘fBasics’ ‘spls’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘mvtnorm’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/supervisedPRIM.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘pROC’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘learnr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rootSolve’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Package in Depends field not imported from: ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

plot.survAUC: no visible global function definition for ‘plot’
plot.survAUC: no visible global function definition for ‘lines’
plot.survErr: no visible global function definition for ‘plot’
plot.survErr: no visible global function definition for ‘lines’
schemper: no visible global function definition for ‘predict’
schemper: no visible global function definition for ‘survfit’
schemper: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx lines plot predict survfit
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
Package suggested but not available for checking: ‘BiocParallel’
pearson: no visible global function definition for ‘cor’
plot.survcorr: no visible global function definition for ‘pnorm’
plot.survcorr: no visible global function definition for ‘par’
plot.survcorr: no visible global function definition for ‘plot’
plot.survcorr: no visible global function definition for ‘points’
survcorr: no visible global function definition for ‘model.frame’
survcorr: no visible global function definition for ‘qnorm’
survcorr: no visible global function definition for ‘runif’
survcorr: no visible global function definition for ‘pnorm’
survcorr: no visible global function definition for ‘var’
survcorr: no visible global function definition for ‘qt’
Undefined global functions or variables:
  cor model.frame par plot pnorm points qnorm qt runif var
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "cor", "model.frame", "pnorm", "qnorm", "qt",
             "runif", "var")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
Package suggested but not available for checking: ‘INLA’
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    doc    2.4Mb
    libs   1.6Mb
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.
'library' or 'require' call to ‘survival’ which was already attached by Depends.
  Please remove these calls from your code.
Survgini: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
Package suggested but not available for checking: ‘INLA’
installed size is 103.6Mb
  sub-directories of 1Mb or more:
    libs  102.8Mb
GNU make is a SystemRequirements.
Packages in Depends field not imported from:
  ‘survC1’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Est.HR.FUN: no visible global function definition for ‘coxph’
Est.HR.FUN: no visible global function definition for ‘basehaz’
Est.HR.FUN: no visible global function definition for ‘approx’
Ghat.FUN: no visible global function definition for ‘survfit’
IDI.INF: no visible global function definition for ‘kmcens’
IDI.INF: no visible global function definition for ‘quantile’
IDI.INF.GRAPH: no visible global function definition for ‘plot’
IDI.INF.GRAPH: no visible global function definition for ‘lines’
IDI.INF.GRAPH: no visible global function definition for ‘abline’
IDI.INF.GRAPH: no visible global function definition for ‘points’
IDI.INF.GRAPH: no visible global function definition for ‘title’
PTB.IDI.FUN: no visible global function definition for ‘rexp’
shade: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  abline approx basehaz coxph kmcens lines plot points polygon quantile
  rexp survfit title
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "points", "polygon",
             "title")
  importFrom("stats", "approx", "quantile", "rexp")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘readr’ ‘rlang’ ‘survival’ ‘tidyverse’ ‘utils’
  All declared Imports should be used.
survMC: no visible global function definition for ‘plot’
survintMC: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   1.9Mb
    doc    3.3Mb
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘forcats’ ‘glue’
  All declared Imports should be used.
Note: found 411 marked UTF-8 strings
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
Package unavailable to check Rd xrefs: ‘survJamda’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  14.6Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs   6.6Mb
Malformed Description field: should contain one or more complete sentences.
dlgMessage.tcltkGUI: no visible global function definition for ‘alarm’
Undefined global functions or variables:
  alarm
Consider adding
  importFrom("utils", "alarm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘lattice’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
svd3dplot: no visible global function definition for ‘wireframe’
svd3dplot: no visible global function definition for ‘levelplot’
Undefined global functions or variables:
  levelplot wireframe
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/svgtools.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
startHttpServer : <anonymous> : Rjsonp: no visible global function
  definition for ‘localeToCharset’
Undefined global functions or variables:
  localeToCharset
Consider adding
  importFrom("utils", "localeToCharset")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
.onAttach : svBrowser: no visible global function definition for
  ‘browseURL’
.onAttach: no visible global function definition for ‘loadhistory’
Undefined global functions or variables:
  browseURL loadhistory
Consider adding
  importFrom("utils", "browseURL", "loadhistory")
to your NAMESPACE file.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
svycox.calibrate: no visible global function definition for ‘quantile’
svycox.calibrate: no visible binding for global variable ‘median’
svycox.calibrate: no visible global function definition for
  ‘as.formula’
svycox.calibrate: no visible global function definition for ‘plot’
svycox.calibrate: no visible global function definition for ‘arrows’
svycox.calibrate: no visible global function definition for ‘abline’
svycox.nomogram: no visible global function definition for ‘predict’
svycox.nomogram: no visible global function definition for ‘as.formula’
svycox.validate : internal.validate.func: no visible global function
  definition for ‘as.formula’
svycox.validate : internal.validate.func: no visible global function
  definition for ‘formula’
Undefined global functions or variables:
  abline arrows as.formula formula median plot predict quantile
Consider adding
  importFrom("graphics", "abline", "arrows", "plot")
  importFrom("stats", "as.formula", "formula", "median", "predict",
             "quantile")
to your NAMESPACE file.
additional_comp: no visible global function definition for ‘aggregate’
additional_compPV : <anonymous>: no visible global function definition
  for ‘aggregate’
cor.aux.func : <anonymous>: no visible global function definition for
  ‘cov.wt’
eta.func : <anonymous>: no visible global function definition for ‘lm’
eta.func : <anonymous>: no visible global function definition for
  ‘anova’
glm.dummy.no.std: no visible global function definition for
  ‘as.formula’
pv_by: no visible binding for global variable ‘var’
pv_perc: no visible binding for global variable ‘var’
pv_quantile: no visible binding for global variable ‘var’
svyPVcor: no visible global function definition for ‘update’
svyPVcor: no visible global function definition for ‘var’
svyPVeta: no visible global function definition for ‘update’
svyPVeta: no visible global function definition for ‘var’
svyPVglm: no visible global function definition for ‘gaussian’
svyPVglm: no visible binding for global variable ‘as.formula’
svyPVglm: no visible binding for global variable ‘var’
svyPVglm: no visible global function definition for ‘pt’
svyPVttest: no visible binding for global variable ‘as.formula’
svyPVttest: no visible global function definition for ‘var’
svyPVttest: no visible global function definition for ‘pt’
svyPVttest: no visible binding for global variable ‘var’
t.test.aux: no visible global function definition for ‘as.formula’
t.test.aux: no visible global function definition for ‘complete.cases’
Undefined global functions or variables:
  aggregate anova as.formula complete.cases cov.wt gaussian lm pt
  update var
Consider adding
  importFrom("stats", "aggregate", "anova", "as.formula",
             "complete.cases", "cov.wt", "gaussian", "lm", "pt",
             "update", "var")
to your NAMESPACE file.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/swag.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘tidyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘swephRdata’
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/swfscMisc.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [47s/47s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    6. ├─dplyr::rowwise(.)
    7. ├─dplyr::mutate(., dplyr::across(dplyr::starts_with("Split"), ~sec_format(.x)))
    8. ├─dplyr::mutate(., F_sec = sec_format(Finals_Time))
    9. ├─dplyr::filter(...)
   10. ├─SwimmeR::swim_parse(read_results(file), splits = TRUE)
   11. │ ├─`%>%`(...)
   12. │ ├─base::transform(...)
   13. │ └─base::transform.data.frame(...)
   14. │   ├─base::do.call("data.frame", c(list(`_data`), e[!matched]))
   15. │   └─base::data.frame(...)
   16. └─dplyr::select(., -Row_Numb)
  
  [ FAIL 3 | WARN 0 | SKIP 13 | PASS 13 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘SwimmeR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

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

Beginning with SwimmeR v0.6.0 the Grade and School output columns are renamed Age and Team respectively.  Please adjust your work flows as needed.
Joining, by = "Row_Numb"
Joining, by = "Row_Numb"
Joining, by = "Row_Numb"
Joining, by = "Row_Numb"
Joining, by = "Row_Numb"
Joining, by = "Row_Numb"
Quitting from lines 106-116 (SwimmeR.Rmd) 
Error: processing vignette 'SwimmeR.Rmd' failed with diagnostics:
arguments imply differing number of rows: 247, 240
--- failed re-building ‘SwimmeR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘MASS’ ‘fda’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fj_pl: no visible global function definition for ‘getbasismatrix’
fj_pl: no visible global function definition for ‘create.bspline.basis’
fj_pl: no visible global function definition for ‘getbasispenalty’
forward_backward.quantities : <anonymous>: no visible global function
  definition for ‘dnorm’
function_cases1AND2: no visible global function definition for ‘dnorm’
function_cases3AND4: no visible global function definition for ‘dnorm’
pij_iid: no visible global function definition for ‘dnorm’
pilj: no visible global function definition for ‘dnorm’
updateLambda: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  create.bspline.basis dnorm getbasismatrix getbasispenalty optimize
Consider adding
  importFrom("stats", "dnorm", "optimize")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
Package suggested but not available for checking: ‘cplexAPI’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
Note: found 1 marked UTF-8 string
Package suggested but not available for checking: ‘cplexAPI’
Packages suggested but not available for checking: 'cplexAPI', 'clpAPI'
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/symbolicDA.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
symbol: no visible global function definition for ‘plot.new’
symbol: no visible global function definition for ‘plot.window’
symbol: no visible global function definition for ‘axis’
symbol: no visible global function definition for ‘box’
symbol: no visible global function definition for ‘title’
symbol: no visible global function definition for ‘rainbow’
symbol: no visible global function definition for ‘hsv’
symbol: no visible global function definition for ‘rect’
symbol: no visible global function definition for ‘polygon’
symbol: no visible global function definition for ‘lines’
symbol: no visible global function definition for ‘text’
Undefined global functions or variables:
  axis box hsv lines plot.new plot.window polygon rainbow rect text
  title
Consider adding
  importFrom("grDevices", "hsv", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "polygon", "rect", "text", "title")
to your NAMESPACE file.
installed size is 41.5Mb
  sub-directories of 1Mb or more:
    libs  40.7Mb
GNU make is a SystemRequirements.
Package in Depends field not imported from: ‘fields’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cwt_fw: no visible global function definition for ‘fft’
cwt_iw: no visible global function definition for ‘fft’
est_riskshrink_thresh: no visible global function definition for
  ‘median’
Undefined global functions or variables:
  fft median
Consider adding
  importFrom("stats", "fft", "median")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘tcltk’ ‘tkrplot’
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
No protocol specified
No protocol specified
Namespace in Imports field not imported from: ‘metR’
  All declared Imports should be used.
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
mainNetFunction: no visible global function definition for ‘png’
mainNetFunction: no visible global function definition for ‘plot’
mainNetFunction: no visible global function definition for ‘lines’
mainNetFunction: no visible global function definition for ‘legend’
mainNetFunction: no visible global function definition for ‘dev.off’
plotPR: no visible global function definition for ‘plot’
plotROC: no visible global function definition for ‘plot’
plotROC: no visible global function definition for ‘lines’
simulatedData: no visible global function definition for ‘rpois’
simulatedData : <anonymous>: no visible global function definition for
  ‘rpois’
simulatedData : rlognormpois: no visible global function definition for
  ‘rnorm’
simulatedData : rlognormpois: no visible global function definition for
  ‘rpois’
Undefined global functions or variables:
  dev.off legend lines plot png rnorm rpois
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "rnorm", "rpois")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘LowRankQP’ ‘rgenoud’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
fn.V: no visible global function definition for ‘LowRankQP’
gaps.plot: no visible global function definition for ‘abline’
path.plot: no visible global function definition for ‘lines’
path.plot: no visible global function definition for ‘abline’
path.plot: no visible global function definition for ‘legend’
synth: no visible binding for global variable ‘sd’
synth: no visible binding for global variable ‘var’
synth: no visible global function definition for ‘LowRankQP’
Undefined global functions or variables:
  LowRankQP abline legend lines sd var
Consider adding
  importFrom("graphics", "abline", "legend", "lines")
  importFrom("stats", "sd", "var")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.1Mb
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/T4cluster.Rcheck/00install.out’ for details.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
prepare_Rd: RGL: unable to open X11 display
prepare_Rd: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
.checkDimAndTest: no visible global function definition for
  ‘chisq.test’
.checkDimAndTest: no visible global function definition for
  ‘fisher.test’
plotTable1Heatmap: no visible global function definition for ‘par’
plotTable1Heatmap: no visible global function definition for ‘image’
plotTable1Heatmap: no visible global function definition for ‘abline’
plotTable1Heatmap: no visible global function definition for ‘axis’
plotTable1Heatmap: no visible global function definition for ‘text’
plotTable1Heatmap: no visible global function definition for ‘legend’
plotTable1Heatmap: no visible global function definition for ‘box’
Undefined global functions or variables:
  abline axis box chisq.test fisher.test image legend par text
Consider adding
  importFrom("graphics", "abline", "axis", "box", "image", "legend",
             "par", "text")
  importFrom("stats", "chisq.test", "fisher.test")
to your NAMESPACE file.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Running ‘test-all.R’ [89s/89s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  Component "col2": target is character, current is factor
  ── Failure (test-modules-print.R:548:9): ModuleConvertNonNormal: respects formatOptions ──
  ModuleConvertNonNormal(...) not equal to data.frame(col1 = eg_median, col2 = " [871D50, 1,980D00]").
  Component "col2": Modes: character, numeric
  Component "col2": Attributes: < target is NULL, current is list >
  Component "col2": target is character, current is factor
  ── Failure (test-modules-print.R:553:9): ModuleConvertNonNormal: respects formatOptions ──
  ModuleConvertNonNormal(...) not equal to data.frame(col1 = eg_median, col2 = " [871D500, 1,980D000]").
  Component "col2": Modes: character, numeric
  Component "col2": Attributes: < target is NULL, current is list >
  Component "col2": target is character, current is factor
  
  [ FAIL 17 | WARN 135 | SKIP 0 | PASS 542 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘iterators’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gee’ ‘survival’
  All declared Imports should be used.
Note: found 81 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘stringr’ ‘tibble’
  All declared Imports should be used.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    java  11.5Mb
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘devEMF’ ‘segmented’ ‘smoother’ ‘tools’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   4.3Mb
Namespace in Imports field not imported from: ‘jiebaR’
  All declared Imports should be used.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
'library' or 'require' calls in package code:
  ‘gdata’ ‘ggplot2’ ‘grid’ ‘lattice’ ‘xtable’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘dplyr’ ‘igraph’ ‘tm’ ‘wordcloud2’
  All declared Imports should be used.
Package suggested but not available for checking: ‘tashudata’
Namespaces in Imports field not imported from:
  ‘drat’ ‘plyr’
  All declared Imports should be used.
Package required but not available: ‘contentid’

Package required and available but unsuitable version: ‘arkdb’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘contentid’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘lazyeval’ ‘rlang’ ‘tidyr’
  All declared Imports should be used.
Note: found 137 marked UTF-8 strings
License components which are templates and need '+ file LICENSE':
  MIT
BootTree: no visible global function definition for ‘hclust’
BootTree: no visible global function definition for ‘dist’
BootTree: no visible global function definition for ‘as.dist’
BootTree: no visible global function definition for ‘cor’
BootTree: no visible binding for global variable ‘var’
Pgpd: no visible global function definition for ‘optim’
Pgpd : <anonymous>: no visible global function definition for ‘optim’
Pgpd: no visible global function definition for ‘var’
Pgpd: no visible global function definition for ‘rnorm’
Pgpd: no visible global function definition for ‘quantile’
Pvalue: no visible global function definition for ‘rnorm’
SigTree: no visible global function definition for ‘data’
TreeStat: no visible global function definition for ‘hclust’
TreeStat: no visible global function definition for ‘as.dist’
TreeStat: no visible global function definition for ‘dist’
TreeStat: no visible global function definition for ‘cor’
plot.best: no visible global function definition for ‘hclust’
plot.best: no visible global function definition for ‘as.dist’
plot.best: no visible global function definition for ‘dist’
plot.best: no visible global function definition for ‘cor’
plot.best: no visible global function definition for ‘plot’
treetext: no visible global function definition for ‘par’
treetext: no visible global function definition for ‘text’
Undefined global functions or variables:
  as.dist cor data dist hclust optim par plot quantile rnorm text var
Consider adding
  importFrom("graphics", "par", "plot", "text")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "optim",
             "quantile", "rnorm", "var")
  importFrom("utils", "data")
to your NAMESPACE file.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘quadprog’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
bayes_control: no visible global function definition for ‘plot’
plot.bayessim: no visible global function definition for ‘plot’
plot.tciinf: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    tklibs   4.7Mb
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/TDAkit.Rcheck/00install.out’ for details.
prepare_Rd: RGL: unable to open X11 display
prepare_Rd: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
cluster_cutoff_at_first_empty_bin: no visible global function
  definition for ‘hist’
mapper1D: no visible global function definition for ‘dist’
mapper1D: no visible global function definition for ‘as.dist’
mapper1D: no visible global function definition for ‘hclust’
mapper1D: no visible global function definition for ‘cutree’
mapper2D: no visible global function definition for ‘dist’
mapper2D: no visible global function definition for ‘as.dist’
mapper2D: no visible global function definition for ‘hclust’
mapper2D: no visible global function definition for ‘cutree’
Undefined global functions or variables:
  as.dist cutree dist hclust hist
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "as.dist", "cutree", "dist", "hclust")
to your NAMESPACE file.
installed size is 37.9Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  36.1Mb
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘RSEIS’ ‘pracma’ ‘signal’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/td.Rcheck/00install.out’ for details.
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    apps   2.3Mb
    libs  10.4Mb
Package suggested but not available for checking: ‘R2wd’
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  15.9Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       3.3Mb
    libs      1.5Mb
    telemac   1.0Mb
Running examples in ‘telemac-Ex.R’ failed
The error most likely occurred in:

> ### Name: optionals
> ### Title: Optional input files
> ### Aliases: optionals optionals.character optionals.list optionals.t2d_opt
> ###   print.t2d_opt print.t2d_opt_LINES
> 
> ### ** Examples
> 
> # t2d_opt object
> opt_obj <- optionals(c("# test file", "col1 col2", "1 2", "3 4"), fname = "optional.txt")
Error in validate_opt(new_opt(optlines, fname)) : 
  inherits(x$file, "character") is not TRUE
Calls: optionals -> optionals.character -> validate_opt -> stopifnot
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘t2d_basics.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: sp
Linking to GEOS 3.7.2, GDAL 2.4.2, PROJ 5.2.0
-- Attaching packages --------------------------------------- tidyverse 1.3.0 --
v ggplot2 3.3.3     v purrr   0.3.4
v tibble  3.1.0     v dplyr   1.0.5
v tidyr   1.1.3     v stringr 1.4.0
v readr   1.4.0     v forcats 0.5.1
-- Conflicts ------------------------------------------ tidyverse_conflicts() --
x tidyr::extract() masks raster::extract()
x dplyr::filter()  masks stats::filter()
x dplyr::lag()     masks stats::lag()
x dplyr::select()  masks raster::select()
--- finished re-building 't2d_basics.Rmd'

--- re-building ‘t2d_rainfall_runoff.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
-- Attaching packages --------------------------------------- tidyverse 1.3.0 --
v ggplot2 3.3.3     v purrr   0.3.4
v tibble  3.1.0     v dplyr   1.0.5
v tidyr   1.1.3     v stringr 1.4.0
v readr   1.4.0     v forcats 0.5.1
-- Conflicts ------------------------------------------ tidyverse_conflicts() --
x dplyr::filter() masks stats::filter()
x dplyr::lag()    masks stats::lag()
Linking to GEOS 3.7.2, GDAL 2.4.2, PROJ 5.2.0
Quitting from lines 219-222 (t2d_rainfall_runoff.Rmd) 
Error: processing vignette 't2d_rainfall_runoff.Rmd' failed with diagnostics:
Values of steering parameters must not be longer than 144 characters!
--- failed re-building 't2d_rainfall_runoff.Rmd'

SUMMARY: processing the following file failed:
  ‘t2d_rainfall_runoff.Rmd’

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

> ### Name: telp
> ### Title: The Base Function of This Package The Free Evocation of Words
> ###   Technique
> ### Aliases: telp
> ### Keywords: function
> 
> ### ** Examples
> 
> telp()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: telp ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
TER.deesc.1.B : A1.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.1.B : A1.f: no visible binding for global variable ‘ID’
TER.deesc.1.B : A2.n.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.1.B : A2.n.f: no visible binding for global variable ‘ID’
TER.deesc.1.B: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.1.B: no visible binding for global variable ‘ID’
TER.deesc.A.B : A1.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : A1.f: no visible binding for global variable ‘ID’
TER.deesc.A.B : A3.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : A3.f: no visible binding for global variable ‘ID’
TER.deesc.A.B : A2.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : A2.f: no visible binding for global variable ‘ID’
TER.deesc.A.B : B1.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : B1.f: no visible binding for global variable ‘ID’
TER.deesc.A.B: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B: no visible binding for global variable ‘ID’
Undefined global functions or variables:
  ID
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
installed size is 195.1Mb
  sub-directories of 1Mb or more:
    R       2.6Mb
    libs  191.8Mb
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs       7.4Mb
    tessdata  14.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘testcorr.Rnw’ using Sweave
Error: processing vignette 'testcorr.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'testcorr.tex' failed.
Messages:
/usr/local/bin/texi2dvi: biber failed
--- failed re-building ‘testcorr.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'Rsymphony', 'gurobi'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
No protocol specified
No protocol specified
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    2.9Mb
    libs   3.9Mb
Note: found 10051 marked UTF-8 strings
  Note: found 10523 strings marked as "bytes"
Namespace in Imports field not imported from: ‘lexicon’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘parallel’ ‘tidyr’
  All declared Imports should be used.
Note: found 40 marked UTF-8 strings
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/textile.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.3Mb
Found the following significant warnings:
  Warning: loading Rplot failed
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/TextMiningGUI.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
Running examples in ‘TextMiningGUI-Ex.R’ failed
The error most likely occurred in:

