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.
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.
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.
Rd file 'Plot.pca.score.Rd':
  \examples lines wider than 100 characters:
             ylab = ylab, xlim = lim, ylim = lim, pch = 19, sub = paste("Cumulative Proportion of Variance Explained = ", 

Rd file 'oplsda.Rd':
  \examples lines wider than 100 characters:
             ylab = ylab, xlim = lim, ylim = lim, pch = 19, sub = paste("Cumulative Proportion of Variance Explained = ", 

Rd file 'univariate.Rd':
  \usage lines wider than 90 characters:
     univariate(file, imputation = FALSE, imput, normalize = TRUE, multi.test = TRUE, plot.volcano = FALSE, save.boxplot=TRUE)

Rd file 'volcano.Rd':
  \examples lines wider than 100 characters:
                         sep = ""), sub = "(Variables in Blue are significant (Pvalue<0.05) and showed Fold Changes >1.2 or <0.8)")
                           j, sep = ""), sub = "(Variables in Blue are significant (Pvalue<0.05) and showed Fold Changes >1.2 or <0.8)")

These lines will be truncated in the PDF manual.
plotFID: no visible global function definition for ‘plot’
plotFID: no visible global function definition for ‘points’
Undefined global functions or variables:
  plot points
Consider adding
  importFrom("graphics", "plot", "points")
to your NAMESPACE file.
prentice.test: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Malformed Description field: should contain one or more complete sentences.
mvb.simu: no visible global function definition for ‘runif’
plot.lps: no visible global function definition for ‘matplot’
unifit: no visible global function definition for ‘model.frame’
unifit: no visible global function definition for ‘model.matrix’
unifit: no visible global function definition for ‘model.response’
unilps: no visible global function definition for ‘model.frame’
unilps: no visible global function definition for ‘model.matrix’
unilps: no visible global function definition for ‘model.response’
Undefined global functions or variables:
  matplot model.frame model.matrix model.response runif
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "runif")
to your NAMESPACE file.
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.
Found the following sources/headers not terminated with a newline:
  src/sitmo/sitmo.hpp
Some compilers warn on such files.
mvnpermute: no visible global function definition for ‘lm’
mvnpermute: no visible global function definition for ‘coef’
mvnpermute: no visible global function definition for ‘resid’
Undefined global functions or variables:
  coef lm resid
Consider adding
  importFrom("stats", "coef", "lm", "resid")
to your NAMESPACE file.
mvorpb: no visible global function definition for ‘pnorm’
mvorpb: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm pnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm")
to your NAMESPACE file.
rtn: no visible global function definition for ‘runif’
rtn: no visible global function definition for ‘qnorm’
rtn: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm runif
Consider adding
  importFrom("stats", "pnorm", "qnorm", "runif")
to your NAMESPACE file.
prepare_Rd: mvsf.Rd:16-17: Dropping empty section \details
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘RColorBrewer’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘RColorBrewer’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plot.matchedwake: no visible global function definition for
  ‘filled.contour’
plot.matchedwake: no visible binding for global variable ‘gray.colors’
plot.matchedwake: no visible global function definition for ‘axis’
plot.matchedwake: no visible global function definition for ‘rect’
slideWakeMatch: no visible binding for global variable ‘lm’
slideWakeMatch: no visible global function definition for ‘as.formula’
slideWakeMatch: no visible global function definition for ‘summary.glm’
Undefined global functions or variables:
  as.formula axis filled.contour gray.colors lm rect summary.glm
Consider adding
  importFrom("grDevices", "gray.colors")
  importFrom("graphics", "axis", "filled.contour", "rect")
  importFrom("stats", "as.formula", "lm", "summary.glm")
to your NAMESPACE file.