> ### Name: TextMiningGUI
> ### Title: TextMiningGUI
> ### Aliases: TextMiningGUI
> 
> ### ** Examples
> 
> library(TextMiningGUI)
> if(TextMiningGUI()){}
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: TextMiningGUI ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
phyper_right: no visible global function definition for ‘dhyper’
progression: no visible global function definition for ‘density’
progression: no visible global function definition for ‘plot’
progression: no visible global function definition for ‘points’
progression: no visible global function definition for ‘legend’
progression: no visible global function definition for ‘text’
specificities.distribution.plot: no visible global function definition
  for ‘dhyper’
specificities.distribution.plot: no visible global function definition
  for ‘plot’
specificities.distribution.plot: no visible global function definition
  for ‘Axis’
specificities.distribution.plot: no visible global function definition
  for ‘arrows’
specificities.distribution.plot: no visible global function definition
  for ‘text’
specificities.distribution.plot: no visible global function definition
  for ‘title’
specificities.probabilities.vector: no visible global function
  definition for ‘phyper’
Undefined global functions or variables:
  Axis arrows density dhyper legend phyper plot points text title
Consider adding
  importFrom("graphics", "Axis", "arrows", "legend", "plot", "points",
             "text", "title")
  importFrom("stats", "density", "dhyper", "phyper")
to your NAMESPACE file.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/text.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
ParseTrueFX: no visible global function definition for ‘read.csv’
TrueFXRef: no visible global function definition for ‘download.file’
TrueFXRef: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL download.file read.csv
Consider adding
  importFrom("utils", "browseURL", "download.file", "read.csv")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘ggm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    7.1Mb
Namespace in Imports field not imported from: ‘proxy’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Thinknum: no visible global function definition for ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘crayon’ ‘purrr’ ‘readr’
  All declared Imports should be used.
coef_traceplot: no visible global function definition for ‘rainbow’
coef_traceplot: no visible global function definition for ‘plot’
coef_traceplot: no visible global function definition for ‘abline’
coef_traceplot : <anonymous>: no visible global function definition for
  ‘lines’
coef_traceplot: no visible global function definition for ‘text’
ee.GEE.aux : <anonymous>: no visible global function definition for
  ‘combn’
Undefined global functions or variables:
  abline combn lines plot rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "plot", "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
summary.tsls: no visible global function definition for ‘printCoefmat’
threesls: no visible global function definition for ‘cor’
threesls: no visible global function definition for ‘pt’
tsls.formula: no visible global function definition for ‘model.matrix’
tsls.formula: no visible global function definition for
  ‘model.response’
Undefined global functions or variables:
  cor model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.matrix", "model.response",
             "printCoefmat", "pt")
to your NAMESPACE file.
installed size is 47.4Mb
  sub-directories of 1Mb or more:
    libs  47.1Mb
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
GNU make is a SystemRequirements.
.LoadTickDataHK: no visible global function definition for ‘read.csv’
.LoadTickDataSHSZ: no visible global function definition for ‘read.csv’
DrawDown: no visible global function definition for ‘na.omit’
PerformanceReport: no visible global function definition for
  ‘aggregate’
PerformanceReport: no visible global function definition for ‘sd’
Undefined global functions or variables:
  aggregate na.omit read.csv sd
Consider adding
  importFrom("stats", "aggregate", "na.omit", "sd")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
newTiddler: no visible global function definition for ‘new’
twImage: no visible global function definition for ‘new’
twLink: no visible global function definition for ‘new’
twList: no visible global function definition for ‘new’
twTable: no visible global function definition for ‘new’
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 113-154 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘tidygeocoder.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 147-152 (tidygeocoder.Rmd) 
Error: processing vignette 'tidygeocoder.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘tidygeocoder.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required and available but unsuitable version: ‘ComplexHeatmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘mix’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Evomorph’ ‘cowplot’ ‘factoextra’ ‘gridExtra’ ‘lme4’ ‘lsr’ ‘plotly’
  ‘png’ ‘shapes’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘modeldata’
  All declared Imports should be used.
Package required and available but unsuitable version: ‘rstanarm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Namespace in Imports field not imported from: ‘janitor’
  All declared Imports should be used.
Note: found 24 marked UTF-8 strings
Package suggested but not available for checking: ‘SingleR’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/tidyseurat.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/tidysq.Rcheck/00install.out’ for details.
Note: found 113 marked UTF-8 strings
Running ‘testthat.R’ [13s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Error: 'formula' missing or incorrect
  Backtrace:
      █
   1. ├─stats::t.test(extra ~ 1, data = sleep) test_htest.R:14:2
   2. └─stats:::t.test.formula(extra ~ 1, data = sleep)
  ── Failure (test_htest.R:168:3): wilcoxon signed rank exact tests works ────────
  `tidy_model` not equal to `tidy_model_test`.
  Component "method": 1 string mismatch
  ── Failure (test_htest.R:212:3): wilcoxon rank sum tests works ─────────────────
  `tidy_model` not equal to `tidy_model_test`.
  Component "method": 1 string mismatch
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 68 ]
  Error: Test failures
  Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   4.4Mb
Namespace in Imports field not imported from: ‘tools’
  All declared Imports should be used.
Note: found 62 marked UTF-8 strings
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘brio’ ‘curl’ ‘diffobj’ ‘gitcreds’ ‘keyring’ ‘nlme’ ‘rgdal’ ‘stringi’
  ‘usethis’ ‘waldo’
  All declared Imports should be used.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Malformed Description field: should contain one or more complete sentences.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/tiledb.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Note: found 341 marked UTF-8 strings
Namespace in Imports field not imported from: ‘lwgeom’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
'library' or 'require' call to ‘shiny’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘ggplot2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
timeline: no visible global function definition for ‘ggplot’
timeline: no visible global function definition for ‘geom_segment’
timeline: no visible global function definition for ‘aes_string’
timeline: no visible global function definition for ‘geom_rect’
timeline: no visible global function definition for ‘geom_text’
timeline: no visible global function definition for ‘theme’
timeline: no visible global function definition for ‘element_blank’
timeline: no visible global function definition for ‘xlab’
timeline: no visible global function definition for ‘ylab’
timeline: no visible global function definition for ‘xlim’
timeline: no visible global function definition for
  ‘scale_y_continuous’
timeline: no visible global function definition for ‘geom_point’
timeline: no visible global function definition for ‘scale_color_grey’
timeline: no visible global function definition for ‘geom_hline’
Undefined global functions or variables:
  aes_string element_blank geom_hline geom_point geom_rect geom_segment
  geom_text ggplot scale_color_grey scale_y_continuous theme xlab xlim
  ylab
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
'library' or 'require' calls in package code:
  ‘ggplot2’ ‘plyr’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Matrix’ ‘lubridate’ ‘timeDate’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
is.Bizday: no visible global function definition for ‘isWeekday’
plotCalendarHeatmap: no visible global function definition for ‘ddply’
plotCalendarHeatmap: no visible global function definition for ‘.’
plotCalendarHeatmap: no visible binding for global variable ‘year’
plotCalendarHeatmap: no visible binding for global variable ‘month’
plotCalendarHeatmap: no visible binding for global variable ‘week’
plotCalendarHeatmap: no visible global function definition for ‘ggplot’
plotCalendarHeatmap: no visible global function definition for ‘aes’
plotCalendarHeatmap: no visible binding for global variable ‘monthweek’
plotCalendarHeatmap: no visible binding for global variable ‘weekday’
plotCalendarHeatmap: no visible global function definition for
  ‘geom_tile’
plotCalendarHeatmap: no visible global function definition for
  ‘facet_grid’
plotCalendarHeatmap: no visible global function definition for
  ‘scale_fill_gradientn’
projectDate: no visible global function definition for ‘holidayNYSE’
projectDate: no visible global function definition for
  ‘sparse.model.matrix’
Undefined global functions or variables:
  . aes ddply facet_grid geom_tile ggplot holidayNYSE isWeekday month
  monthweek scale_fill_gradientn sparse.model.matrix week weekday year
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘boot’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘boot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
boot_autocov: no visible global function definition for ‘is.ts’
boot_autocov: no visible global function definition for ‘tsboot’
boot_autocov: no visible global function definition for ‘quantile’
boot_autocov: no visible global function definition for ‘par’
boot_autocov: no visible global function definition for ‘frequency’
boot_autocov: no visible global function definition for ‘polygon’
boot_autocov: no visible global function definition for ‘lines’
boot_autocov: no visible global function definition for ‘abline’
boot_autocov: no visible global function definition for ‘acf’
boot_spec: no visible global function definition for ‘is.ts’
boot_spec: no visible global function definition for ‘tsboot’
boot_spec: no visible global function definition for ‘spec.pgram’
boot_spec: no visible global function definition for ‘quantile’
boot_spec: no visible global function definition for ‘polygon’
boot_spec: no visible global function definition for ‘lines’
redraw: no visible global function definition for ‘spec.pgram’
statistic: no visible global function definition for ‘acf’
Undefined global functions or variables:
  abline acf frequency is.ts lines par polygon quantile spec.pgram
  tsboot
Consider adding
  importFrom("graphics", "abline", "lines", "par", "polygon")
  importFrom("stats", "acf", "frequency", "is.ts", "quantile",
             "spec.pgram")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘generics’
  All declared Imports should be used.
Note: found 2750 marked UTF-8 strings
author.search: no visible binding for global variable ‘na.omit’
reference.list: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
drawGraph: no visible global function definition for ‘pdf’
drawGraph: no visible global function definition for ‘par’
drawGraph: no visible global function definition for ‘plot’
drawGraph: no visible global function definition for ‘segments’
drawGraph: no visible global function definition for ‘lines’
drawGraph: no visible global function definition for ‘text’
drawGraph: no visible global function definition for ‘dev.off’
drugRank: no visible global function definition for ‘aggregate’
floating2: no visible global function definition for ‘cor’
timma: no visible global function definition for ‘median’
timma: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  aggregate cor dev.off lines median par pdf plot segments text
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot", "segments", "text")
  importFrom("stats", "aggregate", "cor", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
No protocol specified
No protocol specified
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Namespaces in Imports field not imported from:
  ‘cpp11’ ‘dplyr’ ‘magrittr’ ‘stringi’
  All declared Imports should be used.
Note: found 384749 marked UTF-8 strings
tipom.car: no visible global function definition for ‘abline’
tipom.car: no visible global function definition for ‘axis’
tipom.heat: no visible global function definition for ‘image’
tipom.heat: no visible global function definition for ‘gray’
tipom.lw: no visible global function definition for ‘plot’
tipom.lw: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline axis gray image plot
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "image", "plot")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘snow’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘base64enc’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: loading Rplot failed
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/tkrplot.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
Warning: loading Rplot failed

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.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
Running examples in ‘tkRplotR-Ex.R’ failed
The error most likely occurred in:

> ### Name: addTkBind
> ### Title: Add Tk Binds
> ### Aliases: addTkBind
> 
> ### ** Examples
> 
> ## Don't show: 
> if (.isTclImgOk()){
+ tt <- tktoplevel()
+ tt <- tkRplot(tt, function () plot(1:10))
+ FUN <- local({
+   canPos <-.Tcl(paste(tt$env$canvas, "create text 0 0 "))
+     function (x, y) {
+         x <- as.numeric(x)
+         y <- as.numeric(y)
+        tkdelete(tt$env$canvas, tclvalue(canPos))
+            xy <- formatC(tk2usr(x, y),
+                    digits = 2,
+                      format = "f",
+                        width = 5)
+     canPos <<- .Tcl(
+      paste(tt$env$canvas, "create text 40 10 -fill blue -justify left -text { ",
+             xy[1], " ", xy[2],
+             "} -font {Helvetica -10}"))
+   }})
+ 
+ tkbind(tt$env$canvas, "<Motion>", FUN)
+ tkbind(tt$env$canvas, "<Motion>") #to give current bidings
+ FUN1 <- function (x,y) print(tk2usr(x,y))
+ addTkBind(tt$env$canvas, "<Motion>", FUN1)
+ tkbind(tt$env$canvas, "<Motion>") #to give current bidings
+ Sys.sleep(1)
+ tkdestroy(tt)
+ }
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
FLXmclust.Density: no visible global function definition for ‘dmvnorm’
FLXmclust.Estimate: no visible global function definition for ‘flexmix’
FLXmclust.Estimate: no visible global function definition for
  ‘FLXmclust’
coefmclust: no visible global function definition for ‘parameters’
flexmix.Density: no visible global function definition for
  ‘model.matrix’
flexmix.Density: no visible global function definition for
  ‘model.response’
flexmix.Density: no visible global function definition for
  ‘model.frame’
flexmix.Density: no visible global function definition for ‘dnorm’
flexmix.Density: no visible global function definition for ‘dpois’
flexmix.Density: no visible global function definition for ‘dbinom’
flexmix.Estimate: no visible global function definition for ‘flexmix’
flexmix.Estimate: no visible global function definition for ‘FLXglm’
tleplot,TLE-data.frame: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  FLXglm FLXmclust dbinom dmvnorm dnorm dpois flexmix legend
  model.frame model.matrix model.response parameters
Consider adding
  importFrom("graphics", "legend")
  importFrom("stats", "dbinom", "dnorm", "dpois", "model.frame",
             "model.matrix", "model.response")
to your NAMESPACE file.
'library' or 'require' call to ‘mvtnorm’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
EMN: no visible global function definition for ‘dmvnorm’
EMN: no visible global function definition for ‘pmvnorm’
EMT: no visible global function definition for ‘GenzBretz’
EMT: no visible global function definition for ‘dmvt’
EMT: no visible global function definition for ‘pmvt’
MomemNT: no visible global function definition for ‘pnorm’
MomemNT: no visible global function definition for ‘dnorm’
MomemNT: no visible global function definition for ‘pmvnorm’
MomemNT: no visible global function definition for ‘dmvnorm’
TT.moment: no visible global function definition for ‘GenzBretz’
TT.moment: no visible global function definition for ‘pmvt’
TT.moment: no visible global function definition for ‘dt’
TT.moment: no visible global function definition for ‘pt’
TT.moment: no visible global function definition for ‘dmvt’
cdfNI: no visible global function definition for ‘pnorm’
cdfNI: no visible global function definition for ‘pt’
inits: no visible global function definition for ‘lm’
Undefined global functions or variables:
  GenzBretz dmvnorm dmvt dnorm dt lm pmvnorm pmvt pnorm pt
Consider adding
  importFrom("stats", "dnorm", "dt", "lm", "pnorm", "pt")
to your NAMESPACE file.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    examples  12.1Mb
    include    2.9Mb
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    libs  27.8Mb
Note: found 134043 marked UTF-8 strings
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
extractContentDOM: no visible global function definition for
  ‘capture.output’
extractHTMLStrip: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  capture.output
Consider adding
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'Rcampdf', 'Rpoppler', 'tm.lexicon.GeneralInquirer'
Package unavailable to check Rd xrefs: ‘Rpoppler’
Namespace in Imports field not imported from: ‘rjson’
  All declared Imports should be used.
Note: found 4 marked UTF-8 strings
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Note: found 1 marked UTF-8 string
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/tolerance.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘geojsonsf’ ‘lwgeom’
  All declared Imports should be used.
Note: found 160 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘ggplot2’ ‘jsonlite’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘toOrdinal.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-26 (toOrdinal.Rmd) 
Error: processing vignette 'toOrdinal.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘toOrdinal.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘corpus.JSS.papers’
Package suggested but not available for checking: ‘gWidgets2RGtk2’
No protocol specified
Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/topologyGSA.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘rappdirs’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘fs’ ‘stringr’ ‘torch’ ‘torchvision’ ‘zip’
  All declared Imports should be used.
installed size is 108.2Mb
  sub-directories of 1Mb or more:
    R       4.2Mb
    help    3.0Mb
    libs  100.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
Note: found 1946 marked UTF-8 strings
Malformed Description field: should contain one or more complete sentences.
Tosls.formula: no visible global function definition for ‘model.matrix’
Tosls.formula: no visible global function definition for
  ‘model.response’
summary: no visible global function definition for ‘coef’
summary: no visible global function definition for ‘pt’
Undefined global functions or variables:
  coef model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.matrix", "model.response", "pt")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘R6’ ‘jmvcore’
  All declared Imports should be used.
Note: found 100 marked Latin-1 strings
  Note: found 548 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
ConfA: no visible global function definition for ‘qf’
EstM2Sn: no visible global function definition for ‘nlm’
EstM2Sn: no visible global function definition for ‘qnorm’
TV.model: no visible global function definition for ‘dev.new’
TV.model: no visible global function definition for ‘points’
betaBino: no visible global function definition for ‘pbinom’
doseD: no visible global function definition for ‘lm’
doseD: no visible global function definition for ‘dev.new’
doseD: no visible global function definition for ‘par’
doseD: no visible global function definition for ‘plot’
doseD: no visible global function definition for ‘axTicks’
doseD: no visible global function definition for ‘axis’
doseD: no visible global function definition for ‘lines’
doseD: no visible global function definition for ‘abline’
doseD: no visible global function definition for ‘legend’
setD: no visible global function definition for ‘dev.new’
setD: no visible global function definition for ‘par’
setD: no visible global function definition for ‘pbinom’
setD: no visible global function definition for ‘abline’
setD: no visible global function definition for ‘axis’
setD: no visible global function definition for ‘rect’
setD: no visible global function definition for ‘lines’
setD: no visible global function definition for ‘text’
setD: no visible global function definition for ‘axTicks’
setD: no visible global function definition for ‘legend’
spoD : spoD_A: no visible global function definition for ‘chisq.test’
Undefined global functions or variables:
  abline axTicks axis chisq.test dev.new legend lines lm nlm par pbinom
  plot points qf qnorm rect text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axTicks", "axis", "legend", "lines",
             "par", "plot", "points", "rect", "text")
  importFrom("stats", "chisq.test", "lm", "nlm", "pbinom", "qf", "qnorm")
to your NAMESPACE file.
License components which are templates and need '+ file LICENSE':
  MIT
align1d : obj: no visible global function definition for ‘dist’
align2d : obj: no visible global function definition for ‘dist’
align2d : pen: no visible global function definition for ‘dist’
align2d: no visible global function definition for ‘dist’
sumt: no visible global function definition for ‘optim’
tpe1d: no visible global function definition for ‘hclust’
tpe2d: no visible global function definition for ‘hclust’
tpe2d: no visible global function definition for ‘cmdscale’
Undefined global functions or variables:
  cmdscale dist hclust optim
Consider adding
  importFrom("stats", "cmdscale", "dist", "hclust", "optim")
to your NAMESPACE file.
File ‘tpr/libs/tpr.so’:
  Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 153 marked Latin-1 strings
  Note: found 108 marked UTF-8 strings
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/trackeRapp.Rcheck/00install.out’ for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.7Mb
Error(s) in re-building vignettes:
--- re-building ‘TourDetrackeR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric


Attaching package: 'trackeR'

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

    append

Source : http://tile.stamen.com/toner/13/4056/2748.png
Source : http://tile.stamen.com/toner/13/4057/2748.png
Source : http://tile.stamen.com/toner/13/4056/2749.png
Source : http://tile.stamen.com/toner/13/4057/2749.png
Quitting from lines 106-108 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘TourDetrackeR.Rmd’

--- re-building ‘trackeR.Rnw’ using Sweave
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric


Attaching package: 'trackeR'

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

    append

Warning in sanity_checks(dat = dat, silent = silent) :
  Observations with duplicated time stamps have been removed.
Warning in sanity_checks(dat = dat, silent = silent) :
  Observations with duplicated time stamps have been removed.
Loading required package: splines
Loading required package: Matrix

Attaching package: 'fda'

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

    matplot

--- finished re-building 'trackeR.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [21s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(tractor.base)
  > 
  > test_check("tractor.base")
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure (test-30-misc.R:28:5): file functions work ──────────────────────────
  imageFileExists(temp) is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 119 ]
  Error: Test failures
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘basic-usage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'DT'

The following object is masked _by_ '.GlobalEnv':

    datatable

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 49-50 (basic-usage.Rmd) 
Error: processing vignette 'basic-usage.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘basic-usage.Rmd’

SUMMARY: processing the following file failed:
  ‘basic-usage.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘neuralnet’
  All declared Imports should be used.
Package suggested but not available for checking: ‘taxidata’
No protocol specified
No protocol specified
installed size is 48.6Mb
  sub-directories of 1Mb or more:
    libs  46.6Mb
Malformed Description field: should contain one or more complete sentences.
microsoftTranslate: no visible global function definition for
  ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
rtrapezoid: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/trawl.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘tree’
  All declared Imports should be used.
Package suggested but not available for checking: ‘TreeDistData’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Build_JTree: no visible global function definition for ‘flush.console’
Run_JTree: no visible global function definition for ‘cov2cor’
Undefined global functions or variables:
  cov2cor flush.console
Consider adding
  importFrom("stats", "cov2cor")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
LikAge: no visible global function definition for ‘read.table’
bd.ME.optim: no visible global function definition for ‘optim’
bd.ME.optim.rho: no visible global function definition for ‘optim’
bd.ME.optim.rho.all: no visible global function definition for ‘optim’
bd.MEyule.optim: no visible global function definition for ‘optimize’
bd.MEyule.optim: no visible global function definition for ‘optim’
bd.age.optim.matlab: no visible global function definition for
  ‘read.table’
bd.groups.conf: no visible global function definition for ‘uniroot’
bd.shifts.plot: no visible global function definition for ‘plot’
bd.shifts.plot: no visible global function definition for ‘lines’
bdsky.stt.optim: no visible global function definition for ‘optim’
create.mat: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  lines optim optimize plot read.table uniroot write.table
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "optim", "optimize", "uniroot")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
plot.treeperm: no visible global function definition for ‘hist’
plot.treeperm: no visible global function definition for ‘points’
plot.treeperm: no visible global function definition for ‘text’
treeperm.formula: no visible global function definition for
  ‘model.frame’
treeperm.formula: no visible global function definition for
  ‘model.response’
Undefined global functions or variables:
  hist model.frame model.response points text
Consider adding
  importFrom("graphics", "hist", "points", "text")
  importFrom("stats", "model.frame", "model.response")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/treespace.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/treetop.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘boot’ ‘chron’ ‘randtoolbox’
  All declared Imports should be used.
installed size is 101.1Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs  96.3Mb
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘dqrng’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘choropleth_maps_with_tricolore.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 128-137 (choropleth_maps_with_tricolore.Rmd) 
Error: processing vignette 'choropleth_maps_with_tricolore.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘choropleth_maps_with_tricolore.Rmd’