mxkssd: no visible global function definition for ‘txtProgressBar’
mxkssd: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
abcpred_nmer: no visible global function definition for ‘write.table’
algpred: no visible global function definition for ‘read.table’
algpred: no visible global function definition for ‘write.table’
allermatch: no visible global function definition for ‘read.table’
allermatch: no visible global function definition for ‘write.table’
bcepred_nmer: no visible global function definition for ‘write.table’
bimas_nmer: no visible global function definition for ‘write.table’
filter.firstlayer: no visible global function definition for
  ‘read.table’
filter.firstlayer: no visible global function definition for
  ‘write.table’
iedb_arb_mhci_nmer: no visible global function definition for
  ‘write.table’
iedb_arb_mhcii_nmer: no visible global function definition for
  ‘write.table’
iedb_consensus_mhci_nmer: no visible global function definition for
  ‘write.table’
iedb_consensus_mhcii_nmer: no visible global function definition for
  ‘write.table’
netmhcNN_nmer: no visible global function definition for ‘write.table’
netmhcWT_nmer: no visible global function definition for ‘write.table’
propred_nmer: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
update_episode: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
Rd file 'myepisodes_feed_url.Rd':
  \examples lines wider than 100 characters:
     ## Not run: myepisodes_feed_url("foouser", "321654321654321", feed = "mylist", onlyunacquired = TRUE, showignored = FALSE)

Rd file 'shows_from_myepisodes.Rd':
  \examples lines wider than 100 characters:
     ## Not run: shows_from_myepisodes("foouser", "321654321654321", feed = "mylist", onlyunacquired = TRUE, showignored = FALSE)

These lines will be truncated in the PDF manual.
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.
Documented arguments not in \usage in documentation object 'median-methods':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package which this enhances but not available for checking: ‘asreml’
Malformed Description field: should contain one or more complete sentences.
NAPPA: no visible binding for global variable ‘sd’
NAPPA: no visible global function definition for ‘sd’
calibrate.sigmoid.curve : <anonymous> : <anonymous>: no visible global
  function definition for ‘coef’
calibrate.sigmoid.curve : <anonymous> : <anonymous>: no visible global
  function definition for ‘lm’
calibrate.sigmoid.curve: no visible global function definition for
  ‘nls’
calibrate.sigmoid.curve: no visible binding for global variable
  ‘weights’
calibrate.sigmoid.curve: no visible global function definition for
  ‘coef’
calibrate.sigmoid.curve: no visible global function definition for
  ‘plot’
calibrate.sigmoid.curve: no visible global function definition for
  ‘rgb’
calibrate.sigmoid.curve: no visible global function definition for
  ‘box’
calibrate.sigmoid.curve: no visible global function definition for
  ‘axis’
calibrate.sigmoid.curve: no visible global function definition for
  ‘abline’
calibrate.sigmoid.curve: no visible global function definition for
  ‘lines’
calibrate.sigmoid.curve: no visible global function definition for
  ‘predict’
calibrate.sigmoid.curve: no visible global function definition for
  ‘smooth.spline’
calibrate.sigmoid.curve : <anonymous>: no visible global function
  definition for ‘nls’
calibrate.sigmoid.curve : <anonymous>: no visible binding for global
  variable ‘weights’
calibrate.sigmoid.curve: no visible binding for global variable ‘coef’
calibrate.sigmoid.curve: no visible global function definition for ‘pf’
calibrate.sigmoid.curve: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  abline axis box coef legend lines lm nls pf plot predict rgb sd
  smooth.spline weights
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "abline", "axis", "box", "legend", "lines",
             "plot")
  importFrom("stats", "coef", "lm", "nls", "pf", "predict", "sd",
             "smooth.spline", "weights")
to your NAMESPACE file.
NB.estimator: no visible global function definition for ‘optimize’
NB.estimator: no visible global function definition for ‘uniroot’
NB.example.dataset: no visible global function definition for
  ‘write.table’
NB.plot.likelihood: no visible global function definition for ‘plot’
Undefined global functions or variables:
  optimize plot uniroot write.table
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "optimize", "uniroot")
  importFrom("utils", "write.table")
to your NAMESPACE file.
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.
infoNcdfVars: no visible global function definition for ‘na.omit’
modifyNcdfDefAtts: no visible global function definition for ‘na.omit’
plotDatacube: no visible global function definition for ‘runif’
plotDatacube: no visible global function definition for
  ‘colorRampPalette’
plotDatacube: no visible global function definition for ‘dev.cur’
plotDatacube: no visible global function definition for ‘dev.new’
plotDatacube: no visible global function definition for ‘layout’
plotDatacube: no visible global function definition for ‘par’
plotDatacube: no visible global function definition for ‘points’
plotDatacube: no visible global function definition for ‘text’
plotDatacube: no visible global function definition for ‘plot.new’
plotDatacube: no visible global function definition for ‘mtext’
plotDatacube: no visible global function definition for ‘rgb’
plotDatacube: no visible global function definition for ‘legend’
transNcdfRotate: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  colorRampPalette dev.cur dev.new layout legend mtext na.omit par
  plot.new points rgb runif text
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.cur", "dev.new",
             "rgb")
  importFrom("graphics", "layout", "legend", "mtext", "par", "plot.new",
             "points", "text")
  importFrom("stats", "na.omit", "runif")
to your NAMESPACE file.
d0: no visible global function definition for ‘qnorm’
dncgamma: no visible global function definition for ‘dpois’
indncgamma: no visible global function definition for ‘pgamma’
indncgamma: no visible global function definition for ‘dpois’
inxncgamma: no visible global function definition for ‘qnorm’
inxncgamma: no visible global function definition for ‘pgamma’
inxncgamma: no visible global function definition for ‘dpois’
pncgamma: no visible global function definition for ‘pgamma’
pncgamma: no visible global function definition for ‘dpois’
Undefined global functions or variables:
  dpois pgamma qnorm
Consider adding
  importFrom("stats", "dpois", "pgamma", "qnorm")
to your NAMESPACE file.
data.reduction: no visible global function definition for ‘prcomp’
data.reduction: no visible global function definition for ‘hclust’
data.reduction: no visible global function definition for ‘as.dist’
data.reduction: no visible global function definition for ‘cor’
data.reduction: no visible global function definition for ‘dist’
heatmap1: no visible global function definition for ‘sd’
lineplot: no visible global function definition for ‘sd’
normalize: no visible global function definition for ‘sd’
profileplot3d : ColorFunction: no visible global function definition
  for ‘rgb’
profileplot3d : ColorFunction: no visible global function definition
  for ‘colorRamp’
profileplot3d: no visible global function definition for ‘sd’
profileplot3d: no visible global function definition for ‘gray’
Undefined global functions or variables:
  as.dist colorRamp cor dist gray hclust prcomp rgb sd
Consider adding
  importFrom("grDevices", "colorRamp", "gray", "rgb")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "prcomp", "sd")
to your NAMESPACE file.
File ‘NeatMap/libs/NeatMap.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘nMDS_R.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘nMDS_R.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
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.
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘MASS’ which was already attached by Depends.
  Please remove these calls from your code.
The following files look like leftovers/mistakes:
  ‘Rplots.pdf’, ‘Rplots.ps’
Please remove them from your package.
clustConfigurations: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
netVal: no visible global function definition for ‘cutree’
netVal: no visible global function definition for ‘hclust’
netVal: no visible global function definition for ‘as.dist’
Undefined global functions or variables:
  as.dist cutree hclust
Consider adding
  importFrom("stats", "as.dist", "cutree", "hclust")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘buildcmds’
EnvInd: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: ‘fastshp’
simulate.sisnetwork: no visible global function definition for ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
balloon: no visible global function definition for ‘convolve’
physnoise: no visible global function definition for ‘sd’
physnoise: no visible global function definition for ‘rnorm’
rrice: no visible global function definition for ‘rnorm’
simTSrestingstate: no visible global function definition for ‘runif’
simTSrestingstate: no visible global function definition for ‘fft’
spatialnoise: no visible global function definition for ‘rnorm’
spatialnoise: no visible global function definition for ‘qgamma’
spatialnoise: no visible global function definition for ‘pnorm’
specifydesign: no visible global function definition for ‘convolve’
systemnoise: no visible global function definition for ‘rnorm’
tasknoise: no visible global function definition for ‘rnorm’
tasknoise: no visible global function definition for ‘sd’
temporalnoise: no visible global function definition for ‘arima.sim’
Undefined global functions or variables:
  arima.sim convolve fft pnorm qgamma rnorm runif sd
Consider adding
  importFrom("stats", "arima.sim", "convolve", "fft", "pnorm", "qgamma",
             "rnorm", "runif", "sd")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘MASS’ ‘boot’ ‘lattice’ ‘psych’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
nfca : nFCAmain: no visible global function definition for ‘hist’
nfca : nFCAmain: no visible global function definition for
  ‘flush.console’
nfca : nFCAmain: no visible global function definition for ‘qnorm’
nfca : nFCAmain: no visible global function definition for ‘read.csv’
nfca : nFCAmain: no visible global function definition for ‘cor’
nfca : nFCAmain: no visible global function definition for ‘as.dist’
nfca : nFCAmain: no visible global function definition for ‘cophenetic’
nfca : nFCAmain: no visible global function definition for ‘hclust’
nfca : thresholdTEST: no visible global function definition for
  ‘read.csv’
nfca : gScript: no visible global function definition for ‘read.csv’
nfca : gScript0: no visible global function definition for ‘read.csv’
nfca : gMatrix: no visible global function definition for ‘read.csv’
nfca: no visible global function definition for ‘cor’
Undefined global functions or variables:
  as.dist cophenetic cor flush.console hclust hist qnorm read.csv
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "as.dist", "cophenetic", "cor", "hclust", "qnorm")
  importFrom("utils", "flush.console", "read.csv")
to your NAMESPACE file.