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

Error: Vignette re-building failed.
Execution halted
cinbag: no visible global function definition for ‘var’
trimTrees: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict var
Consider adding
  importFrom("stats", "predict", "var")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/trinROC.Rcheck/00install.out’ for details.
'library' or 'require' calls to packages already attached by Depends:
  ‘gtools’ ‘mgcv’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘gtools’ ‘mgcv’ ‘msm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HtoGp: no visible global function definition for ‘odd’
HtoGp: no visible global function definition for ‘even’
plot.pirls.gam: no visible global function definition for ‘par’
plot.pirls.gam: no visible global function definition for ‘plot’
plot.pirls.gam: no visible global function definition for ‘title’
plot.pirls.gam: no visible global function definition for ‘lines’
plot.pirls.gam: no visible global function definition for ‘rug’
plot.pirls.gam: no visible global function definition for ‘mtext’
test.trioGxE: no visible global function definition for ‘write.table’
trioGxE: no visible global function definition for ‘quantile’
trioGxE: no visible global function definition for ‘qtnorm’
trioplot: no visible global function definition for ‘quantile’
trioplot: no visible global function definition for ‘formula’
trioplot: no visible global function definition for ‘gam’
trioplot: no visible global function definition for ‘binomial’
Undefined global functions or variables:
  binomial even formula gam lines mtext odd par plot qtnorm quantile
  rug title write.table
Consider adding
  importFrom("graphics", "lines", "mtext", "par", "plot", "rug", "title")
  importFrom("stats", "binomial", "formula", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘countrycode’ ‘haven’ ‘readstata13’ ‘stringr’ ‘tibble’ ‘tidyr’
  All declared Imports should be used.
Note: found 118 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Hmisc’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
DrawMargin: no visible global function definition for ‘qnorm’
DrawProbability: no visible global function definition for ‘pnorm’
Factor: no visible global function definition for ‘new’
Gaussian: no visible global function definition for ‘new’
LikelihoodFactor: no visible global function definition for ‘new’
Parameters: no visible global function definition for ‘new’
Player: no visible global function definition for ‘new’
PriorFactor: no visible global function definition for ‘new’
SumFactor: no visible global function definition for ‘new’
TruncateFactor: no visible global function definition for ‘new’
Variable: no visible global function definition for ‘new’
Vdraw: no visible global function definition for ‘dnorm’
Vdraw: no visible global function definition for ‘pnorm’
Vwin: no visible global function definition for ‘dnorm’
Vwin: no visible global function definition for ‘pnorm’
Wdraw: no visible global function definition for ‘dnorm’
Wdraw: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dnorm new pnorm qnorm
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dnorm", "pnorm", "qnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘MASS’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cdens: no visible global function definition for ‘head’
dplot: no visible global function definition for ‘knots’
dplot: no visible global function definition for ‘median’
dplot: no visible global function definition for ‘par’
dplot: no visible global function definition for ‘plot.stepfun’
dplot: no visible global function definition for ‘abline’
edf: no visible global function definition for ‘approxfun’
mctest : rdist: no visible global function definition for ‘runif’
mctest : S: no visible global function definition for ‘optim’
qplot: no visible global function definition for ‘plot’
qplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline approxfun head knots median optim par plot plot.stepfun runif
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "approxfun", "knots", "median", "optim",
             "plot.stepfun", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘ez’ ‘forcats’ ‘ggplot2’
  All declared Imports should be used.
Note: found 118 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tseries’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/TSclust.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘TSodbc’
tfDetails: no visible global function definition for ‘start’
tfDetails: no visible global function definition for ‘end’
Undefined global functions or variables:
  end start
Consider adding
  importFrom("stats", "end", "start")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘tsglm.Rnw’ using Sweave
Error: processing vignette 'tsglm.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'tsglm.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'tsglm.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Qhat: no visible global function definition for ‘pnorm’
plrt: no visible global function definition for ‘uniroot’
plrt: no visible global function definition for ‘optimize’
simulatedata: no visible global function definition for ‘rnorm’
tsc.test: no visible global function definition for ‘shapiro.test’
tsc.test: no visible global function definition for ‘p.adjust’
tsc.test: no visible global function definition for ‘glm’
tsc.test : f: no visible global function definition for ‘pnorm’
tsc.test: no visible global function definition for ‘uniroot’
tsc.test: no visible global function definition for ‘optimize’
variance: no visible global function definition for ‘density’
variance: no visible global function definition for ‘ecdf’
Undefined global functions or variables:
  density ecdf glm optimize p.adjust pnorm rnorm shapiro.test uniroot
Consider adding
  importFrom("stats", "density", "ecdf", "glm", "optimize", "p.adjust",
             "pnorm", "rnorm", "shapiro.test", "uniroot")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/TSCS.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘TSodbc’
Package unavailable to check Rd xrefs: ‘TSodbc’
Errors in running code in vignettes:
when running code in ‘Guide.Stex’
  ...
> z <- TSget("ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT", 
+     eurostat)
Apr 16, 2019 10:07:08 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/dataflow/ESTAT/ei_nama_q/latest/
Apr 16, 2019 10:07:08 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
SEVERE: Internal Server Error

  When sourcing ‘Guide.R’:
Error: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.exceptions.SdmxResponseException: (500): Error on the provider side.
Execution halted
when running code in ‘GuideAppendix.Stex’
  ...

> options(continue = "  ")

> user <- Sys.getenv("MYSQL_USER")

> setup <- RMySQL::dbConnect(RMySQL::MySQL(), dbname = "test")

  When sourcing ‘GuideAppendix.R’:
Error: Failed to connect to database: Error: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)
Execution halted
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   8.5Mb
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/TSdist.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
No protocol specified
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘zoo’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
vintageMap: no visible global function definition for ‘read.table’
TSget,character-TSfameLocalConnection: no visible global function
  definition for ‘as.ts’
TSget,character-TSfameLocalConnection: no visible global function
  definition for ‘zoo’
TSget,character-TSfameLocalConnection: no visible global function
  definition for ‘frequency’
TSget,character-TSfameServerConnection: no visible global function
  definition for ‘as.ts’
TSget,character-TSfameServerConnection: no visible global function
  definition for ‘zoo’
TSget,character-TSfameServerConnection: no visible global function
  definition for ‘frequency’
Undefined global functions or variables:
  as.ts frequency read.table zoo
Consider adding
  importFrom("stats", "as.ts", "frequency")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘tsibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘crosstalk’
  All declared Imports should be used.
Func.SAX: no visible global function definition for ‘sd’
Func.SAX: no visible global function definition for ‘qnorm’
Func.matrix: no visible global function definition for ‘qnorm’
Func.motif: no visible global function definition for ‘sd’
Func.motif: no visible global function definition for ‘na.omit’
Func.motif: no visible global function definition for ‘combn’
Func.motif.multivariate: no visible global function definition for
  ‘txtProgressBar’
Func.motif.multivariate: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  combn na.omit qnorm sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit", "qnorm", "sd")
  importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
dLag : dlag.f: no visible global function definition for
  ‘complete.cases’
distmat: no visible global function definition for ‘dist’
fitCity: no visible global function definition for ‘glm.control’
fitCity: no visible global function definition for ‘terms’
ldmvnorm: no visible global function definition for ‘mahalanobis’
lspline: no visible global function definition for ‘quantile’
plot.tsdecomp: no visible global function definition for ‘par’
plot.tsdecomp: no visible global function definition for ‘plot’
setupFormula: no visible global function definition for ‘as.formula’
spatialgibbs: no visible global function definition for ‘rnorm’
spatialgibbs: no visible global function definition for ‘rgamma’
spatialgibbs: no visible global function definition for ‘runif’
tsdecomp: no visible global function definition for ‘fft’
Undefined global functions or variables:
  as.formula complete.cases dist fft glm.control mahalanobis par plot
  quantile rgamma rnorm runif terms
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.formula", "complete.cases", "dist", "fft",
             "glm.control", "mahalanobis", "quantile", "rgamma", "rnorm",
             "runif", "terms")
to your NAMESPACE file.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
    libs   2.6Mb
GNU make is a SystemRequirements.
Malformed Title field: should not end in a period.
covTranspose11: warning in glasso(sc, 2 * rhoc/n, wi.init = gc$wi,
  w.init = gc$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
covTranspose11: warning in glasso(sr, 2 * rhor/p, wi.init = gr$wi,
  w.init = gr$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
.help.ESS: no visible global function definition for ‘index.search’
TransSphere : ttin: no visible global function definition for ‘t.test’
TransSphere: no visible global function definition for ‘sd’
TransSphere: no visible global function definition for ‘quantile’
TransSphere: no visible global function definition for ‘pt’
Undefined global functions or variables:
  index.search pt quantile sd t.test
Consider adding
  importFrom("stats", "pt", "quantile", "sd", "t.test")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘EMD’ ‘vars’
  All declared Imports should be used.
plotarimapred: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘forecastHybrid’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Plotting_Time_Series.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshot100af396368a2.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot100af396368a2.png': No such file or directory
Quitting from lines 39-44 (Plotting_Time_Series.Rmd) 
Error: processing vignette 'Plotting_Time_Series.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Plotting_Time_Series.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘shinyAce’ ‘shinyjs’
  All declared Imports should be used.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
TT.GS : TT.GS.sp: no visible global function definition for ‘qt’
TT.GS : TT.GS.sp: no visible global function definition for ‘runif’
TT.GS : TT.GS.sp: no visible global function definition for ‘pt’
TT.moment: no visible global function definition for ‘dt’
TT.moment: no visible global function definition for ‘pt’
Undefined global functions or variables:
  dt pt qt runif
Consider adding
  importFrom("stats", "dt", "pt", "qt", "runif")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘latticeExtra’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: package ‘BiocParallel’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ttScreening.Rcheck/00install.out’ for details.
.saveDevice: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off
Consider adding
  importFrom("grDevices", "dev.off")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
ttwa: no visible global function definition for ‘aggregate’
ttwa: no visible global function definition for ‘txtProgressBar’
ttwa: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  aggregate setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "aggregate")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/TukeyRegion.Rcheck/00install.out’ for details.
turf: no visible global function definition for ‘read.table’
turf: no visible global function definition for ‘flush.console’
turf.combos: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn flush.console read.table
Consider adding
  importFrom("utils", "combn", "flush.console", "read.table")
to your NAMESPACE file.
Package required and available but unsuitable version: ‘stats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
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.
Note: found 34 marked Latin-1 strings
Note: found 9 marked UTF-8 strings
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/TwoArmSurvSim.Rcheck/00install.out’ for details.
TwoCop: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘sl3’
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
check_arg: no visible global function definition for ‘deparse1’
check_output: no visible global function definition for ‘deparse1’
declare: no visible global function definition for ‘deparse1’
get_assertion: no visible global function definition for
  ‘activeBindingFunction’
print.typed: no visible global function definition for ‘deparse1’
process_assertion_factory_dots: no visible global function definition
  for ‘deparse1’
Undefined global functions or variables:
  activeBindingFunction deparse1
Running examples in ‘typed-Ex.R’ failed
The error most likely occurred in:

> ### Name: ?
> ### Title: Set Variable Types, Argument Types and Return Types.
> ### Aliases: ? declare
> 
> ### ** Examples
> 
> Integer() ? function (x= ? Integer()) {
+   Integer() ? y <- 2L
+   res <- x + y
+   res
+ }
# typed function
function (x) 
{
    check_arg(x, Integer())
    declare("y", Integer(), value = 2L)
    res <- x + y
    check_output(res, Integer())
}
Error in deparse1(attr(x, "return_type")) : 
  could not find function "deparse1"
Calls: <Anonymous> -> print.typed -> writeLines -> paste0
Execution halted
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   4. ├─base::print(fun2)
   5. └─typed:::print.typed(fun2)
   6.   ├─base::writeLines(...)
   7.   └─base::paste0("# Return type: ", deparse1(attr(x, "return_type")))
  ── Error (test-qm.R:8:3): question mark works ──────────────────────────────────
  Error: invalid (NULL) left side of assignment
  Backtrace:
      █
   1. └─testthat::expect_equal((`?`(Double(), x) = 1), 1) test-qm.R:8:2
   2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
   3.     └─rlang::eval_bare(expr, quo_get_env(quo))
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 172 ]
  Error: Test failures
  Execution halted
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Crm: no visible global function definition for ‘integrate’
Crm : <anonymous>: no visible global function definition for
  ‘integrate’
Crm: no visible global function definition for ‘optimize’
ail1: no visible global function definition for ‘uniroot’
ail2 : fu : <anonymous>: no visible global function definition for
  ‘integrate’
ail2: no visible global function definition for ‘uniroot’
aip : fu : <anonymous>: no visible global function definition for
  ‘integrate’
aip: no visible global function definition for ‘uniroot’
ait1: no visible global function definition for ‘uniroot’
ait2 : fu : <anonymous>: no visible global function definition for
  ‘integrate’
ait2: no visible global function definition for ‘uniroot’
sim3p3: no visible global function definition for ‘rbinom’
simCrm: no visible global function definition for ‘rbinom’
simCrm: no visible global function definition for ‘palette’
simCrm: no visible global function definition for ‘gray’
simCrm: no visible global function definition for ‘plot’
simCrm: no visible global function definition for ‘abline’
simCrm: no visible global function definition for ‘lines’
ssim3p3: no visible global function definition for ‘txtProgressBar’
ssim3p3: no visible global function definition for ‘setTxtProgressBar’
ssimCrm: no visible global function definition for ‘txtProgressBar’
ssimCrm: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  abline gray integrate lines optimize palette plot rbinom
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("grDevices", "gray", "palette")
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "integrate", "optimize", "rbinom", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc     6.5Mb
    ubinc   2.1Mb
installed size is 54.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs  52.3Mb
GNU make is a SystemRequirements.
Package required but not available: ‘ChemmineR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
rmd2pdf: no visible global function definition for ‘tail’
rnw2pdf: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Found the following executable files:
  inst/examples/ko.txt
  inst/examples/ru/koi8-r.txt
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
GNU make is a SystemRequirements.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
plot.UComp: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘plotly’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyjs’
  ‘shinythemes’ ‘zip’
  All declared Imports should be used.
Note: found 162 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
installed size is 32.5Mb
  sub-directories of 1Mb or more:
    doc         5.8Mb
    dummydata   1.4Mb
    libs       23.7Mb
installed size is 149.5Mb
  sub-directories of 1Mb or more:
    data       2.0Mb
    extdata    2.3Mb
    libs     144.9Mb
No protocol specified
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    help   4.1Mb
ubRacing : predCandidate: no visible global function definition for
  ‘predict’
ubRacing : aux2.friedman.edit: no visible global function definition
  for ‘pchisq’
ubRacing : aux2.friedman.edit: no visible global function definition
  for ‘qt’
ubRacing : aux.friedman.edit: no visible global function definition for
  ‘wilcox.test’
ubRacing : aux.ttest.edit: no visible global function definition for
  ‘t.test’
ubRacing : aux.ttest.edit: no visible global function definition for
  ‘p.adjust’
ubRacing : idFolds: no visible global function definition for
  ‘quantile’
ubRacing: no visible binding for global variable ‘sd’
ubSmoteExs: no visible global function definition for ‘runif’
Undefined global functions or variables:
  p.adjust pchisq predict qt quantile runif sd t.test wilcox.test
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "predict", "qt", "quantile",
             "runif", "sd", "t.test", "wilcox.test")
to your NAMESPACE file.
med: no visible global function definition for ‘quantile’
uh: no visible global function definition for ‘mad’
uh.bu: no visible global function definition for ‘mad’
Undefined global functions or variables:
  mad quantile
Consider adding
  importFrom("stats", "mad", "quantile")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ungroup.Rcheck/00install.out’ for details.
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
plot.pclm: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
prepare_Rd: RGL: unable to open X11 display
prepare_Rd: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
Error(s) in re-building vignettes:
  ...
--- re-building ‘convexhull.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 93-98 (convexhull.Rmd) 
Error: processing vignette 'convexhull.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘convexhull.Rmd’

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

Error: Vignette re-building failed.
Execution halted
dudewicz.unif.test: no visible global function definition for ‘runif’
frosini.unif.test: no visible global function definition for ‘runif’
hegazy.unif.test: no visible global function definition for ‘runif’
kolmogorov.unif.test: no visible global function definition for ‘runif’
kuiper.unif.test: no visible global function definition for ‘runif’
neyman.unif.test: no visible global function definition for ‘runif’
quesenberry.unif.test: no visible global function definition for
  ‘runif’
sarkadi.unif.test: no visible global function definition for ‘runif’
sherman.unif.test: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Note: found 548 marked UTF-8 strings
cumcount: no visible global function definition for ‘setNames’
uniqtag: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘extraDistr’ ‘logitnorm’ ‘nakagami’ ‘tibble’
  All declared Imports should be used.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.6Mb
    libs   9.3Mb
GNU make is a SystemRequirements.
Note: found 3345 marked UTF-8 strings
Note: found 7872 marked UTF-8 strings
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.6Mb
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
Note: found 488 marked UTF-8 strings
No protocol specified
No protocol specified
.geomap: no visible global function definition for ‘list2DF’
Undefined global functions or variables:
  list2DF
Package suggested but not available for checking: ‘USAboundariesData’
readSEER: no visible global function definition for ‘read.fwf’
Undefined global functions or variables:
  read.fwf
Consider adding
  importFrom("utils", "read.fwf")
to your NAMESPACE file.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘UScensus2000cdp/R/zzz.R’:
  .First.lib calls:
    cat(paste("'", ehelp[4], "'\n", "Version ", ehelp[2], " created on ",     ehelp[3], ".\n", sep = ""))
    cat(paste(substring(ehelp[3], first = 16), "\n", "Version ",     substring(ehelp[4], first = 16), " created on ", substring(ehelp[5],         first = 16), ".\n", sep = ""))
    cat(paste("copyright (c) 2009, Zack W. Almquist, University of California-Irvine\n",     sep = ""))
    cat("For citation information, type citation(\"UScensus2000cdp\").\n")
    cat("Type help(package=\"UScensus2000cdp\") to get started.\n")

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    data  26.4Mb
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘UScensus2000tract/R/zzz.R’:
  .First.lib calls:
    cat(paste("'", ehelp[4], "'\n", "Version ", ehelp[2], " created on ",     ehelp[3], ".\n", sep = ""))
    cat(paste(substring(ehelp[3], first = 16), "\n", "Version ",     substring(ehelp[4], first = 16), " created on ", substring(ehelp[5],         first = 16), ".\n", sep = ""))
    cat(paste("copyright (c) 2009, Zack W. Almquist, University of California-Irvine\n",     sep = ""))
    cat("For citation information, type citation(\"UScensus2000tract\").\n")
    cat("Type help(package=\"UScensus2000tract\") to get started.\n")

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.
Found the following hidden files and directories:
  data/.Rhistory
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘rgdal’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘foreign’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘cli’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tsibble’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   6.4Mb
Note: found 1 marked UTF-8 string
Malformed Title field: should not end in a period.
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘stringdist’ ‘utils’
  All declared Imports should be used.
histw: no visible global function definition for ‘plot.new’
histw: no visible global function definition for ‘plot.window’
histw: no visible global function definition for ‘axis’
histw: no visible global function definition for ‘rect’
histw: no visible global function definition for ‘lines’
uwham.boot: no visible binding for global variable ‘var’
Undefined global functions or variables:
  axis lines plot.new plot.window rect var
Consider adding
  importFrom("graphics", "axis", "lines", "plot.new", "plot.window",
             "rect")
  importFrom("stats", "var")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘rio’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  20.5Mb
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/VALERIE.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘Cairo’
  All declared Imports should be used.
Found the following significant warnings:
  Note: possible error in 'bquote(dplyr::transmute(x$query, ': unused argument (splice = TRUE) 
  Note: possible error in 'bquote(dplyr::transmute(tbl, ': unused argument (splice = TRUE) 
  Note: possible error in 'bquote({': unused argument (splice = TRUE) 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/validatedb.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
aggregate_by_record: possible error in bquote(dplyr::transmute(x$query,
  ..(key_expr), nfails = .(fails), nNA = .(nas)), splice = TRUE):
  unused argument (splice = TRUE)
confront_tbl: possible error in bquote(dplyr::transmute(tbl,
  ..(key_expr), ..(exprs[working])), splice = TRUE): unused argument
  (splice = TRUE)
confront_tbl_sparse : <anonymous>: possible error in bquote({: unused
  argument (splice = TRUE)
confront_tbl_sparse : <anonymous>: possible error in d <-
  dplyr::transmute(tbl, ..(key_expr), rule = .(rule_name), fail =
  !.(e)): unused argument (splice = TRUE)
confront_tbl_sparse : <anonymous>: possible error in dplyr::filter(d,
  dplyr::coalesce(fail, TRUE)): unused argument (splice = TRUE)
confront_tbl_sparse : <anonymous>: possible error in }, splice = TRUE):
  unused argument (splice = TRUE)
Running examples in ‘validatedb-Ex.R’ failed
The error most likely occurred in:

> ### Name: aggregate.tbl_validation
> ### Title: Count the number of invalid rules or records.
> ### Aliases: aggregate.tbl_validation
> 
> ### ** Examples
> 
> income <- data.frame(id = 1:2, age=c(12,35), salary = c(1000,NA))
> con <- dbplyr::src_memdb()
> tbl_income <- dplyr::copy_to(con, income, overwrite=TRUE)
> print(tbl_income)
# Source:   table<income> [?? x 3]
# Database: sqlite 3.35.2 [:memory:]
     id   age salary
  <int> <dbl>  <dbl>
1     1    12   1000
2     2    35     NA
> 
> # Let's define a rule set and confront the table with it:
> rules <- validator( is_adult   = age >= 18
+                     , has_income = salary > 0
+ )
> 
> # and confront!
> # in general with a db table it is handy to use a key
> cf <- confront(tbl_income, rules, key="id")
Error in bquote({ : unused argument (splice = TRUE)
Calls: confront ... rule_works_on_tbl -> confront_tbl_sparse -> lapply -> FUN
Execution halted
Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Backtrace:
      █
   1. ├─validate::confront(tbl_d, rules, key = "id") test-values.R:122:4
   2. └─validatedb::confront(tbl_d, rules, key = "id")
   3.   └─validatedb:::.local(dat, x, ref, ...)
   4.     └─validatedb::confront.tbl_sql(...)
   5.       └─validatedb:::confront_tbl(tbl = tbl, x = x, key = key)
   6.         └─validatedb:::rule_works_on_tbl(tbl, x)
   7.           └─validatedb:::confront_tbl_sparse(...)
   8.             └─base::lapply(...)
   9.               └─validatedb:::FUN(X[[i]], ...)
  
  [ FAIL 19 | WARN 0 | SKIP 0 | PASS 1 ]
  Error: Test failures
  Execution halted
Running ‘tinytest.R’ [3s/3s]
Running the tests in ‘tests/tinytest.R’ failed.
Last 13 lines of output:
  Running test_validator.R..............   13 tests [0;32mOK[0m 
  Running test_validator.R..............   13 tests [0;32mOK[0m 
  Running test_validator.R..............   13 tests [0;32mOK[0m [0;34m0.1s[0m
  ----- FAILED[data]: test_genericrules.R<259--260>
   call| expect_equal(as.logical(values(confront(transactions, rule))), 
   call| c(TRUE, FALSE, TRUE, TRUE), info = "regex in does_not_contain")
   diff| Lengths (4, 0) differ (comparison on first 0 components)
   info| regex in does_not_contain
  ----- FAILED[data]: test_genericrules.R<264--265>
   call| expect_equal(as.logical(values(confront(transactions, rule))), 
   call| c(TRUE, FALSE, TRUE, TRUE), info = "regex in does_not_contain")
   diff| Lengths (4, 0) differ (comparison on first 0 components)
   info| regex in does_not_contain
  Error: 2 out of 399 tests failed
  Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/valmetrics.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘car’ ‘rlang’ ‘tidyverse’
  All declared Imports should be used.
installed size is 144.9Mb
  sub-directories of 1Mb or more:
    extdata    1.0Mb
    libs     143.3Mb
Malformed Description field: should contain one or more complete sentences.
Mammen: no visible global function definition for ‘runif’
PR2: no visible global function definition for ‘ar.burg’
PR2: no visible global function definition for ‘pt’
PR2: no visible global function definition for ‘pf’
PR3: no visible global function definition for ‘ar.burg’
PR3: no visible global function definition for ‘pt’
PR3: no visible global function definition for ‘pf’
VAR.FOR: no visible global function definition for ‘qnorm’
VAR.ForeB: no visible global function definition for ‘runif’
VAR.LRtest: no visible global function definition for ‘pchisq’
VAR.LRtest: no visible global function definition for ‘pf’
VAR.PI: no visible global function definition for ‘quantile’
VAR.Waldtest: no visible global function definition for ‘pf’
VAR.irf: no visible global function definition for ‘par’
VAR.irf: no visible global function definition for ‘plot’
VAR.irf: no visible global function definition for ‘abline’
VAR1.sim: no visible global function definition for ‘rnorm’
resamp: no visible global function definition for ‘runif’
Undefined global functions or variables:
  abline ar.burg par pchisq pf plot pt qnorm quantile rnorm runif
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "ar.burg", "pchisq", "pf", "pt", "qnorm",
             "quantile", "rnorm", "runif")
to your NAMESPACE file.
No protocol specified
No protocol specified
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/VARMER.Rcheck/00install.out’ for details.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Namespace in Imports field not imported from: ‘rio’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘basic_usage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

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

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshota8c46dff7787.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshota8c46dff7787.png': No such file or directory
Quitting from lines 54-55 (basic_usage.Rmd) 
Error: processing vignette 'basic_usage.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘basic_usage.Rmd’

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

Error: Vignette re-building failed.
Execution halted
black_scholes: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘matrixcalc’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespace in Imports field not imported from: ‘DiceKriging’
  All declared Imports should be used.
burdenPlot: no visible global function definition for ‘density’
burdenPlot: no visible global function definition for ‘axis’
burdenPlot: no visible global function definition for ‘points’
burdenPlot: no visible global function definition for ‘lines’
burdenPlot: no visible global function definition for ‘abline’
burdenPlot: no visible global function definition for ‘text’
burdenPlot: no visible global function definition for ‘sd’
burdenPlot: no visible global function definition for ‘segments’
vbdm: no visible global function definition for ‘var’
vbdm: no visible global function definition for ‘pchisq’
vbdmR : run_discrete_mixture_vanilla: no visible global function
  definition for ‘var’
vbdmR: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  abline axis density lines pchisq points sd segments text var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "points", "segments",
             "text")
  importFrom("stats", "density", "pchisq", "sd", "var")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
compute_KL : rtnorm: no visible global function definition for ‘runif’
compute_KL : rtnorm: no visible global function definition for ‘dnorm’
compute_KL: no visible global function definition for ‘qnorm’
compute_KL: no visible global function definition for ‘dnorm’
compute_KL: no visible global function definition for ‘pnorm’
compute_KL: no visible global function definition for ‘var’
compute_KL: no visible global function definition for ‘rbinom’
compute_KL: no visible global function definition for ‘rnorm’
compute_KL: no visible global function definition for ‘sd’
vbsr: no visible global function definition for ‘qchisq’
vbsr: no visible global function definition for ‘var’
vbsr: no visible global function definition for ‘pchisq’
vbsr: no visible global function definition for ‘sd’
vbsr: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  dnorm pchisq pnorm qchisq qnorm rbinom rnorm runif sd var
Consider adding
  importFrom("stats", "dnorm", "pchisq", "pnorm", "qchisq", "qnorm",
             "rbinom", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
GetTestPlot.Boot: no visible global function definition for ‘plot’
GetTestPlot.Vuong: no visible global function definition for ‘plot’
VC_MOSUM_Boot: no visible global function definition for ‘plot’
VC_MOSUM_Vuong: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.1Mb
Compare2FDS: no visible global function definition for ‘runif’
Compare2FDS: no visible global function definition for ‘lm’
Compare2FDS: no visible global function definition for ‘model.matrix’
Compare2FDS: no visible global function definition for ‘plot’
Compare2FDS: no visible global function definition for ‘abline’
Compare2FDS: no visible global function definition for ‘lines’
Compare2FDS: no visible global function definition for ‘text’
Compare2Vdg: no visible global function definition for ‘par’
Compare2Vdg: no visible global function definition for ‘plot’
Compare2Vdg: no visible global function definition for ‘lines’
Compare2Vdg: no visible global function definition for ‘legend’
FDSPlot: no visible global function definition for ‘runif’
FDSPlot: no visible global function definition for ‘lm’
FDSPlot: no visible global function definition for ‘model.matrix’
FDSPlot: no visible global function definition for ‘plot’
FDSPlot: no visible global function definition for ‘abline’
Vdgraph: no visible global function definition for ‘par’
Vdgraph: no visible global function definition for ‘plot’
Vdgraph: no visible global function definition for ‘lines’
Vdgraph: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline legend lines lm model.matrix par plot runif text
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "plot",
             "text")
  importFrom("stats", "lm", "model.matrix", "runif")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘freetypeharfbuzz’
  All declared Imports should be used.
calculateParameters,AffineTransformation: no visible global function
  definition for ‘lm’
calculateParameters,AffineTransformation: no visible global function
  definition for ‘coef’
calculateParameters,SimilarityTransformation: no visible global
  function definition for ‘lm’
calculateParameters,SimilarityTransformation: no visible global
  function definition for ‘coef’
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for ‘points’
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for ‘legend’
Undefined global functions or variables:
  coef legend lm points
Consider adding
  importFrom("graphics", "legend", "points")
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/VecStatGraphs3D.Rcheck/00install.out’ for details.
DrawDensity3D: no visible global function definition for ‘colorRamp’
DrawDensity3D: no visible global function definition for ‘rgb’
ReadFromFile3D: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  colorRamp read.table rgb
Consider adding
  importFrom("grDevices", "colorRamp", "rgb")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Running examples in ‘VecStatGraphs3D-Ex.R’ failed
The error most likely occurred in:

> ### Name: DrawModuleAndAngleDistribution3D
> ### Title: Graphic representation of Module and Angle Distribution.
> ### Aliases: DrawModuleAndAngleDistribution3D
> ### Keywords: graphics
> 
> ### ** Examples
> 
>    FileName<-system.file("data/XYZcoor.txt", package="VecStatGraphs3D")
>    dat<-LoadData3D(FileName, Type=1)
>    DrawModuleAndAngleDistribution3D(dat, plane="XY");
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: DrawModuleAndAngleDistribution3D ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘foreach’ ‘iterators’ ‘maps’ ‘spam’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_to_vegalite.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 24-36 (intro_to_vegalite.Rmd) 
Error: processing vignette 'intro_to_vegalite.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘intro_to_vegalite.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/vegan3d.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
Running examples in ‘vegawidget-Ex.R’ failed
The error most likely occurred in:

> ### Name: vw_set_base_url
> ### Title: Set base URL
> ### Aliases: vw_set_base_url
> 
> ### ** Examples
> 
>  # this is the URL used for Vega datasets
>  previous <- vw_set_base_url("https://cdn.jsdelivr.net/npm/vega-datasets@2")
> 
>  # reset to previous value
>  vw_set_base_url(previous)
Error in vega_embed_local[["loader"]][["baseURL"]] <- url : 
  replacement has length zero
Calls: vw_set_base_url
Execution halted
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
      is_false, is_null, is_true
  
  ══ Skipped tests ═══════════════════════════════════════════════════════════════
  ● On CRAN (7)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-set-base-url.R:18:3): vw_set_base_url() works ───────────────────
  Error: replacement has length zero
  Backtrace:
      █
   1. └─vegawidget::vw_set_base_url(NULL) test-set-base-url.R:18:2
  
  [ FAIL 1 | WARN 0 | SKIP 7 | PASS 71 ]
  Error: Test failures
  Execution halted
Note: found 128 marked UTF-8 strings
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R   3.6Mb
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Checking should be performed on sources prepared by ‘R CMD build’.
plot.VennDiagram : <anonymous>: no visible global function definition
  for ‘hcl’
plot.VennDiagram: no visible global function definition for ‘plot.new’
plot.VennDiagram: no visible global function definition for
  ‘plot.window’
plot.VennDiagram: no visible global function definition for ‘col2rgb’
plot.VennDiagram: no visible global function definition for ‘rgb’
plot.VennDiagram: no visible global function definition for ‘polygon’
plot.VennDiagram: no visible global function definition for ‘text’
plot.VennDiagram: no visible global function definition for ‘title’
Undefined global functions or variables:
  col2rgb hcl plot.new plot.window polygon rgb text title
Consider adding
  importFrom("grDevices", "col2rgb", "hcl", "rgb")
  importFrom("graphics", "plot.new", "plot.window", "polygon", "text",
             "title")
to your NAMESPACE file.
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    libs  27.5Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/vennplot.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    help   2.9Mb
spikeplot: no visible global function definition for ‘deparse1’
Undefined global functions or variables:
  deparse1
Missing link or links in documentation object 'spikeplot.Rd':
  ‘[base]{plot}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
Package required but not available: ‘coRdon’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Malformed Title field: should not end in a period.
Note: found 2 marked UTF-8 strings
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/vICC.Rcheck/00install.out’ for details.
Note: found 60 marked UTF-8 strings
No protocol specified
No protocol specified
Namespaces in Imports field not imported from:
  ‘plotrix’ ‘sp’ ‘viridis’
  All declared Imports should be used.
vif: no visible global function definition for ‘sd’
vif: no visible global function definition for ‘lm’
vif: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  lm pnorm sd
Consider adding
  importFrom("stats", "lm", "pnorm", "sd")
to your NAMESPACE file.
hyperpara: no visible binding for global variable ‘var’
hyperpara: no visible global function definition for ‘hist’
Undefined global functions or variables:
  hist var
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "var")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘mclust’ ‘rlang’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Note: found 2754 marked UTF-8 strings
Running ‘testthat.R’ [18s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  `ir <- irmi(test_df, mixed = "m", count = "co")` did not produce any warnings.
  ── Failure (test_IRMI_ordered.R:15:3): irmi step ───────────────────────────────
  `ir <- irmi(test_df, mixed = "m", count = "co", step = TRUE)` did not produce any warnings.
  ── Failure (test_IRMI_ordered.R:20:3): irmi step noise ─────────────────────────
  `ir <- irmi(test_df, mixed = "m", count = "co", step = TRUE, noise = TRUE)` did not produce any warnings.
  ── Failure (test_IRMI_ordered.R:25:3): irmi robust ─────────────────────────────
  `ir <- irmi(test_df, robust = TRUE, mixed = "m", count = "co")` did not produce any warnings.
  ── Failure (test_IRMI_ordered.R:34:3): irmi robust noise ───────────────────────
  `... <- NULL` did not produce any warnings.
  ── Failure (test_IRMI_ordered.R:39:3): irmi robust noise with no imp_var ───────
  `... <- NULL` did not produce any warnings.
  
  [ FAIL 6 | WARN 0 | SKIP 0 | PASS 144 ]
  Error: Test failures
  Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/vindecodr.Rcheck/00install.out’ for details.
installed size is 54.9Mb
  sub-directories of 1Mb or more:
    libs  54.6Mb
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'library' or 'require' call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
viopoints.default: no visible global function definition for ‘par’
viopoints.default: no visible global function definition for ‘plot.new’
viopoints.default: no visible global function definition for
  ‘plot.window’
viopoints.default: no visible global function definition for ‘axis’
viopoints.default: no visible global function definition for ‘arrows’
viopoints.default: no visible global function definition for
  ‘getFromNamespace’
viopoints.default: no visible global function definition for ‘title’
viopoints.default: no visible global function definition for ‘box’
Undefined global functions or variables:
  arrows axis box getFromNamespace par plot.new plot.window title
Consider adding
  importFrom("graphics", "arrows", "axis", "box", "par", "plot.new",
             "plot.window", "title")
  importFrom("utils", "getFromNamespace")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/viromeBrowser.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘diptest’
  All declared Imports should be used.
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ● has_virtuoso() is not TRUE (1)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test-vos_odbc.R:25:3): We can generate an odbcinst file ──────────────
  Error: cannot open the connection
  Backtrace:
      █
   1. └─virtuoso:::vos_odbcinst() test-vos_odbc.R:25:2
   2.   └─base::write(...)
   3.     └─base::cat(...)
   4.       └─base::file(file, ifelse(append, "a", "w"))
  
  [ FAIL 1 | WARN 1 | SKIP 9 | PASS 14 ]
  Error: Test failures
  Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/viscomplexr.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’
  All declared Imports should be used.
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    libs  27.3Mb
Namespace in Imports field not imported from: ‘sqldf’
  All declared Imports should be used.
GNU make is a SystemRequirements.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc           4.3Mb
    docjs         1.4Mb
    htmlwidgets   3.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction-to-visNetwork.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 22-27 (Introduction-to-visNetwork.Rmd) 
Error: processing vignette 'Introduction-to-visNetwork.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Introduction-to-visNetwork.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
Error(s) in re-building vignettes:
--- re-building ‘gg_vistime-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
--- finished re-building ‘gg_vistime-vignette.Rmd’

--- re-building ‘hc_vistime-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 33-40 (hc_vistime-vignette.Rmd) 
Error: processing vignette 'hc_vistime-vignette.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘hc_vistime-vignette.Rmd’

--- re-building ‘vistime-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 31-39 (vistime-vignette.Rmd) 
Error: processing vignette 'vistime-vignette.Rmd' failed with diagnostics:
invalid 'path' argument
--- failed re-building ‘vistime-vignette.Rmd’

SUMMARY: processing the following files failed:
  ‘hc_vistime-vignette.Rmd’ ‘vistime-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘glue’ ‘tidyr’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘introduction.Rmd’

--- re-building ‘shiny-example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 61-63 (shiny-example.Rmd) 
Error: processing vignette 'shiny-example.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘shiny-example.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Decile.Plot: no visible global function definition for ‘barplot’
Decile.Plot: no visible global function definition for ‘axis’
Sliding.Window: no visible global function definition for ‘plot’
Sliding.Window: no visible global function definition for ‘lines’
Sliding.Window: no visible global function definition for ‘legend’
Undefined global functions or variables:
  axis barplot legend lines plot
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines", "plot")
to your NAMESPACE file.
Package required but not available: ‘gWidgets2RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 56.7Mb
  sub-directories of 1Mb or more:
    libs  56.3Mb
Note: found 4954 marked UTF-8 strings
Malformed Description field: should contain one or more complete sentences.
voss1d: no visible global function definition for ‘approx’
voss1d: no visible global function definition for ‘rnorm’
voss1g: no visible global function definition for ‘dchisq’
voss1g: no visible global function definition for ‘approx’
voss1g: no visible global function definition for ‘rnorm’
voss2d: no visible global function definition for ‘rnorm’
voss2g: no visible global function definition for ‘dchisq’
voss2g: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  approx dchisq rnorm
Consider adding
  importFrom("stats", "approx", "dchisq", "rnorm")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘glue’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    extdata   8.4Mb
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
'library' or 'require' call to ‘misc3d’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   6.9Mb
Malformed Description field: should contain one or more complete sentences.
plot.vscc: no visible global function definition for ‘rainbow’
plot.vscc: no visible global function definition for ‘pairs’
Undefined global functions or variables:
  pairs rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "pairs")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘XML’ ‘checkmate’ ‘gstat’ ‘intervals’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘EnvStats’ ‘shiny’ ‘stats’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘lattice’ ‘latticeExtra’ ‘stringdist’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ald: no visible global function definition for ‘detectCores’
ald: no visible global function definition for ‘mclapply’
coltheart.N: no visible global function definition for ‘detectCores’
coltheart.N: no visible global function definition for ‘mclapply’
hamming.distance: no visible global function definition for
  ‘stringdist’
ldknn: no visible global function definition for ‘detectCores’
ldknn: no visible global function definition for ‘mclapply’
ldknn.odds: no visible global function definition for ‘glm’
ldknn.odds: no visible binding for global variable ‘binomial’
ldknn.odds: no visible global function definition for ‘coefficients’
levenshtein.damerau.distance: no visible global function definition for
  ‘stringdist’
levenshtein.distance: no visible global function definition for
  ‘stringdist’
plot.ldknn.run: no visible global function definition for ‘histogram’
plot.ldknn.run: no visible global function definition for
  ‘theEconomist.theme’
plot.ldknn.run: no visible global function definition for ‘xyplot’
plot.ldknn.run: no visible global function definition for ‘as.layer’
Undefined global functions or variables:
  as.layer binomial coefficients detectCores glm histogram mclapply
  stringdist theEconomist.theme xyplot
Consider adding
  importFrom("stats", "binomial", "coefficients", "glm")
to your NAMESPACE file.
Note: found 358074 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘R6’
  All declared Imports should be used.
summary.whc: no visible global function definition for ‘printCoefmat’
wahc.fit: no visible global function definition for ‘pt’
wahc.fit: no visible global function definition for ‘cor’
whc: no visible global function definition for ‘model.frame’
whc: no visible global function definition for ‘model.matrix’
whc: no visible global function definition for ‘model.response’
Undefined global functions or variables:
  cor model.frame model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.frame", "model.matrix",
             "model.response", "printCoefmat", "pt")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is 68.7Mb
  sub-directories of 1Mb or more:
    libs  67.4Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘ENMeval’ ‘RColorBrewer’ ‘XML’ ‘dismo’ ‘dplyr’ ‘leaflet.extras’
  ‘maptools’ ‘raster’ ‘rgbif’ ‘rgdal’ ‘rgeos’ ‘rmarkdown’ ‘shinyjs’
  ‘shinythemes’ ‘spThin’ ‘spocc’ ‘testthat’ ‘zip’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘WRS2’ ‘ggplot2’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   5.5Mb
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘vctrs’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rPeaks’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/waveformlidar.Rcheck/00install.out’ for details.
plot_local.multiple.cross.correlation: no visible global function
  definition for ‘plot’
plot_wave.local.multiple.cross.correlation : blocki: no visible global
  function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘zoo’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Note: found 3133 marked UTF-8 strings
onesamplemeantest: no visible global function definition for ‘pnorm’
twosamplemeantest: no visible global function definition for ‘pnorm’
wcq: no visible global function definition for ‘var’
wcq: no visible global function definition for ‘pnorm’
wcq.fdrc: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  p.adjust pnorm var
Consider adding
  importFrom("stats", "p.adjust", "pnorm", "var")
to your NAMESPACE file.
Note: found 1537 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘tools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
Note: found 3 marked UTF-8 strings
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/webfakes.Rcheck/00install.out’ for details.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    client   9.4Mb
    doc      1.0Mb
Namespaces in Imports field not imported from:
  ‘shiny’ ‘tidyselect’
  All declared Imports should be used.
installed size is 28.8Mb
  sub-directories of 1Mb or more:
    libs  28.6Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘here’ ‘rgeos’ ‘tibble’
  All declared Imports should be used.
Weighted.Box.test: no visible global function definition for ‘acf’
Weighted.Box.test: no visible binding for global variable ‘na.pass’
Weighted.Box.test: no visible global function definition for ‘pgamma’
Weighted.Box.test: no visible global function definition for ‘pchisq’
Weighted.LM.test: no visible global function definition for ‘acf’
Weighted.LM.test: no visible binding for global variable ‘na.pass’
Weighted.LM.test: no visible global function definition for ‘pgamma’
Undefined global functions or variables:
  acf na.pass pchisq pgamma
Consider adding
  importFrom("stats", "acf", "na.pass", "pchisq", "pgamma")
to your NAMESPACE file.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
Package required but not available: ‘GO.db’

Packages suggested but not available for checking:
  'org.Hs.eg.db', 'org.Mm.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 4102 marked UTF-8 strings
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
Bundesliga.Mannschaft: no visible global function definition for ‘data’
Bundesliga.Mannschaft: no visible binding for global variable
  ‘Bundesliga’
Bundesliga.Tabelle: no visible global function definition for ‘data’
Bundesliga.Tabelle: no visible binding for global variable ‘Bundesliga’
Bundesliga.XML: no visible global function definition for ‘data’
Bundesliga.XML: no visible binding for global variable ‘Bundesliga’
sens.spec: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Running ‘testthat.R’ [2s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
       █
    1. ├─testthat::expect_s3_class(...) test-lake_wiki.R:34:2
    2. │ └─testthat::quasi_label(enquo(object), arg = "object")
    3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
    4. └─wikilake::lake_wiki(c("Elk River Chain of Lakes Watershed", "Lake Mendota"))
    5.   └─wikilake::lake_clean(res)
    6.     └─base::sapply(dt[, var], function(x) parse_unit_brackets(x, unit_key_numeric$units[i]))
    7.       └─base::lapply(X = X, FUN = FUN, ...)
    8.         └─wikilake:::FUN(X[[i]], ...)
    9.           └─wikilake::parse_unit_brackets(x, unit_key_numeric$units[i])
   10.             └─base::strsplit(x, " ")
  
  [ FAIL 1 | WARN 0 | SKIP 3 | PASS 0 ]
  Error: Test failures
  Execution halted
wilcox.selection.split: no visible global function definition for
  ‘pnorm’
wilcox.test2: no visible global function definition for ‘wilcox.test’
Undefined global functions or variables:
  pnorm wilcox.test
Consider adding
  importFrom("stats", "pnorm", "wilcox.test")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘drc’ ‘imputeTestbench’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/WinRatio.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    bn   7.1Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘DescTools’ ‘HydeNet’ ‘RBGL’ ‘Rgraphviz’ ‘arules’ ‘bnlearn’
  ‘dplyr’ ‘graph’ ‘igraph’ ‘linkcomm’ ‘missRanger’ ‘parallel’ ‘psych’
  ‘rhandsontable’ ‘rintrojs’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’
  ‘shinycssloaders’ ‘shinydashboard’ ‘tools’ ‘visNetwork’
  All declared Imports should be used.
dbayes: no visible global function definition for ‘mahalanobis’
dbayes: no visible global function definition for ‘var’
wmd: no visible global function definition for ‘cor’
wmd: no visible global function definition for ‘var’
Undefined global functions or variables:
  cor mahalanobis var
Consider adding
  importFrom("stats", "cor", "mahalanobis", "var")
to your NAMESPACE file.
fit,Leader: no visible global function definition for ‘lm’
plotfit,Leader: no visible global function definition for ‘par’
plotfit,Leader: no visible global function definition for ‘plot’
Undefined global functions or variables:
  lm par plot
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/wordbankr.Rcheck/00install.out’ for details.
Note: found 933 marked UTF-8 strings
Error(s) in re-building vignettes:
  ...
--- re-building ‘wordcloud.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 37-39 (wordcloud.Rmd) 
Error: processing vignette 'wordcloud.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘wordcloud.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Note: found 2 marked UTF-8 strings
Note: found 6738 marked UTF-8 strings
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  ‘plyr’ ‘reshape2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
wordmatch: no visible global function definition for ‘llply’
wordmatch : <anonymous>: no visible global function definition for
  ‘llply’
wordmatch: no visible global function definition for ‘melt’
wordmatch: no visible global function definition for ‘count’
Undefined global functions or variables:
  count llply melt
Warning in initDict() :
  cannot find WordNet 'dict' directory: please set the environment variable WNHOME to its parent

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

Probably some imports need to be declared in the NAMESPACE file.
Note: found 3 marked UTF-8 strings
Note: found 2 marked UTF-8 strings
Malformed Description field: should contain one or more complete sentences.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.7Mb
Malformed Description field: should contain one or more complete sentences.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.3Mb
No protocol specified
No protocol specified
Namespaces in Imports field not imported from:
  ‘fdadensity’ ‘locfit’ ‘locpol’ ‘modeest’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Package suggested but not available for checking: ‘ROTS’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    extdata   2.9Mb
Error(s) in re-building vignettes:
--- re-building ‘overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
Warning: Removed 10 rows containing non-finite values (stat_smooth).
Warning: Removed 8 rows containing missing values (geom_point).
Warning: Removed 5 rows containing missing values (geom_path).
Warning: Removed 10 rows containing missing values (geom_point).

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshot13f204f5efc8.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot13f204f5efc8.png': No such file or directory
Quitting from lines 214-234 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
Package suggested but not available for checking: ‘Rsymphony’
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
File
  LICENCE
is not mentioned in the DESCRIPTION file.
'library' or 'require' call to ‘MASS’ which was already attached by Depends.
  Please remove these calls from your code.
simul.wsvm: no visible binding for global variable ‘mixture.example’
wsvm.boost: no visible global function definition for ‘plot’
Undefined global functions or variables:
  mixture.example plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   5.9Mb
Namespace in Imports field not imported from: ‘simts’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
File
  inst/LICENCE
will install at top-level and is not mentioned in the DESCRIPTION file.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/wyz.code.metaTesting.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/x13binary.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    bin   4.1Mb
    lib   2.1Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/x3ptools.Rcheck/00install.out’ for details.
Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred.
installed size is 40.3Mb
  sub-directories of 1Mb or more:
    libs  39.4Mb
GNU make is a SystemRequirements.
File
  LICENCE
is not mentioned in the DESCRIPTION file.
quadplot: no visible global function definition for ‘median’
xgobi: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  median write.table
Consider adding
  importFrom("stats", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
XHWE: no visible global function definition for ‘read.table’
result: no visible global function definition for ‘pchisq’
result: no visible global function definition for ‘rbinom’
result: no visible global function definition for ‘rmultinom’
Undefined global functions or variables:
  pchisq rbinom read.table rmultinom
Consider adding
  importFrom("stats", "pchisq", "rbinom", "rmultinom")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘psychTools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
installed size is 36.4Mb
  sub-directories of 1Mb or more:
    java  34.2Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
R5.value.default: no visible binding for global variable ‘data.table’
R5.value.default: no visible global function definition for
  ‘as.data.table’
R5.value.parse: no visible binding for global variable ‘data.table’
R5.value.parse: no visible global function definition for
  ‘is.data.table’
R5.value.parse: no visible global function definition for
  ‘as.data.table’
stampme: no visible global function definition for ‘flush.console’
stampmsg: no visible global function definition for ‘flush.console’
write.data.table: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  as.data.table data.table flush.console is.data.table write.table
Consider adding
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/XML.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘qpdf’ ‘rlang’ ‘tibble’
  All declared Imports should be used.
Packages suggested but not available for checking: 'ChemmineR', 'fmcsR'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/xplain.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Xplortext.Rcheck/00install.out’ for details.
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    libs  25.7Mb
Note: found 268 marked UTF-8 strings
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    include   4.0Mb
    libs      2.0Mb
Malformed Title field: should not end in a period.
big.read.table: no visible global function definition for ‘read.table’
big.read.table: no visible global function definition for ‘object.size’
sparkline: no visible global function definition for ‘is.ts’
sparkline: no visible global function definition for ‘time’
sparkline: no visible global function definition for ‘boxplot’
Undefined global functions or variables:
  boxplot is.ts object.size read.table time
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "is.ts", "time")
  importFrom("utils", "object.size", "read.table")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Yamm.Rcheck/00install.out’ for details.
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    libs  25.6Mb
Package in Depends field not imported from: ‘compiler’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bootstrapswapcurve: no visible global function definition for ‘ts’
fitted: no visible global function definition for ‘ts’
forwardrates: no visible global function definition for ‘ts’
residuals: no visible global function definition for ‘ts’
tZC_NS: no visible global function definition for ‘cmpfun’
tZC_NS_extra: no visible global function definition for ‘cmpfun’
tZC_SV: no visible global function definition for ‘cmpfun’
tZC_SV_extra: no visible global function definition for ‘cmpfun’
ycextra: no visible global function definition for ‘new’
ycinter: no visible global function definition for ‘new’
ycplot: no visible global function definition for ‘par’
ycplot: no visible global function definition for ‘points’
ycplot: no visible global function definition for ‘abline’
ycplot: no visible global function definition for ‘hist’
ycplot: no visible global function definition for ‘lines’
ycplot: no visible global function definition for ‘density’
ycplot: no visible global function definition for ‘qqnorm’
ycplot: no visible global function definition for ‘qqline’
ycsummary: no visible global function definition for ‘shapiro.test’
ycsummary: no visible global function definition for ‘pf’
Undefined global functions or variables:
  abline cmpfun density hist lines new par pf points qqline qqnorm
  shapiro.test ts
Consider adding
  importFrom("graphics", "abline", "hist", "lines", "par", "points")
  importFrom("methods", "new")
  importFrom("stats", "density", "pf", "qqline", "qqnorm",
             "shapiro.test", "ts")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.NS.estimator: no visible global function definition for ‘lm’
.NS.estimator: no visible global function definition for ‘coef’
.NS.estimator: no visible global function definition for ‘na.omit’
.NS.estimator: no visible global function definition for ‘resid’
.NSS.estimator: no visible global function definition for ‘lm’
.NSS.estimator: no visible global function definition for ‘coef’
.NSS.estimator: no visible global function definition for ‘na.omit’
.NSS.estimator: no visible global function definition for ‘resid’
NSrates: no visible global function definition for ‘time’
Nelson.Siegel: no visible global function definition for ‘optimize’
Srates: no visible global function definition for ‘time’
Svensson: no visible global function definition for ‘median’
Svensson: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  coef lm median na.omit optimize resid time
Consider adding
  importFrom("stats", "coef", "lm", "median", "na.omit", "optimize",
             "resid", "time")
to your NAMESPACE file.
kmeansN: no visible global function definition for ‘kmeans’
kmeansN: no visible global function definition for ‘aggregate’
kmeansN2: no visible global function definition for ‘aggregate’
kmeansN2: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  aggregate kmeans sd
Consider adding
  importFrom("stats", "aggregate", "kmeans", "sd")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘miniUI’ ‘shinyBS’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/yotover.Rcheck/00install.out’ for details.
installed size is 42.7Mb
  sub-directories of 1Mb or more:
    libs  42.5Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Running examples in ‘YPmodel-Ex.R’ failed
The error most likely occurred in:

> ### Name: YPmodel-package
> ### Title: The short-term and long-term hazard ratio model for survival
> ###   data
> ### Aliases: YPmodel-package
> ### Keywords: Survival analysis
> 
> ### ** Examples
> 
> 	library(YPmodel)
> 	data(gastric)
> 	YPmodel(gastric, repNum=100)
Error in if (class(data)[1] != "matrix" || class(data)[2] != "array") { : 
  missing value where TRUE/FALSE needed
Calls: YPmodel ... fun.adlgrk -> fun.flipud -> fun.cumsum -> fun.flipud
Execution halted
installed size is 35.8Mb
  sub-directories of 1Mb or more:
    libs  35.5Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Found the following significant warnings:
  Warning: package ‘mixOmics’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/YuGene.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘ghyp’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   3.1Mb
Malformed Description field: should contain one or more complete sentences.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/zenplots.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Note: found 47 marked UTF-8 strings
Note: found 5 marked UTF-8 strings
Note: found 146804 marked UTF-8 strings
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘testthat’
  All declared Imports should be used.
Package suggested but not available for checking: ‘zdat’
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘lubridate’
  All declared Imports should be used.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  'Rglpk' 'corrplot' 'lattice' 'rgl'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
multiplot: no visible global function definition for 'rainbow'
multiplot: no visible global function definition for 'plot'
multiplot: no visible global function definition for 'text'
multiplot: no visible global function definition for 'lines'
multiplot: no visible global function definition for 'par'
plot.abf2: no visible global function definition for 'plot'
plot.abf2: no visible global function definition for 'abline'
plot.abf2: no visible global function definition for 'text'
plot.abf2split: no visible global function definition for 'plot'
Undefined global functions or variables:
  abline lines par plot rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "par", "plot", "text")
to your NAMESPACE file.
Missing or unexported object: 'devtools::use_package'
Malformed Description field: should contain one or more complete sentences.
print.funlinWLS: no visible global function definition for 'pchisq'
print.linML: no visible global function definition for 'pchisq'
print.loglinML: no visible global function definition for 'pchisq'
print.satMarML: no visible global function definition for 'pchisq'
print.satMcarWLS: no visible global function definition for 'pchisq'
summary.funlinWLS: no visible global function definition for 'pchisq'
summary.linML: no visible global function definition for 'pchisq'
summary.loglinML: no visible global function definition for 'pchisq'
summary.satMarML: no visible global function definition for 'pchisq'
summary.satMcarWLS: no visible global function definition for 'pchisq'
summary.waldTest: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets  11.6Mb
Aggregate: no visible global function definition for 'aggregate'
Aggregate: no visible binding for global variable 'tail'
Aggregate: no visible binding for global variable 'var'
cocktailEnsemble: no visible global function definition for 'glm'
cocktailEnsemble: no visible global function definition for 'binomial'
cocktailEnsemble: no visible global function definition for 'step'
cocktailEnsemble: no visible binding for global variable 'na.omit'
imputeMissings : <anonymous>: no visible global function definition for
  'median'
predict.cocktailEnsemble: no visible global function definition for
  'predict'
Undefined global functions or variables:
  aggregate binomial glm median na.omit predict step tail var
Consider adding
  importFrom("stats", "aggregate", "binomial", "glm", "median",
             "na.omit", "predict", "step", "var")
  importFrom("utils", "tail")
to your NAMESPACE file.
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    R  13.7Mb
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'SemiPar' 'nlme'
  Please remove these calls from your code.
asp: no visible global function definition for 'as.formula'
asp: no visible global function definition for 'var'
aspm: no visible binding for global variable 'X.Declan'
aspm: no visible binding for global variable 'Z.Jaida'
aspm: no visible binding for global variable 'group.vec.Handan'
aspm: no visible global function definition for 'as.formula'
aspm: no visible global function definition for 'glm'
aspm: no visible global function definition for 'binomial'
aspm: no visible global function definition for 'poisson'
Undefined global functions or variables:
  X.Declan Z.Jaida as.formula binomial glm group.vec.Handan poisson var
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "poisson", "var")
to your NAMESPACE file.
Depends: includes the non-default packages:
  'Matrix', 'coda', 'mvtnorm', 'MCMCpack', 'spatstat', 'parallel'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  'MCMCpack' 'Matrix' 'coda' 'mvtnorm' 'parallel' 'spatstat'
  Please remove these calls from your code.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   7.1Mb
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.
critical.values: no visible global function definition for 'rnorm'
critical.values: no visible global function definition for 'quantile'
mandel.test: no visible global function definition for 'qf'
mtukey.test : p.test: no visible global function definition for 'qf'
mtukey.test: no visible binding for global variable 'quantile'
mtukey.test: no visible global function definition for 'rnorm'
tukey.test: no visible global function definition for 'qf'
Undefined global functions or variables:
  qf quantile rnorm
Consider adding
  importFrom("stats", "qf", "quantile", "rnorm")
to your NAMESPACE file.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.7Mb
    pictures   2.1Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
Malformed Description field: should contain one or more complete sentences.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    tutorials   5.5Mb
Running examples in 'aftgee-Ex.R' failed
The error most likely occurred in:

> ### Name: aftsrr
> ### Title: Accelerated Failure Time with Smooth Rank Regression
> ### Aliases: aftsrr
> 
> ### ** Examples
> 
> data(kidney, package = "survival")
Warning in data(kidney, package = "survival") :
  data set 'kidney' not found
> fit <- aftsrr(Surv(time, status) ~ age + sex, id = id,
+               data = kidney, se = c("ISMB", "ZLMB"), B = 10)
Error in is.data.frame(data) : object 'kidney' not found
Calls: aftsrr ... model.frame -> model.frame.default -> is.data.frame
Execution halted
Running examples in 'aftgee-Ex.R' failed
The error most likely occurred in:

> ### Name: aftsrr
> ### Title: Accelerated Failure Time with Smooth Rank Regression
> ### Aliases: aftsrr
> 
> ### ** Examples
> 
> data(kidney, package = "survival")
Warning in data(kidney, package = "survival") :
  data set 'kidney' not found
> fit <- aftsrr(Surv(time, status) ~ age + sex, id = id,
+               data = kidney, se = c("ISMB", "ZLMB"), B = 10)
Error in is.data.frame(data) : object 'kidney' not found
Calls: aftsrr ... model.frame -> model.frame.default -> is.data.frame
Execution halted
Malformed Description field: should contain one or more complete sentences.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    ShinyGR   6.8Mb
Running examples in 'akc-Ex.R' failed
The error most likely occurred in:

> ### Name: doc_group
> ### Title: Construct network of documents based on keyword co-occurrence
> ### Aliases: doc_group
> 
> ### ** Examples
> 
>  library(akc)
>  bibli_data_table %>%
+    keyword_clean(id = "id",keyword = "keyword") %>%
+    doc_group(id = "id",keyword = "keyword") -> grouped_doc
Warning: `distinct_()` was deprecated in dplyr 0.7.0.
Please use `distinct()` instead.
See vignette('programming') for more help
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Warning: `tbl_df()` was deprecated in dplyr 1.0.0.
Please use `tibble::as_tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Error in `colnames<-`(`*tmp*`, value = c("item1", "item2", "value")) : 
  attempt to set 'colnames' on an object with less than two dimensions
Calls: %>% ... %>% -> tbl_df -> as_tibble -> custom_melt -> colnames<-
Execution halted
Error(s) in re-building vignettes:
--- re-building 'akc_vignette.Rmd' using rmarkdown
Quitting from lines 75-79 (akc_vignette.Rmd) 
Error: processing vignette 'akc_vignette.Rmd' failed with diagnostics:
attempt to set 'colnames' on an object with less than two dimensions
--- failed re-building 'akc_vignette.Rmd'

--- re-building 'tutorial_raw_text.Rmd' using rmarkdown
Quitting from lines 63-65 (tutorial_raw_text.Rmd) 
Error: processing vignette 'tutorial_raw_text.Rmd' failed with diagnostics:
attempt to set 'colnames' on an object with less than two dimensions
--- failed re-building 'tutorial_raw_text.Rmd'

SUMMARY: processing the following files failed:
  'akc_vignette.Rmd' 'tutorial_raw_text.Rmd'

Error: Vignette re-building failed.
Execution halted
dke.fun.default: no visible global function definition for 'hist'
kef: no visible global function definition for 'dbinom'
kef: no visible global function definition for 'dgamma'
kef: no visible global function definition for 'dlnorm'
plot.dke.fun: no visible global function definition for 'hist'
plot.dke.fun: no visible global function definition for 'lines'
plot.hcvc.fun1d: no visible global function definition for
  'plot.default'
plot.hcvd.fun1d: no visible global function definition for
  'plot.default'
plot.kern.fun1d: no visible global function definition for
  'plot.default'
plot.kpmfe.fun1d: no visible global function definition for
  'plot.default'
plot.reg.fun1d: no visible global function definition for
  'plot.default'
simp_int: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx dbinom dgamma dlnorm hist lines plot.default
Consider adding
  importFrom("graphics", "hist", "lines", "plot.default")
  importFrom("stats", "approx", "dbinom", "dgamma", "dlnorm")
to your NAMESPACE file.
'library' or 'require' call to 'stats' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
akmeans: no visible global function definition for 'kmeans'
Undefined global functions or variables:
  kmeans
Consider adding
  importFrom("stats", "kmeans")
to your NAMESPACE file.
adpbar: no visible global function definition for 'optim'
alabama: no visible global function definition for 'optim'
auglag: no visible global function definition for 'modifyList'
auglag1: no visible global function definition for 'optim'
auglag1: no visible global function definition for 'nlminb'
auglag2: no visible global function definition for 'optim'
auglag2: no visible global function definition for 'nlminb'
auglag3: no visible global function definition for 'optim'
auglag3: no visible global function definition for 'nlminb'
augpen: no visible global function definition for 'optim'
constrOptim.nl: no visible global function definition for 'modifyList'
Undefined global functions or variables:
  modifyList nlminb optim
Consider adding
  importFrom("stats", "nlminb", "optim")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
batch.possSpells.fnc: no visible binding for global variable 'words'
possSpells.fnc: no visible binding for global variable 'len.phons'
possSpells.fnc: no visible binding for global variable 'phon1'
possSpells.fnc: no visible binding for global variable 'len.total'
possSpells.fnc: no visible binding for global variable 'poss.spells'
Undefined global functions or variables:
  len.phons len.total phon1 poss.spells words
ahull_track: no visible global function definition for 'psp'
ahull_track: no visible global function definition for 'owin'
ahull_track: no visible global function definition for
  'runifpointOnLines'
dw_track: no visible global function definition for 'psp'
dw_track: no visible global function definition for 'owin'
dw_track: no visible global function definition for 'runifpointOnLines'
Undefined global functions or variables:
  owin psp runifpointOnLines
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
EXP.step: no visible global function definition for 'rgamma'
EXP.step: no visible global function definition for 'rnorm'
MAX.step: no visible global function definition for 'uniroot'
Norm.GMedian: no visible binding for global variable 'median'
RNASeq.Data.Gene: no visible binding for global variable 'quantile'
decom.initial: no visible global function definition for 'kmeans'
decom.initial: no visible global function definition for 'quantile'
decom.initial: no visible global function definition for 'var'
dispersion.nb.QL: no visible binding for global variable 'quantile'
est.mu.nb.mle: no visible global function definition for 'runif'
est.v.nb.QL: no visible global function definition for 'runif'
pdf2grid: no visible global function definition for 'dnorm'
pdf2grid: no visible global function definition for 'dgamma'
prior.grid: no visible global function definition for 'sd'
prior.grid: no visible global function definition for 'dnorm'
test.AMAP: no visible global function definition for 'rgamma'
test.AMAP: no visible global function definition for 'rnorm'
test.AMAP: no visible global function definition for 'quantile'
Undefined global functions or variables:
  dgamma dnorm kmeans median quantile rgamma rnorm runif sd uniroot var
Consider adding
  importFrom("stats", "dgamma", "dnorm", "kmeans", "median", "quantile",
             "rgamma", "rnorm", "runif", "sd", "uniroot", "var")
to your NAMESPACE file.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   8.2Mb
Malformed Title field: should not end in a period.
amltest: no visible global function definition for 'var'
amltest: no visible global function definition for 'optim'
amltest: no visible global function definition for 'lm'
cleanclust: no visible global function definition for 'cor'
cleanclust: no visible global function definition for 'hclust'
cleanclust: no visible global function definition for 'as.dist'
cleanclust: no visible global function definition for 'cutree'
Undefined global functions or variables:
  as.dist cor cutree hclust lm optim var
Consider adding
  importFrom("stats", "as.dist", "cor", "cutree", "hclust", "lm",
             "optim", "var")
to your NAMESPACE file.
AMOEBA : Classi: no visible global function definition for 'sd'
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    data   3.5Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
plottr: no visible global function definition for 'plot'
print.analyzerPlot: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Analyz.loadSteps,Analyz: no visible global function definition for
  'read.csv'
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'discretization' 'foreign' 'functional' 'stringr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
aode: no visible global function definition for 'Compose'
mdl: no visible global function definition for 'cutPoints'
setVar: no visible global function definition for 'Compose'
Undefined global functions or variables:
  Compose cutPoints
Malformed Description field: should contain one or more complete sentences.
andrews: no visible global function definition for 'plot.new'
andrews: no visible global function definition for 'plot.window'
andrews: no visible global function definition for 'title'
andrews: no visible global function definition for 'axis'
andrews: no visible global function definition for 'box'
andrews: no visible global function definition for 'lines'
andrews: no visible global function definition for 'rainbow'
andrews: no visible global function definition for 'hsv'
selectand: no visible global function definition for 'lines'
Undefined global functions or variables:
  axis box hsv lines plot.new plot.window rainbow title
Consider adding
  importFrom("grDevices", "hsv", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "title")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Missing or unexported object: 'grid::unitType'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs     4.2Mb
Malformed Title field: should not end in a period.
'library' or 'require' call to 'tcltk' which was already attached by Depends.
  Please remove these calls from your code.
annot : annotlist: no visible global function definition for
  'read.table'
annot : annotlist: no visible global function definition for
  'write.table'
annot: no visible global function definition for 'flush.console'
annot: no visible global function definition for 'read.table'
annot: no visible global function definition for 'choose.dir'
Undefined global functions or variables:
  choose.dir flush.console read.table write.table
Consider adding
  importFrom("utils", "choose.dir", "flush.console", "read.table",
             "write.table")
to your NAMESPACE file.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    libs   1.8Mb
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
aw_map: no visible global function definition for 'browseURL'
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
'library' or 'require' call to 'boot' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
varbin: no visible global function definition for 'boot'
Undefined global functions or variables:
  boot
Packages in Depends field not imported from:
  'boot' 'lme4'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 73.0Mb
  sub-directories of 1Mb or more:
    gdal   3.8Mb
    libs  68.8Mb
apci.plot.hexagram: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
apc.plot.data.sparsity : function.sparsity.plot: no visible global
  function definition for 'plot'
apc.plot.data.sums: no visible global function definition for 'plot'
apc.plot.fit : function.plot.est.sdv: no visible global function
  definition for 'plot'
apc.plot.fit.pt: no visible global function definition for 'plot'
new.apc.plot.fit : function.plot.est.sdv: no visible global function
  definition for 'plot'
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
runAPSIM: warning in scan(reports_file[i], "", sep = "", skip =
  length(temp), nline = 1): partial argument match of 'nline' to
  'nlines'
runAPSIM: no visible global function definition for 'write.table'
runAPSIM: no visible global function definition for 'read.table'
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    extdata   6.3Mb
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.
frag.graph.plot: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Running examples in 'ARCokrig-Ex.R' failed
The error most likely occurred in:

> ### Name: ARCokrig
> ### Title: Fit the AR-Cokriging model and make predictions
> ### Aliases: ARCokrig
> 
> ### ** Examples
> 
> 
> ##############################################################
> ##############################################################
> ############ Example
> Funcc = function(x){
+   return(0.5*(6*x-2)^2*sin(12*x-4)+10*(x-0.5)-5)
+ }
> 
> Funcf = function(x){
+   z1 = Funcc(x)
+   z2 = 2*z1-20*x+20 + sin(10*cos(5*x))
+   return(z2)
+ }
> 
> #####################################################################
> ###### Nested design 
> #####################################################################
> Dc <- seq(-1,1,0.1)
> indDf <- c(1, 3, 6, 8, 10, 13, 17, 21)
> zc <- Funcc(Dc)
> Df <- Dc[indDf]
> zf <- Funcf(Df)
> 
> input.new = as.matrix(seq(-1,1,length.out=200))
> 
> 
> ## fit and predict with the AR-Cokriging model
> 
> out = ARCokrig(formula=list(~1,~1+x1), output=list(c(zc), c(zf)),
+               input=list(as.matrix(Dc), as.matrix(Df)),
+               cov.model="matern_5_2",
+               input.new=input.new)
[1] "optimization error, skip t=1"
[1] "Error in chol.default(R) : \n  the leading minor of order 2 is not positive definite\n"
attr(,"class")
[1] "try-error"
attr(,"condition")
<simpleError in chol.default(R): the leading minor of order 2 is not positive definite>
[1] "optimization error, skip t=2"
[1] "Error in chol.default(R) : \n  the leading minor of order 2 is not positive definite\n"
attr(,"class")
[1] "try-error"
attr(,"condition")
<simpleError in chol.default(R): the leading minor of order 2 is not positive definite>
Error in chol.default(R) : 
  the leading minor of order 2 is not positive definite
Calls: ARCokrig -> cokm.predict -> chol -> chol.default
Execution halted
Running examples in 'ARCokrig-Ex.R' failed
The error most likely occurred in:

> ### Name: ARCokrig
> ### Title: Fit the AR-Cokriging model and make predictions
> ### Aliases: ARCokrig
> 
> ### ** Examples
> 
> 
> ##############################################################
> ##############################################################
> ############ Example
> Funcc = function(x){
+   return(0.5*(6*x-2)^2*sin(12*x-4)+10*(x-0.5)-5)
+ }
> 
> Funcf = function(x){
+   z1 = Funcc(x)
+   z2 = 2*z1-20*x+20 + sin(10*cos(5*x))
+   return(z2)
+ }
> 
> #####################################################################
> ###### Nested design 
> #####################################################################
> Dc <- seq(-1,1,0.1)
> indDf <- c(1, 3, 6, 8, 10, 13, 17, 21)
> zc <- Funcc(Dc)
> Df <- Dc[indDf]
> zf <- Funcf(Df)
> 
> input.new = as.matrix(seq(-1,1,length.out=200))
> 
> 
> ## fit and predict with the AR-Cokriging model
> 
> out = ARCokrig(formula=list(~1,~1+x1), output=list(c(zc), c(zf)),
+               input=list(as.matrix(Dc), as.matrix(Df)),
+               cov.model="matern_5_2",
+               input.new=input.new)
[1] "optimization error, skip t=1"
[1] "Error in chol.default(R) : \n  the leading minor of order 2 is not positive definite\n"
attr(,"class")
[1] "try-error"
attr(,"condition")
<simpleError in chol.default(R): the leading minor of order 2 is not positive definite>
[1] "optimization error, skip t=2"
[1] "Error in chol.default(R) : \n  the leading minor of order 2 is not positive definite\n"
attr(,"class")
[1] "try-error"
attr(,"condition")
<simpleError in chol.default(R): the leading minor of order 2 is not positive definite>
Error in chol.default(R) : 
  the leading minor of order 2 is not positive definite
Calls: ARCokrig -> cokm.predict -> chol -> chol.default
Execution halted
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ARCokrig)
  > 
  > test_check("ARCokrig")
  [1] "optimization error, skip t=1"
  [1] "Error in chol.default(R) : \n  the leading minor of order 2 is not positive definite\n"
  attr(,"class")
  [1] "try-error"
  attr(,"condition")
  <simpleError in chol.default(R): the leading minor of order 2 is not positive definite>
  [1] "optimization error, skip t=2"
  [1] "Error in chol.default(R) : \n  the leading minor of order 2 is not positive definite\n"
  attr(,"class")
  [1] "try-error"
  attr(,"condition")
  <simpleError in chol.default(R): the leading minor of order 2 is not positive definite>
  == Failed tests ================================================================
  -- Error (test_ARCokrig.R:28:1): (code run outside of `test_that()`) -----------
  Error: the leading minor of order 2 is not positive definite
  Backtrace:
      x
   1. \-ARCokrig::cokm.predict(obj, input.new) test_ARCokrig.R:28:0
   2.   +-base::chol(R)
   3.   \-base::chol.default(R)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ARCokrig)
  > 
  > test_check("ARCokrig")
  [1] "optimization error, skip t=1"
  [1] "Error in chol.default(R) : \n  the leading minor of order 2 is not positive definite\n"
  attr(,"class")
  [1] "try-error"
  attr(,"condition")
  <simpleError in chol.default(R): the leading minor of order 2 is not positive definite>
  [1] "optimization error, skip t=2"
  [1] "Error in chol.default(R) : \n  the leading minor of order 2 is not positive definite\n"
  attr(,"class")
  [1] "try-error"
  attr(,"condition")
  <simpleError in chol.default(R): the leading minor of order 2 is not positive definite>
  == Failed tests ================================================================
  -- Error (test_ARCokrig.R:28:1): (code run outside of `test_that()`) -----------
  Error: the leading minor of order 2 is not positive definite
  Backtrace:
      x
   1. \-ARCokrig::cokm.predict(obj, input.new) test_ARCokrig.R:28:0
   2.   +-base::chol(R)
   3.   \-base::chol.default(R)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted
'library' or 'require' call to 'stats' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
ardec: no visible global function definition for 'filter'
ardec.lm: no visible global function definition for 'ar'
ardec.lm: no visible global function definition for 'lm'
Undefined global functions or variables:
  ar filter lm
Consider adding
  importFrom("stats", "ar", "filter", "lm")
to your NAMESPACE file.
areabiplot: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   1.1Mb
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Package required and available but unsuitable version: 'stats4'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 28.8Mb
  sub-directories of 1Mb or more:
    R      3.4Mb
    libs  24.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.5Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    bin   12.0Mb
    misc   2.1Mb
Package suggested but not available for checking: 'REBayes'
signTest: no visible global function definition for 'deparse1'
Undefined global functions or variables:
  deparse1
Running examples in 'asht-Ex.R' failed
The error most likely occurred in:

> ### Name: signTest
> ### Title: Exact Sign Test with Confidence Intervals
> ### Aliases: signTest
> ### Keywords: htest
> 
> ### ** Examples
> 
> x<-c(rep(-1,10),rep(0,60),rep(1,30))
> signTest(x, stat='cd')
Error in deparse1(substitute(x)) : could not find function "deparse1"
Calls: signTest
Execution halted
'library' or 'require' calls to packages already attached by Depends:
  'Hmisc' 'splancs'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Hmisc' 'shapefiles' 'splancs'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ASP.Score: no visible global function definition for 'pnorm'
Graphs.Bayesian: no visible global function definition for 'dev.new'
colorhex: no visible global function definition for 'gray'
colorhex: no visible global function definition for 'rgb'
Undefined global functions or variables:
  dev.new gray pnorm rgb
Consider adding
  importFrom("grDevices", "dev.new", "gray", "rgb")
  importFrom("stats", "pnorm")
to your NAMESPACE file.
Package which this enhances but not available for checking: 'asreml'
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: 'mvtnorm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CALPHA: no visible global function definition for 'dbinom'
CALPHA: no visible global function definition for 'pchisq'
CAST: no visible global function definition for 'fisher.test'
CAST: no visible global function definition for 'chisq.test'
CMC: no visible global function definition for 'pf'
MULTI: no visible global function definition for 'complete.cases'
RVT1: no visible global function definition for 'pchisq'
RVT2: no visible global function definition for 'pchisq'
RWAS: no visible global function definition for 'pnorm'
SKAT: no visible global function definition for 'dbeta'
SKAT: no visible global function definition for 'pchisq'
TTEST: no visible global function definition for 'complete.cases'
TTEST: no visible global function definition for 'pf'
WST: no visible global function definition for 'mvfft'
WST: no visible global function definition for 'pnorm'
my_cmc_method: no visible global function definition for
  'complete.cases'
my_getUV: no visible global function definition for 'complete.cases'
my_orwss_method: no visible global function definition for 'sd'
my_rarecov_method: no visible global function definition for
  'chisq.test'
my_rbt_method: no visible global function definition for 'ppois'
my_score_method: no visible global function definition for 'pchisq'
my_ssu_method: no visible global function definition for 'pchisq'
my_ssuw_method: no visible global function definition for 'pchisq'
my_sum_method: no visible global function definition for 'pchisq'
my_uminp_method: no visible global function definition for 'pchisq'
my_uminp_method: no visible global function definition for 'pmvnorm'
Undefined global functions or variables:
  chisq.test complete.cases dbeta dbinom fisher.test mvfft pchisq pf
  pmvnorm pnorm ppois sd
Consider adding
  importFrom("stats", "chisq.test", "complete.cases", "dbeta", "dbinom",
             "fisher.test", "mvfft", "pchisq", "pf", "pnorm", "ppois",
             "sd")
to your NAMESPACE file.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
beamDiskOverlap: no visible global function definition for 'integrate'
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
fm_unred: no visible global function definition for 'spline'
galage: no visible global function definition for 'integrate'
lumdist: no visible global function definition for 'integrate'
Undefined global functions or variables:
  integrate spline
Consider adding
  importFrom("stats", "integrate", "spline")
to your NAMESPACE file.
VPC.graph : findQuantile: no visible global function definition for
  'quantile'
VPC.graph : findQuantileCI : <anonymous>: no visible global function
  definition for 'quantile'
asVPC.binW: no visible global function definition for 'median'
asVPC.binW : <anonymous>: no visible global function definition for
  'quantile'
asVPC.binW: no visible global function definition for 'quantile'
asVPC.distanceW: no visible global function definition for 'median'
asVPC.distanceW : <anonymous>: no visible global function definition
  for 'quantile'
asVPC.distanceW: no visible global function definition for 'quantile'
makeCOVbin: no visible global function definition for 'quantile'
makeCOVbin: no visible global function definition for 'median'
read_Simdata: no visible global function definition for 'read.table'
Undefined global functions or variables:
  median quantile read.table
Consider adding
  importFrom("stats", "median", "quantile")
  importFrom("utils", "read.table")
to your NAMESPACE file.
get.est.ATT: no visible global function definition for 'tail'
get.est.MT: no visible global function definition for 'tail'
get.est.simple: no visible global function definition for 'tail'
newton.r: no visible global function definition for 'tail'
plot.ATE: no visible global function definition for 'par'
plot.ATE: no visible global function definition for 'plot'
plot.ATE: no visible global function definition for 'axis'
plot.ATE: no visible global function definition for 'abline'
plot.ATE: no visible global function definition for 'lines'
plot.ATE: no visible global function definition for 'legend'
plot.ATE: no visible global function definition for 'points'
print.summary.ATE: no visible global function definition for
  'printCoefmat'
summary.ATE: no visible global function definition for 'qnorm'
summary.ATE: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline axis legend lines par plot pnorm points printCoefmat qnorm
  tail
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "points")
  importFrom("stats", "pnorm", "printCoefmat", "qnorm")
  importFrom("utils", "tail")
to your NAMESPACE file.
atmcmc : rmvtnorm: no visible global function definition for 'rnorm'
atmcmc: no visible global function definition for 'rnorm'
atmcmc: no visible global function definition for 'runif'
atmcmc: no visible global function definition for 'par'
atmcmc: no visible global function definition for 'lm'
atmcmc: no visible global function definition for 'lines'
atmcmc: no visible global function definition for 'var'
atmcmc: no visible global function definition for 'cov'
atmcmc: no visible global function definition for 'quantile'
atmcmc: no visible global function definition for 'sd'
plotmcmc: no visible global function definition for 'pdf'
plotmcmc: no visible global function definition for 'par'
plotmcmc: no visible global function definition for 'dev.new'
plotmcmc: no visible global function definition for 'png'
plotmcmc: no visible global function definition for 'hist'
plotmcmc: no visible global function definition for 'dev.off'
plotmcmc: no visible global function definition for 'plot'
plotmcmc: no visible global function definition for 'lines'
Undefined global functions or variables:
  cov dev.new dev.off hist lines lm par pdf plot png quantile rnorm
  runif sd var
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf", "png")
  importFrom("graphics", "hist", "lines", "par", "plot")
  importFrom("stats", "cov", "lm", "quantile", "rnorm", "runif", "sd",
             "var")
to your NAMESPACE file.
PlotAtm.lin : scale_image: no visible global function definition for
  'heat.colors'
PlotAtm.lin : scale_image: no visible global function definition for
  'par'
PlotAtm.lin : scale_image: no visible global function definition for
  'sd'
PlotAtm.lin : scale_image: no visible global function definition for
  'approx'
PlotAtm.lin : scale_image: no visible global function definition for
  'image'
PlotAtm.lin : scale_image: no visible global function definition for
  'axis'
PlotAtm.lin : scale_image: no visible global function definition for
  'mtext'
PlotAtm.lin: no visible global function definition for 'arrows'
PlotAtm.lin: no visible global function definition for 'text'
PlotAtm.lin: no visible global function definition for 'polygon'
sky.colors: no visible global function definition for 'rgb'
Undefined global functions or variables:
  approx arrows axis heat.colors image mtext par polygon rgb sd text
Consider adding
  importFrom("grDevices", "heat.colors", "rgb")
  importFrom("graphics", "arrows", "axis", "image", "mtext", "par",
             "polygon", "text")
  importFrom("stats", "approx", "sd")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
plot.AUC: no visible global function definition for 'plot'
plot.AUC: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines plot
Consider adding
  importFrom("graphics", "lines", "plot")
to your NAMESPACE file.
AUCRFcv: no visible global function definition for 'predict'
plot.AUCRF: no visible global function definition for 'par'
plot.AUCRF: no visible global function definition for 'dotchart'
plot.AUCRF: no visible global function definition for 'title'
plot.AUCRF: no visible global function definition for 'text'
Undefined global functions or variables:
  dotchart par predict text title
Consider adding
  importFrom("graphics", "dotchart", "par", "text", "title")
  importFrom("stats", "predict")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  'RJSONIO' 'hexbin' 'plotrix'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
audioHist: no visible global function definition for 'hist'
audioHist: no visible global function definition for 'rescale'
audioHist: no visible global function definition for 'toJSON'
audioScatter: no visible binding for global variable 'formula'
audioScatter: no visible global function definition for 'hexbinplot'
audioScatter: no visible global function definition for 'cor'
audioScatter: no visible global function definition for 'toJSON'
audioSplom: no visible global function definition for 'hexplom'
audioSplom: no visible binding for global variable 'BTY'
audioSplom: no visible binding for global variable 'panel.hexboxplot'
audioSplom: no visible global function definition for 'combn'
audioSplom : <anonymous>: no visible global function definition for
  'cor'
audioSplom : <anonymous>: no visible global function definition for
  'toJSON'
audiolyzRcheck: no visible global function definition for
  'download.file'
audiolyzRcheck: no visible global function definition for 'unzip'
matricize: no visible global function definition for 'hexbin'
panel.audiolyzR: no visible global function definition for
  'panel.hexbinplot'
Undefined global functions or variables:
  BTY combn cor download.file formula hexbin hexbinplot hexplom hist
  panel.hexbinplot panel.hexboxplot rescale toJSON unzip
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "cor", "formula")
  importFrom("utils", "combn", "download.file", "unzip")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
simulateD: no visible global function definition for 'rgamma'
simulateT: no visible global function definition for 'runif'
simulateT: no visible global function definition for 'rbeta'
simulateT: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  rbeta rbinom rgamma runif
Consider adding
  importFrom("stats", "rbeta", "rbinom", "rgamma", "runif")
to your NAMESPACE file.
Package which this enhances but not available for checking: 'rPython'
'library' or 'require' calls in package code:
  'ggplot2' 'gpclib' 'maptools'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
gLog.ep: no visible global function definition for 'quantile'
gedestp: no visible global function definition for 'na.omit'
gedestp: no visible global function definition for 'optim'
gets.mean: no visible global function definition for 'start'
gets.mean: no visible global function definition for 'end'
gets.mean: no visible global function definition for 'window'
gets.mean: no visible global function definition for 'pt'
gets.mean: no visible global function definition for 'Box.test'
gets.mean: no visible global function definition for 'pchisq'
gets.vol: no visible global function definition for 'start'
gets.vol: no visible global function definition for 'end'
gets.vol: no visible global function definition for 'window'
gets.vol: no visible global function definition for 'pt'
gets.vol: no visible global function definition for 'Box.test'
gets.vol: no visible global function definition for 'pchisq'
jb.test: no visible global function definition for 'pchisq'
skewness.test: no visible global function definition for 'pchisq'
sm: no visible global function definition for 'start'
sm: no visible global function definition for 'end'
sm: no visible global function definition for 'window'
sm: no visible global function definition for 'pt'
sm: no visible global function definition for 'pchisq'
sm: no visible global function definition for 'Box.test'
Undefined global functions or variables:
  Box.test end na.omit optim pchisq pt quantile start window
Consider adding
  importFrom("stats", "Box.test", "end", "na.omit", "optim", "pchisq",
             "pt", "quantile", "start", "window")
to your NAMESPACE file.
Package required and available but unsuitable version: 'parallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 56.6Mb
  sub-directories of 1Mb or more:
    libs  55.8Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
Running examples in 'AWR.Kinesis-Ex.R' failed
The error occurred in:


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> pkgname <- "AWR.Kinesis"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> options(pager = "console")
> library('AWR.Kinesis')
> 
> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
> base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
> cleanEx()
Error: connections left open:
	stdin (file)
Execution halted
installed size is 67.2Mb
  sub-directories of 1Mb or more:
    java  67.2Mb
CRexp_set: no visible global function definition for 'runif'
b6e6rl: no visible global function definition for 'runif'
derand_RL: no visible global function definition for 'runif'
derandexp_RL: no visible global function definition for 'runif'
nahvyb_expt: no visible global function definition for 'runif'
roulete: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
.generateTransform: no visible global function definition for 'sd'
.generateUnitHyperCube: no visible global function definition for
  'runif'
.makeBoundedSingleStep: no visible global function definition for
  'runif'
.makeBoundedStep: no visible global function definition for 'runif'
.makeStep: no visible global function definition for 'runif'
.staircaseSampling: no visible global function definition for 'runif'
GaussianPrior: no visible global function definition for 'qnorm'
LogNormalPrior: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  qnorm runif sd
Consider adding
  importFrom("stats", "qnorm", "runif", "sd")
to your NAMESPACE file.
Error(s) in re-building vignettes:
--- re-building 'babsim-vignette-introduction.Rmd' using rmarkdown
Quitting from lines 618-626 (babsim-vignette-introduction.Rmd) 
Error: processing vignette 'babsim-vignette-introduction.Rmd' failed with diagnostics:
'origin' must be supplied
--- failed re-building 'babsim-vignette-introduction.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   1.8Mb
Running examples in 'backbone-Ex.R' failed
The error most likely occurred in:

> ### Name: backbone.extract
> ### Title: Extracts the backbone of a weighted network using results from a
> ###   null model
> ### Aliases: backbone.extract
> 
> ### ** Examples
> 
> probs <- sdsm(davis)
This matrix object looks like an unweighted bipartite network of 18 agents and 14 artifacts.
> bb <- backbone.extract(probs, alpha = .2, signed = TRUE, fwer = "none")
Error in frommatrix(backbone, class[1]) : object 'G' not found
Calls: backbone.extract -> frommatrix
Execution halted
BACprior.CV: no visible global function definition for 'na.fail'
BACprior.CV: no visible global function definition for 'plot'
BACprior.CV: no visible global function definition for 'abline'
BACprior.boot: no visible global function definition for 'na.fail'
BACprior.boot: no visible global function definition for 'plot'
BACprior.boot: no visible global function definition for 'abline'
BACprior.lm: no visible global function definition for 'na.fail'
BACprior.lm: no visible global function definition for 'coef'
BACprior.lm: no visible global function definition for 'vcov'
Undefined global functions or variables:
  abline coef na.fail plot vcov
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("stats", "coef", "na.fail", "vcov")
to your NAMESPACE file.
'library' or 'require' call to 'mvtnorm' which was already attached by Depends.
  Please remove these calls from your code.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
GNU make is a SystemRequirements.
Unexported objects imported by ':::' calls:
  'erah:::avoid.processing' 'erah:::convertMSPspectra'
  'erah:::convertMSPspectra.dot' 'erah:::getC.rq' 'erah:::getS.OSD'
  'erah:::load.file' 'erah:::pre.process' 'erah:::sparse.to.vector'
  See the note in ?`:::` about the use of this operator.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     2.4Mb
    doc   1.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
best_binomial_bandit : f: no visible global function definition for
  'dbeta'
best_binomial_bandit : f: no visible global function definition for
  'pbeta'
best_binomial_bandit: no visible global function definition for
  'integrate'
best_poisson_bandit : f: no visible global function definition for
  'dgamma'
best_poisson_bandit : f: no visible global function definition for
  'pgamma'
best_poisson_bandit: no visible global function definition for
  'integrate'
deseasonalized_trend: no visible global function definition for
  'predict'
distribution_estimate: no visible global function definition for
  'quantile'
distribution_estimate: no visible global function definition for
  'qbeta'
significance_analysis: no visible global function definition for
  'prop.test'
sim_post: no visible global function definition for 'rbeta'
summarize_metrics: no visible global function definition for 'median'
summarize_metrics: no visible global function definition for
  'prop.test'
Undefined global functions or variables:
  dbeta dgamma integrate median pbeta pgamma predict prop.test qbeta
  quantile rbeta
Consider adding
  importFrom("stats", "dbeta", "dgamma", "integrate", "median", "pbeta",
             "pgamma", "predict", "prop.test", "qbeta", "quantile",
             "rbeta")
to your NAMESPACE file.
Running examples in 'banter-Ex.R' failed
The error most likely occurred in:

> ### Name: plotDetectorTrace
> ### Title: Plot BANTER Detector Traces
> ### Aliases: plotDetectorTrace
> 
> ### ** Examples
> 
> data(train.data)
> # initialize BANTER model with event data
> bant.mdl <- initBanterModel(train.data$events)
> # add all detector models
> bant.mdl <- addBanterDetector(
+   bant.mdl, train.data$detectors, 
+   ntree = 50, sampsize = 1, num.cores = 1
+ )
> 
> plotDetectorTrace(bant.mdl)
Error: object 'as.data.frame.ppp' is not exported by 'namespace:spatstat'
Execution halted
extractAffybatch: no visible global function definition for 'new'
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' calls to packages already attached by Depends:
  'grid' 'lattice'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'grid' 'lattice'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
barcode: no visible global function definition for 'unit'
barcode: no visible global function definition for 'grid.newpage'
barcode: no visible global function definition for 'grid.text'
barcode: no visible global function definition for 'gpar'
barcode: no visible global function definition for 'pushViewport'
barcode: no visible global function definition for 'viewport'
barcode: no visible global function definition for 'convertHeight'
barcode: no visible global function definition for 'convertWidth'
barcode: no visible global function definition for 'grid.rect'
barcode: no visible global function definition for 'popViewport'
barcode.panel: no visible global function definition for 'unit'
barcode.panel: no visible global function definition for 'hist'
barcode.panel: no visible global function definition for 'pushViewport'
barcode.panel: no visible global function definition for 'viewport'
barcode.panel: no visible global function definition for 'grid.xaxis'
barcode.panel: no visible global function definition for 'gpar'
barcode.panel: no visible global function definition for 'grid.text'
barcode.panel: no visible global function definition for 'popViewport'
barcode.panel: no visible global function definition for
  'grid.segments'
barcode.panel: no visible global function definition for 'grid.points'
Undefined global functions or variables:
  convertHeight convertWidth gpar grid.newpage grid.points grid.rect
  grid.segments grid.text grid.xaxis hist popViewport pushViewport unit
  viewport
Consider adding
  importFrom("graphics", "hist")
to your NAMESPACE file.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.9Mb
Running 'spelling.R' [0s]
  Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(BaseSet)
  
  Attaching package: 'BaseSet'
  
  The following object is masked from 'package:stats':
  
      filter
  
  The following object is masked from 'package:base':
  
      union
  
  > 
  > test_check("BaseSet")
  == Failed tests ================================================================
  -- Failure (test-element_size.R:18:5): element_size works ----------------------
  nrow(out) not equal to 2L.
  1/1 mismatches
  [1] 7 - 2 == 5
  -- Failure (test-element_size.R:19:5): element_size works ----------------------
  out$size not equal to c(0, 1).
  Lengths differ: 7 is not 2
  -- Failure (test-pull.R:29:5): pull works --------------------------------------
  `out` not equal to c("a", "b", "a2", "b2").
  'current' is not a factor
  -- Failure (test-pull.R:59:5): pull uses active --------------------------------
  `out` not equal to c("a", "b", "a2", "b2").
  'current' is not a factor
  
  [ FAIL 4 | WARN 0 | SKIP 0 | PASS 407 ]
  Error: Test failures
  Execution halted
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.
Packages which this enhances but not available for checking:
  'doMC', 'rPython'
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(batata)
  > 
  > test_check("batata")
  == Skipped tests ===============================================================
  * On CRAN (1)
  
  == Failed tests ================================================================
  -- Failure (test-test-latest-packages.R:87:3): the first column of latest_packages() is of type character --
  data$packages has type 'integer', not 'character'.
  
  [ FAIL 1 | WARN 0 | SKIP 1 | PASS 40 ]
  Error: Test failures
  Execution halted
Package suggested but not available for checking: 'doMC'
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
--- re-building 'adaptation_level.Rmd' using rmarkdown
Loading required package: Rcpp

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 83-85 (adaptation_level.Rmd) 
Error: processing vignette 'adaptation_level.Rmd' failed with diagnostics:
result would be too long a vector
--- failed re-building 'adaptation_level.Rmd'

--- re-building 'afterimages.Rmd' using rmarkdown
Loading required package: Rcpp

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

--- finished re-building 'afterimages.Rmd'

--- re-building 'flanker.Rmd' using rmarkdown
Loading required package: Rcpp

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

--- finished re-building 'flanker.Rmd'

--- re-building 'stroop.Rmd' using rmarkdown
Loading required package: Rcpp
Scale for 'fill' is already present. Adding another scale for 'fill', which will replace the existing scale.
--- finished re-building 'stroop.Rmd'

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

Error: Vignette re-building failed.
Execution halted
GNU make is a SystemRequirements.
FECRT: no visible global function definition for 'pdf'
FECRT: no visible global function definition for 'hist'
FECRT: no visible global function definition for 'abline'
FECRT: no visible global function definition for 'dev.off'
FECRT.analysis: no visible global function definition for 'pdf'
FECRT.analysis: no visible global function definition for 'hist'
FECRT.analysis: no visible global function definition for 'abline'
FECRT.analysis: no visible global function definition for 'dev.off'
fecrt: no visible global function definition for 'pdf'
fecrt: no visible global function definition for 'hist'
fecrt: no visible global function definition for 'abline'
fecrt: no visible global function definition for 'dev.off'
fecrt.analysis: no visible global function definition for 'pdf'
fecrt.analysis: no visible global function definition for 'hist'
fecrt.analysis: no visible global function definition for 'abline'
fecrt.analysis: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  abline dev.off hist pdf
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "hist")
to your NAMESPACE file.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
GNU make is a SystemRequirements.
Package suggested but not available for checking: 'doMC'
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs   2.1Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
GNU make is a SystemRequirements.
BMAnimalTrack: no visible global function definition for 'nlm'
BMAnimalTrack: no visible global function definition for 'qnorm'
dataSim: no visible global function definition for 'rnorm'
rBBridge: no visible global function definition for 'rnorm'
rBMotion: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  nlm qnorm rnorm
Consider adding
  importFrom("stats", "nlm", "qnorm", "rnorm")
to your NAMESPACE file.
Package suggested but not available for checking: 'BBcor'
NeedsCompilation field should likely be 'yes'
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   4.1Mb
Package suggested but not available for checking: 'cyjShiny'
Malformed Description field: should contain one or more complete sentences.
noninform_prior : a : f1: no visible global function definition for
  'pbeta'
noninform_prior : a : f1: no visible global function definition for
  'dbeta'
noninform_prior : a: no visible global function definition for
  'integrate'
noninform_prior: no visible global function definition for 'rbeta'
noninform_prior: no visible global function definition for 'optim'
postNullFun : b : f1: no visible global function definition for 'pbeta'
postNullFun : b : f1: no visible global function definition for 'dbeta'
postNullFun : b: no visible global function definition for 'integrate'
prior_prob : a : f1: no visible global function definition for 'pbeta'
prior_prob : a : f1: no visible global function definition for 'dbeta'
prior_prob : a: no visible global function definition for 'integrate'
Undefined global functions or variables:
  dbeta integrate optim pbeta rbeta
Consider adding
  importFrom("stats", "dbeta", "integrate", "optim", "pbeta", "rbeta")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   3.4Mb
plot.mcmcRocPrc: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
MHratioPopPref: no visible global function definition for 'runif'
MratioPopMult: no visible global function definition for 'dunif'
MratioPopMult: no visible global function definition for 'runif'
bayesPref: no visible global function definition for 'runif'
calcP: no visible global function definition for 'dunif'
calcP: no visible global function definition for 'dmultinom'
calcdic: no visible global function definition for 'median'
calcdic: no visible binding for global variable 'median'
calcdic: no visible global function definition for 'dmultinom'
calcdicExtern: no visible global function definition for 'median'
calcdicExtern: no visible global function definition for 'dmultinom'
calcdicExtern: no visible binding for global variable 'median'
credibleIntervals: no visible global function definition for 'quantile'
prefPlot: no visible global function definition for 'postscript'
prefPlot: no visible global function definition for 'plot'
prefPlot: no visible global function definition for 'lines'
prefPlot: no visible global function definition for 'density'
prefPlot: no visible global function definition for 'median'
prefPlot: no visible global function definition for 'legend'
prefPlot: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  density dev.off dmultinom dunif legend lines median plot postscript
  quantile runif
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "density", "dmultinom", "dunif", "median",
             "quantile", "runif")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'MASS' 'combinat' 'gplots' 'mnormt'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.8Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    7.2Mb
    help   1.3Mb
validate: no visible binding for global variable 'qnorm'
validate: no visible global function definition for 'pchisq'
validate: no visible global function definition for 'qnorm'
validate: no visible global function definition for 'plot'
validate: no visible global function definition for 'axis'
validate: no visible global function definition for 'points'
validate: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline axis pchisq plot points qnorm
Consider adding
  importFrom("graphics", "abline", "axis", "plot", "points")
  importFrom("stats", "pchisq", "qnorm")
to your NAMESPACE file.
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    libs  23.7Mb
GNU make is a SystemRequirements.
'library' or 'require' call to 'coda' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'fields' 'poibin' 'rjags'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
BMR.plot: no visible global function definition for 'heat.colors'
BMR.plot: no visible global function definition for 'image.plot'
BMR.plot: no visible global function definition for 'title'
BMR.plot: no visible global function definition for 'mtext'
BMR.plot: no visible global function definition for 'par'
baysic.data: no visible global function definition for 'layout'
baysic.data: no visible global function definition for 'barplot'
baysic.data: no visible global function definition for 'rainbow'
baysic.fit: no visible global function definition for 'jags.model'
baysic.fit: no visible global function definition for 'update'
baysic.fit: no visible global function definition for 'coda.samples'
baysic.test: no visible global function definition for 'ppois'
baysic.test : <anonymous>: no visible global function definition for
  'ppoibin'
baysic.test: no visible global function definition for 'pbinom'
fuzzy.FDR.approx: no visible global function definition for 'p.adjust'
fuzzy.FDR.approx: no visible global function definition for 'runif'
Undefined global functions or variables:
  barplot coda.samples heat.colors image.plot jags.model layout mtext
  p.adjust par pbinom ppoibin ppois rainbow runif title update
Consider adding
  importFrom("grDevices", "heat.colors", "rainbow")
  importFrom("graphics", "barplot", "layout", "mtext", "par", "title")
  importFrom("stats", "p.adjust", "pbinom", "ppois", "runif", "update")
to your NAMESPACE file.
BAYSTAR: no visible global function definition for 'median'
BAYSTAR: no visible global function definition for 'ar'
BAYSTAR: no visible global function definition for 'quantile'
BAYSTAR: no visible global function definition for 'dev.new'
BAYSTAR: no visible global function definition for 'ts.plot'
BAYSTAR: no visible global function definition for 'title'
BAYSTAR: no visible global function definition for 'par'
BAYSTAR: no visible global function definition for 'plot.ts'
BAYSTAR: no visible global function definition for 'lines'
BAYSTAR: no visible global function definition for 'acf'
TAR.lagd: no visible global function definition for 'runif'
TAR.sigma: no visible global function definition for 'rgamma'
TAR.simu: no visible global function definition for 'rnorm'
TAR.summary: no visible global function definition for 'quantile'
TAR.summary: no visible global function definition for 'sd'
TAR.thres: no visible global function definition for 'rnorm'
TAR.thres: no visible global function definition for 'runif'
Undefined global functions or variables:
  acf ar dev.new lines median par plot.ts quantile rgamma rnorm runif
  sd title ts.plot
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "lines", "par", "title")
  importFrom("stats", "acf", "ar", "median", "plot.ts", "quantile",
             "rgamma", "rnorm", "runif", "sd", "ts.plot")
to your NAMESPACE file.
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(baytrends)
  Loading required package: lubridate
  
  Attaching package: 'lubridate'
  
  The following objects are masked from 'package:base':
  
      date, intersect, setdiff, union
  
  Loading:baytrends v2.0.2
  
  Attaching package: 'baytrends'
  
  The following object is masked from 'package:stats':
  
      nobs
  
  > 
  > test_check("baytrends")
  == Failed tests ================================================================
  -- Failure (test-makeSurvDF.R:16:3): makeSurvDF, colnames default --------------
  colnames(df2) not equal to `qc_col`.
  Lengths differ: 35 is not 17
  -- Failure (test-makeSurvDF.R:34:3): makeSurvDF, colnames user -----------------
  colnames(df4) not equal to `qc_col`.
  Lengths differ: 35 is not 17
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 12 ]
  Error: Test failures
  Execution halted
Package in Depends field not imported from: 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Malformed Description field: should contain one or more complete sentences.
LaplaceMetropolis_admkr: no visible binding for global variable
  'median'
LaplaceMetropolis_admkr: no visible global function definition for
  'mad'
LaplaceMetropolis_gaussian: no visible binding for global variable
  'median'
LaplaceMetropolis_gaussian: no visible global function definition for
  'mad'
cost_admkr: no visible global function definition for 'sd'
cov_chol: no visible global function definition for 'qchisq'
cov_chol_admkr: no visible global function definition for 'qchisq'
gibbs_admkr_erro: no visible global function definition for 'rnorm'
gibbs_admkr_erro: no visible global function definition for 'runif'
gibbs_admkr_nw: no visible global function definition for 'qnorm'
gibbs_admkr_nw: no visible global function definition for 'rnorm'
gibbs_admkr_nw: no visible global function definition for 'runif'
loglikelihood_admkr: no visible global function definition for 'sd'
margin_like_admkr: no visible global function definition for 'sd'
np_gibbs: no visible global function definition for 'qnorm'
np_gibbs: no visible global function definition for 'rnorm'
np_gibbs: no visible global function definition for 'runif'
np_gibbs: no visible global function definition for 'rgamma'
Undefined global functions or variables:
  mad median qchisq qnorm rgamma rnorm runif sd
Consider adding
  importFrom("stats", "mad", "median", "qchisq", "qnorm", "rgamma",
             "rnorm", "runif", "sd")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      2.3Mb
bbmm.contour: no visible global function definition for 'na.omit'
bbmm.contour: no visible global function definition for 'optimize'
bbmm.contour: no visible global function definition for 'contour'
bbmm.contour: no visible global function definition for 'points'
bbmm.contour: no visible global function definition for 'lines'
brownian.bridge: no visible global function definition for 'sd'
brownian.motion.variance: no visible global function definition for
  'optimize'
Undefined global functions or variables:
  contour lines na.omit optimize points sd
Consider adding
  importFrom("graphics", "contour", "lines", "points")
  importFrom("stats", "na.omit", "optimize", "sd")
to your NAMESPACE file.
bbo: no visible global function definition for 'runif'
bbo: no visible global function definition for 'tail'
plot.bbo: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot runif tail
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
  importFrom("utils", "tail")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to 'rgl' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
pairs.bce : panel.cor: no visible global function definition for 'text'
pairs.bce : panel.cor: no visible global function definition for 'cor'
pairs.bce : panel.hist: no visible global function definition for 'par'
pairs.bce : panel.hist: no visible global function definition for
  'hist'
pairs.bce : panel.hist: no visible global function definition for
  'rect'
pairs.bce: no visible global function definition for 'pairs'
panel.cor: no visible global function definition for 'par'
panel.cor: no visible global function definition for 'cor'
panel.cor: no visible global function definition for 'strwidth'
panel.cor: no visible global function definition for 'text'
rdirichlet2: no visible global function definition for 'rgamma'
summary.bce: no visible global function definition for 'cov'
summary.bce: no visible binding for global variable 'sd'
summary.bce: no visible binding for global variable 'quantile'
Undefined global functions or variables:
  cor cov hist pairs par quantile rect rgamma sd strwidth text
Consider adding
  importFrom("graphics", "hist", "pairs", "par", "rect", "strwidth",
             "text")
  importFrom("stats", "cor", "cov", "quantile", "rgamma", "sd")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'kBET', 'lisi', 'harmony', 'dlfUtils'
mise: no visible global function definition for 'integrate'
density,BrVitale : density.vitale : <anonymous>: no visible global
  function definition for 'dbeta'
density,Chen99Kernel : <anonymous>: no visible global function
  definition for 'dbeta'
density,HirukawaJLNKernel : <anonymous>: no visible global function
  definition for 'dbeta'
density,MicroBetaChen99Kernel : <anonymous>: no visible global function
  definition for 'dbeta'
density,Vitale : <anonymous>: no visible global function definition for
  'dbeta'
distribution,BernsteinPolynomials : <anonymous>: no visible global
  function definition for 'integrate'
distribution,KernelDensity : <anonymous>: no visible global function
  definition for 'integrate'
print,BoundedDensity: no visible global function definition for 'str'
print,KernelDensity: no visible global function definition for 'str'
rsample,BoundedDensity: no visible global function definition for
  'runif'
setNormalizationConst,MacroBetaChen99Kernel: no visible global function
  definition for 'integrate'
setNormalizationConst,MacroBetaHirukawaTSKernel: no visible global
  function definition for 'integrate'
setNormalizationConstant,MacroBetaHirukawaJLNKernel: no visible global
  function definition for 'integrate'
setNormalizationConstants,MicroBetaChen99Kernel :
  density.kernelFunction: no visible global function definition for
  'dbeta'
setNormalizationConstants,MicroBetaChen99Kernel : <anonymous>: no
  visible global function definition for 'integrate'
show,BoundedDensity: no visible global function definition for 'str'
show,KernelDensity: no visible global function definition for 'str'
Undefined global functions or variables:
  dbeta integrate runif str
Consider adding
  importFrom("stats", "dbeta", "integrate", "runif")
  importFrom("utils", "str")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'RColorBrewer' 'beadarray'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
beadtypeFilter: no visible global function definition for 'na.omit'
beadtypeFilter: no visible global function definition for 'exprs'
beadtypeFilter: no visible global function definition for 'se.exprs'
beadtypeFilter: no visible global function definition for 'beadNum'
beadtypeFilter: no visible global function definition for 'fData'
emCDF: no visible global function definition for 'brewer.pal'
emCDF: no visible global function definition for 'plot'
emCDF: no visible global function definition for 'ecdf'
emCDF: no visible global function definition for 'legend'
emCDF: no visible global function definition for 'lines'
emCDF: no visible global function definition for 'text'
emCDF: no visible global function definition for 'reshape'
iccFun : <anonymous>: no visible global function definition for
  'quantile'
varianceplot: no visible global function definition for 'reshape'
varianceplot: no visible global function definition for 'plot'
varianceplot: no visible global function definition for 'points'
varianceplot: no visible global function definition for 'legend'
Undefined global functions or variables:
  beadNum brewer.pal ecdf exprs fData legend lines na.omit plot points
  quantile reshape se.exprs text
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points", "text")
  importFrom("stats", "ecdf", "na.omit", "quantile", "reshape")
to your NAMESPACE file.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
GNU make is a SystemRequirements.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
Error(s) in re-building vignettes:
--- re-building 'belg1.Rmd' using rmarkdown
Quitting from lines 13-32 (belg1.Rmd) 
Error: processing vignette 'belg1.Rmd' failed with diagnostics:
package 'lattice' 0.20.38 was found, but >= 0.20.41 is required by 'rasterVis'
--- failed re-building 'belg1.Rmd'

SUMMARY: processing the following file failed:
  'belg1.Rmd'

Error: Vignette re-building failed.
Execution halted
GNU make is a SystemRequirements.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   2.2Mb
betafam: no visible global function definition for 'pnorm'
betafam: no visible global function definition for 'pchisq'
betafam: no visible global function definition for 'lm'
betafam: no visible global function definition for 'coefficients'
betafam: no visible global function definition for 'glm.fit'
betafam: no visible global function definition for 'gaussian'
betafam: no visible global function definition for 'glmnet'
Undefined global functions or variables:
  coefficients gaussian glm.fit glmnet lm pchisq pnorm
Consider adding
  importFrom("stats", "coefficients", "gaussian", "glm.fit", "lm",
             "pchisq", "pnorm")
to your NAMESPACE file.
Checking should be performed on sources prepared by 'R CMD build'.
Malformed Title field: should not end in a period.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   1.1Mb
    libs   2.4Mb
block.gibbs: no visible global function definition for 'rmultinom'
rdirichlet: no visible global function definition for 'rgamma'
Undefined global functions or variables:
  rgamma rmultinom
Consider adding
  importFrom("stats", "rgamma", "rmultinom")
to your NAMESPACE file.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.0Mb
Malformed Description field: should contain one or more complete sentences.
global: no visible global function definition for 'par'
global: no visible global function definition for 'runif'
global: no visible global function definition for 'cov'
mymcmc: no visible global function definition for 'par'
mymcmc: no visible global function definition for 'rnorm'
mymcmc: no visible global function definition for 'runif'
mymcmc: no visible global function definition for 'cov'
mymcmc: no visible global function definition for 'lines'
plkhci: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  cov lines par qchisq rnorm runif
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "cov", "qchisq", "rnorm", "runif")
to your NAMESPACE file.
installed size is 145.8Mb
  sub-directories of 1Mb or more:
    include  144.8Mb
Package in Depends field not imported from: 'betareg'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bias: no visible global function definition for 'predict'
bias: no visible global function definition for 'pnorm'
bias: no visible global function definition for 'model.matrix'
Undefined global functions or variables:
  model.matrix pnorm predict
Consider adding
  importFrom("stats", "model.matrix", "pnorm", "predict")
to your NAMESPACE file.
Package required and available but unsuitable version: 'graphics'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   1.9Mb
    libs      1.7Mb
GNU make is a SystemRequirements.
Checking should be performed on sources prepared by 'R CMD build'.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      3.2Mb
Packages in Depends field not imported from:
  'gbm' 'glmnet' 'randomForest' 'tree'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
LDCAEst: no visible global function definition for 'glmnet'
cv.LDCA: no visible global function definition for 'cv.glmnet'
predict.LDCA: no visible global function definition for 'predict'
predict.cv.LDCA: no visible global function definition for 'predict'
predict.tsp.gbm: no visible global function definition for 'predict'
predict.tsp.randomForest: no visible global function definition for
  'predict'
predict.tsp.tree: no visible global function definition for 'predict'
tsp.gbm: no visible global function definition for 'gbm.fit'
tsp.randomForest: no visible global function definition for
  'randomForest'
tsp.tree: no visible global function definition for 'tree.control'
tsp.tree: no visible global function definition for 'tree'
Undefined global functions or variables:
  cv.glmnet gbm.fit glmnet predict randomForest tree tree.control
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
chisq.sim.factory : chisq.sim.func: no visible global function
  definition for 'chisq.test'
rmultnom: no visible global function definition for 'runif'
Undefined global functions or variables:
  chisq.test runif
Consider adding
  importFrom("stats", "chisq.test", "runif")
to your NAMESPACE file.
bin_ps: no visible global function definition for 'runif'
bin_ps: no visible global function definition for 'dbinom'
draw_i: no visible global function definition for 'runif'
Undefined global functions or variables:
  dbinom runif
Consider adding
  importFrom("stats", "dbinom", "runif")
to your NAMESPACE file.
IndivdRUMIndMH: no visible global function definition for
  'flush.console'
dRUMAuxMix: no visible global function definition for 'flush.console'
dRUMHAM: no visible global function definition for 'flush.console'
dRUMIndMH: no visible global function definition for 'flush.console'
print.binomlogit: no visible global function definition for 'is'
summary.binomlogit: no visible global function definition for 'is'
Undefined global functions or variables:
  flush.console is
Consider adding
  importFrom("methods", "is")
  importFrom("utils", "flush.console")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls in package code:
  'ggplot2' 'lattice' 'polynom' 'tcltk'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
bins.quantiles: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
plot.binseg_normal: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   1.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
Found the following significant warnings:
  Warning: namespace 'Rcpp' is not available and has been replaced
See 'd:/Rcompile/CRANpkg/local/3.6/bioimagetools.Rcheck/00install.out' for details.
mlsolve: no visible global function definition for 'plot'
view.te: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
describeRNA: no visible global function definition for 'plot'
revealRNA: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
'library' or 'require' call to 'MGRASTer' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.onAttach: no visible global function definition for 'packageVersion'
biom.matrix: no visible global function definition for 'packageVersion'
Undefined global functions or variables:
  packageVersion
Consider adding
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    doc       1.2Mb
    extdata   1.7Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Depends: includes the non-default packages:
  'colorspace', 'deldir', 'rgl', 'tcltk', 'tcltk2', 'tkrplot'
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:
  'colorspace'
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  'deldir' 'rgl' 'tcltk' 'tcltk2' 'tkrplot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
biwt.cor: no visible global function definition for 'covMcd'
biwt.cor: no visible binding for global variable 'mad'
biwt.est: no visible global function definition for 'covMcd'
biwt.est: no visible global function definition for 'mahalanobis'
chi.int: no visible global function definition for 'pchisq'
chi.int.p: no visible global function definition for 'dchisq'
chi.int2: no visible global function definition for 'pchisq'
chi.int2.p: no visible global function definition for 'dchisq'
rejpt.bw: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  covMcd dchisq mad mahalanobis pchisq
Consider adding
  importFrom("stats", "dchisq", "mad", "mahalanobis", "pchisq")
to your NAMESPACE file.
Running examples in 'blandr-Ex.R' failed
The error most likely occurred in:

> ### Name: blandr.dataset.fibre
> ### Title: Function to load D'arbela mean velocity of circumferential fibre
> ###   shortening dataset from internet
> ### Aliases: blandr.dataset.fibre
> 
> ### ** Examples
> 
> blandr.dataset.fibre()
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in file(con, "r") : cannot open the connection
Calls: blandr.dataset.fibre -> readLines -> file
Execution halted
install_blat: no visible global function definition for 'download.file'
install_blat: no visible global function definition for 'unzip'
Undefined global functions or variables:
  download.file unzip
Consider adding
  importFrom("utils", "download.file", "unzip")
to your NAMESPACE file.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
GNU make is a SystemRequirements.
hhj: no visible global function definition for 'plot'
plot.pwsd: no visible global function definition for 'plot'
pwsd: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Missing link or links in documentation object 'plot.hhj.Rd':
  '[base:plot]{base::plot}'

Missing link or links in documentation object 'plot.pwsd.Rd':
  '[base:plot]{base::plot}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
Malformed Description field: should contain one or more complete sentences.
blockMessage : <anonymous>: no visible global function definition for
  'head'
blockMessage: no visible global function definition for 'head'
blockMessage: no visible global function definition for 'tail'
Undefined global functions or variables:
  head tail
Consider adding
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Running examples in 'blscrapeR-Ex.R' failed
The error most likely occurred in:

> ### Name: inflation_adjust
> ### Title: Convert the Value of a US Dollar to a Given Year
> ### Aliases: inflation_adjust
> ### Keywords: api bls cpi economics inflation unemployment
> 
> ### ** Examples
> 
> 
> ## Get historical USD values based on a 2010 dollar.
> values <- inflation_adjust(base_year = 2015)
trying URL 'https://download.bls.gov/pub/time.series/cu/cu.data.1.AllItems'
Warning in download.file("https://download.bls.gov/pub/time.series/cu/cu.data.1.AllItems",  :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in download.file("https://download.bls.gov/pub/time.series/cu/cu.data.1.AllItems",  : 
  cannot open URL 'https://download.bls.gov/pub/time.series/cu/cu.data.1.AllItems'
Calls: inflation_adjust -> download.file
Execution halted
File
  inst/LICENCE
will install at top-level and is not mentioned in the DESCRIPTION file.
Package in Depends field not imported from: 'drc'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bmd: no visible global function definition for 'qnorm'
bmd: no visible global function definition for 'predict'
bmd: no visible global function definition for 'LL.2'
bmd: no visible global function definition for 'LN.2'
bmd: no visible global function definition for 'W1.2'
bmd: no visible global function definition for 'W2.2'
bmd: no visible global function definition for 'LL.5'
bmd: no visible global function definition for 'LN.4'
bmd: no visible global function definition for 'W1.4'
bmd: no visible global function definition for 'W2.4'
bmd: no visible global function definition for 'FPL.4'
bmd: no visible global function definition for 'maED'
bmd: no visible global function definition for 'ED'
Undefined global functions or variables:
  ED FPL.4 LL.2 LL.5 LN.2 LN.4 W1.2 W1.4 W2.2 W2.4 maED predict qnorm
Consider adding
  importFrom("stats", "predict", "qnorm")
to your NAMESPACE file.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls to packages already attached by Depends:
  'coda' 'functional' 'plyr'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'coda' 'functional' 'plyr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HDistNoSize: no visible global function definition for 'density'
HDistSize: no visible global function definition for 'density'
bmkconverge: no visible global function definition for 'Compose'
bmksensitive: no visible global function definition for 'Compose'
bmksummary: no visible global function definition for 'Compose'
bmksummary: no visible global function definition for 'Curry'
bmksummary: no visible binding for global variable 'quantile'
bmksummary : std.error: no visible global function definition for 'var'
bmksummary: no visible global function definition for 'mcmc'
bmksummary: no visible global function definition for 'mcmc.list'
bmksummary: no visible global function definition for 'median'
bmksummary: no visible global function definition for 'effectiveSize'
bmksummary: no visible global function definition for 'gelman.diag'
Undefined global functions or variables:
  Compose Curry density effectiveSize gelman.diag mcmc mcmc.list median
  quantile var
Consider adding
  importFrom("stats", "density", "median", "quantile", "var")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
bmmix : LL.y: no visible global function definition for 'dmultinom'
bmmix : LL.x : <anonymous>: no visible global function definition for
  'dmultinom'
bmmix : LPrior.alpha: no visible global function definition for 'dexp'
bmmix : alpha.move: no visible global function definition for 'rnorm'
bmmix : alpha.move: no visible global function definition for 'runif'
bmmix : phi.move: no visible global function definition for 'rnorm'
bmmix : phi.move: no visible global function definition for 'runif'
bmmix: no visible global function definition for 'read.table'
Undefined global functions or variables:
  dexp dmultinom read.table rnorm runif
Consider adding
  importFrom("stats", "dexp", "dmultinom", "rnorm", "runif")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
make_topology: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
bnlr: no visible global function definition for 'dnorm'
bnlr: no visible global function definition for 'runif'
chainsum : <anonymous>: no visible global function definition for
  'quantile'
infocrit: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm quantile runif
Consider adding
  importFrom("stats", "dnorm", "quantile", "runif")
to your NAMESPACE file.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.7Mb
BOGest: no visible global function definition for 'read.table'
BOGstat: no visible global function definition for 'phyper'
BOGstat: no visible global function definition for 'wilcox.test'
BOGstat: no visible global function definition for 'p.adjust'
gseaplot: no visible global function definition for 'par'
gseaplot: no visible global function definition for 'plot'
gseaplot: no visible global function definition for 'points'
gseaplot: no visible global function definition for 'axis'
gseaplot: no visible global function definition for 'segments'
hgplot: no visible global function definition for 'par'
hgplot: no visible global function definition for 'barplot'
Undefined global functions or variables:
  axis barplot p.adjust par phyper plot points read.table segments
  wilcox.test
Consider adding
  importFrom("graphics", "axis", "barplot", "par", "plot", "points",
             "segments")
  importFrom("stats", "p.adjust", "phyper", "wilcox.test")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
installed size is 60.6Mb
  sub-directories of 1Mb or more:
    include   8.7Mb
    lib      51.5Mb
GNU make is a SystemRequirements.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Malformed Title field: should not end in a period.
boostBackend: no visible global function definition for 'model.frame'
findFormulaIn: no visible global function definition for 'as.formula'
kFoldCV: no visible binding for global variable 'par'
predictResponseFromWeightedAverage: no visible global function
  definition for 'weighted.mean'
print.boostr: no visible global function definition for 'str'
Undefined global functions or variables:
  as.formula model.frame par str weighted.mean
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "as.formula", "model.frame", "weighted.mean")
  importFrom("utils", "str")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
specdens: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
boot.stepAIC: no visible global function definition for 'update'
boot.stepAIC: no visible binding for global variable 'coef'
boot.stepAIC : <anonymous>: no visible global function definition for
  'anova'
boot.stepAIC: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  anova coef pnorm update
Consider adding
  importFrom("stats", "anova", "coef", "pnorm", "update")
to your NAMESPACE file.
Package suggested but not available for checking: 'doMC'
boottol: no visible global function definition for 'setNames'
boottol : shift: no visible global function definition for 'tail'
boottol : shift: no visible global function definition for 'head'
boottol: no visible global function definition for 'na.omit'
vastol: no visible global function definition for 'setNames'
vastol: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  head na.omit setNames tail
Consider adding
  importFrom("stats", "na.omit", "setNames")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
bPeaksAnalysis: no visible global function definition for 'write.table'
dataReading: no visible global function definition for 'read.table'
dataSmoothing: no visible global function definition for 'filter'
peakDetection: no visible global function definition for 'quantile'
peakDetection: no visible global function definition for 'pdf'
peakDetection: no visible global function definition for 'par'
peakDetection: no visible global function definition for 'plot'
peakDetection: no visible global function definition for 'text'
peakDetection: no visible global function definition for 'abline'
peakDetection: no visible global function definition for 'points'
peakDetection: no visible global function definition for 'dev.off'
peakDetection: no visible global function definition for 'write.table'
peakDrawing: no visible global function definition for 'par'
peakDrawing: no visible global function definition for 'plot'
peakDrawing: no visible global function definition for 'abline'
peakLocation: no visible global function definition for 'read.table'
peakLocation: no visible global function definition for 'pdf'
peakLocation: no visible global function definition for 'barplot'
peakLocation: no visible global function definition for 'dev.off'
peakLocation: no visible global function definition for 'write.table'
Undefined global functions or variables:
  abline barplot dev.off filter par pdf plot points quantile read.table
  text write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "barplot", "par", "plot", "points",
             "text")
  importFrom("stats", "filter", "quantile")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
apply.breaks: no visible binding for global variable 'median'
break.clust: no visible global function definition for 'plot'
break.clust: no visible global function definition for 'median'
breakage.plot: no visible binding for global variable 'median'
breakage.plot: no visible global function definition for 'plot'
breakage.plot: no visible global function definition for 'abline'
breakage.plot: no visible global function definition for 'lm'
find.bottom: no visible global function definition for 'filter'
fit.breakage: no visible global function definition for 'optim'
fit.breakage: no visible global function definition for 'plot'
fit.breakage: no visible global function definition for 'points'
fit.sensitivity.plot: no visible global function definition for
  'contour'
fit.sensitivity.plot: no visible global function definition for
  'points'
fit.sensitivity.plot: no visible global function definition for 'text'
Undefined global functions or variables:
  abline contour filter lm median optim plot points text
Consider adding
  importFrom("graphics", "abline", "contour", "plot", "points", "text")
  importFrom("stats", "filter", "lm", "median", "optim")
to your NAMESPACE file.
Package suggested but not available for checking: 'cmdstanr'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R     2.9Mb
    doc   2.4Mb
excel_fig: no visible global function definition for 'plot'
grayplot : hidegrayplot: no visible global function definition for
  'plot'
grayplot_na : hidegrayplot_na: no visible global function definition
  for 'plot'
mypairs: no visible global function definition for 'plot'
plot_crayons: no visible global function definition for 'plot'
triplot: no visible global function definition for 'plot'
venn: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Package suggested but not available for checking: 'glmmADMB'
Foreign function calls to a different package:
  .C("CharArray", ..., PACKAGE = "libOpenBUGS")
  .C("CmdInterpreter", ..., PACKAGE = "libOpenBUGS")
  .C("Integer", ..., PACKAGE = "libOpenBUGS")
  .C("RealArray", ..., PACKAGE = "libOpenBUGS")
  .C("SetTempDir", ..., PACKAGE = "libOpenBUGS")
  .C("SetWorkingDir", ..., PACKAGE = "libOpenBUGS")
Undeclared package in foreign function calls:
   'libOpenBUGS'
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    doc    7.7Mb
    libs  12.5Mb
GNU make is a SystemRequirements.
BSGS.Sample: no visible global function definition for 'rgamma'
BSGS.Simple: no visible global function definition for 'rgamma'
CompWiseGibbs: no visible global function definition for 'runif'
CompWiseGibbs: no visible global function definition for 'rnorm'
CompWiseGibbsSMP: no visible global function definition for 'rbinom'
CompWiseGibbsSMP: no visible global function definition for 'runif'
CompWiseGibbsSMP: no visible global function definition for 'rnorm'
CompWiseGibbsSimple: no visible global function definition for 'runif'
CompWiseGibbsSimple: no visible global function definition for 'rnorm'
CompWiseGibbsSimple: no visible global function definition for 'rgamma'
GroupMH: no visible global function definition for 'runif'
GroupZ.MH: no visible global function definition for 'runif'
Undefined global functions or variables:
  rbinom rgamma rnorm runif
Consider adding
  importFrom("stats", "rbinom", "rgamma", "rnorm", "runif")
to your NAMESPACE file.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    fonts   2.4Mb
    lib     3.4Mb
plot.bspec: no visible global function definition for 'par'
plot.bspec: no visible global function definition for 'plot'
plot.bspec: no visible global function definition for 'matlines'
plot.bspec: no visible global function definition for 'points'
plot.bspec: no visible global function definition for 'axis'
plot.bspec: no visible global function definition for 'mtext'
plot.bspec: no visible global function definition for 'axTicks'
plot.bspec: no visible global function definition for 'box'
plot.bspecACF: no visible global function definition for 'plot'
plot.bspecACF: no visible global function definition for 'abline'
plot.bspecACF: no visible global function definition for 'matlines'
Undefined global functions or variables:
  abline axTicks axis box matlines mtext par plot points
Consider adding
  importFrom("graphics", "abline", "axTicks", "axis", "box", "matlines",
             "mtext", "par", "plot", "points")
to your NAMESPACE file.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   5.7Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
alpha.proxy: no visible global function definition for 'filled.contour'
alpha.proxy: no visible global function definition for 'axis'
alpha.proxy: no visible global function definition for 'contour'
factor.model.stat: no visible global function definition for 'quantile'
factor.model.stat: no visible global function definition for 'lsfit'
partial.rainbow: no visible binding for global variable 'rainbow'
var.shrink.eqcor: no visible global function definition for 'var'
var.shrink.eqcor: no visible global function definition for 'quantile'
var.shrink.eqcor: no visible global function definition for 'cov2cor'
Undefined global functions or variables:
  axis contour cov2cor filled.contour lsfit quantile rainbow var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "contour", "filled.contour")
  importFrom("stats", "cov2cor", "lsfit", "quantile", "var")
to your NAMESPACE file.
plot.bursts: no visible global function definition for 'plot'
plot.bursts: no visible global function definition for 'axis'
plot.bursts: no visible global function definition for 'arrows'
Undefined global functions or variables:
  arrows axis plot
Consider adding
  importFrom("graphics", "arrows", "axis", "plot")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
makemim: no visible global function definition for 'cor'
sigtestMTC: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  cor p.adjust
Consider adding
  importFrom("stats", "cor", "p.adjust")
to your NAMESPACE file.
File 'cairoDevice/R/zzz.R':
  .onLoad calls:
    message("R session is headless; GTK+ not initialized.")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
bplot: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Package suggested but not available for checking: 'ReGenesees'
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc        4.0Mb
    pictures   3.9Mb
diffplot: no visible global function definition for 'plot'
get_comptab: no visible global function definition for 'plot'
qdist: no visible global function definition for 'plot'
qdist : pfun: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
bootstrapCapwire: no visible global function definition for 'quantile'
drawCapRatesBeta : <anonymous>: no visible global function definition
  for 'rbeta'
drawCapRatesExp : <anonymous>: no visible global function definition
  for 'rexp'
drawCapRatesGamma : <anonymous>: no visible global function definition
  for 'rgamma'
drawCapRatesGeom : <anonymous>: no visible global function definition
  for 'rgeom'
drawCapRatesUnif : <anonymous>: no visible global function definition
  for 'runif'
partitionCountData : find.3.way.partitions: no visible global function
  definition for 'dmultinom'
Undefined global functions or variables:
  dmultinom quantile rbeta rexp rgamma rgeom runif
Consider adding
  importFrom("stats", "dmultinom", "quantile", "rbeta", "rexp", "rgamma",
             "rgeom", "runif")
to your NAMESPACE file.
plot.cosinor: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Sub.pair: no visible global function definition for 'qnorm'
as.record: no visible global function definition for 'capture.output'
estN: no visible global function definition for 'sd'
estN: no visible global function definition for 'qnorm'
estN.bootstrap: no visible global function definition for 'runif'
Undefined global functions or variables:
  capture.output qnorm runif sd
Consider adding
  importFrom("stats", "qnorm", "runif", "sd")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R        1.1Mb
    data     1.5Mb
    models   2.4Mb
abundance: no visible global function definition for 'D'
Undefined global functions or variables:
  D
Consider adding
  importFrom("stats", "D")
to your NAMESPACE file.
barplotEQR: no visible global function definition for 'barplot'
barplotEQR: no visible global function definition for 'abline'
barplotEQR: no visible global function definition for 'par'
barplotEQR: no visible global function definition for 'text'
Undefined global functions or variables:
  abline barplot par text
Consider adding
  importFrom("graphics", "abline", "barplot", "par", "text")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'MASS' 'RSQLite' 'grid' 'sm'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
MDR.high.forward1: no visible global function definition for 'combn'
MDR.sing.mod1: no visible global function definition for 'combn'
MDR.sing.mod1: no visible global function definition for
  'complete.cases'
MDR.sing.mod1: no visible global function definition for 'lm'
MDR.sing.mod1: no visible global function definition for 'aov'
MDR.sing.mod1: no visible global function definition for 'anova'
MDR.stage.forward1: no visible global function definition for 'combn'
MDR.stage.forward1: no visible global function definition for
  'complete.cases'
MDR.stage.forward1: no visible global function definition for 'lm'
MDR.stage.forward1: no visible global function definition for 'resid'
MDR.stage.forward1: no visible global function definition for 'pf'
MDR_forward1: no visible global function definition for
  'complete.cases'
MDR_forward1: no visible global function definition for 'lm'
MDR_forward1: no visible global function definition for 'aov'
low.anova: no visible global function definition for 'complete.cases'
low.anova: no visible global function definition for 'lm'
sing.mod1: no visible global function definition for 'combn'
sing.mod1: no visible global function definition for 'complete.cases'
sing.mod1: no visible global function definition for 'lm'
sing.mod1: no visible global function definition for 'pf'
Undefined global functions or variables:
  anova aov combn complete.cases lm pf resid
Consider adding
  importFrom("stats", "anova", "aov", "complete.cases", "lm", "pf",
             "resid")
  importFrom("utils", "combn")
to your NAMESPACE file.
installed size is 37.4Mb
  sub-directories of 1Mb or more:
    doc  37.2Mb
Malformed Description field: should contain one or more complete sentences.
mi.inference: no visible binding for global variable 'var'
mi.inference: no visible global function definition for 'qt'
mi.inference: no visible global function definition for 'pt'
Undefined global functions or variables:
  pt qt var
Consider adding
  importFrom("stats", "pt", "qt", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
ctab: no visible global function definition for 'xtabs'
mob.eqmain: no visible global function definition for 'model.matrix'
mob.qi: no visible global function definition for 'C'
mob.qi: no visible binding for global variable 'contr.treatment'
mob.rc1: no visible global function definition for 'C'
mob.rc1: no visible binding for global variable 'contr.treatment'
mob.rc1: no visible global function definition for 'model.matrix'
mob.symint: no visible global function definition for 'model.matrix'
print.ctab: no visible global function definition for 'ftable'
Undefined global functions or variables:
  C contr.treatment ftable model.matrix xtabs
Consider adding
  importFrom("stats", "C", "contr.treatment", "ftable", "model.matrix",
             "xtabs")
to your NAMESPACE file.