Package suggested but not available for checking: ‘NFPdata’
Malformed Description field: should contain one or more complete sentences.
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.
Missing or unexported object: ‘cleanNLP::cnlp_get_token’
Package in Depends field not imported from: ‘proto’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘stats:::nlsModel’ ‘stats:::nlsModel.plinear’
  See the note in ?`:::` about the use of this operator.
nls2: no visible global function definition for ‘nls.control’
nls2: no visible global function definition for ‘as.formula’
nls2: no visible global function definition for ‘coef’
nls2: no visible global function definition for ‘runif’
nls2 : <anonymous>: no visible global function definition for
  ‘deviance’
Undefined global functions or variables:
  as.formula coef deviance nls.control runif
Consider adding
  importFrom("stats", "as.formula", "coef", "deviance", "nls.control",
             "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
nnmf_als: no visible global function definition for ‘rnorm’
nnmf_mm: no visible global function definition for ‘rnorm’
nnmf_prob: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Package suggested but not available for checking: ‘hurricaneexposuredata’
makeRules: no visible global function definition for ‘sd’
makeRules: no visible global function definition for ‘rnorm’
nodeHarvest: no visible global function definition for ‘capture.output’
nodeHarvest: no visible global function definition for ‘lm’
nodeHarvest: no visible global function definition for ‘coef’
plot.nodeHarvest: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  capture.output coef lm rgb rnorm sd
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "coef", "lm", "rnorm", "sd")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Depends: includes the non-default packages:
  'lpSolve', 'gdata', 'Hmisc', 'rms', 'geometry', 'psych', 'pwt'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  ‘Hmisc’ ‘gdata’ ‘geometry’ ‘lpSolve’ ‘psych’ ‘rms’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Hmisc’ ‘gdata’ ‘geometry’ ‘lpSolve’ ‘psych’ ‘pwt’ ‘rms’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
additive: no visible global function definition for ‘lp’
ar.dual.dea: no visible global function definition for ‘lp’
cost.dea: no visible global function definition for ‘lp’
ddf: no visible global function definition for ‘lp’
dea: no visible global function definition for ‘lp’
direc.dea: no visible global function definition for ‘lp’
dual.dea: no visible global function definition for ‘lp’
effdea.b.f: no visible global function definition for ‘convhulln’
effdea.b.f: no visible global function definition for ‘lp’
faremalm2: no visible binding for global variable ‘Lag’
faremalm2: no visible global function definition for ‘na.omit’
int.dea: no visible global function definition for ‘lp’
lp2: no visible global function definition for ‘lp’
revenue.dea: no visible global function definition for ‘lp’
sbm.tone: no visible global function definition for ‘lp’
sbm.vrs: no visible global function definition for ‘lp’
Undefined global functions or variables:
  Lag convhulln lp na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
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.
Rd file 'notifyR-package.Rd':
  \examples lines wider than 100 characters:
     send_push(userkey,message="finished.",title="World Simulation",url="http://www.myRresults.com/",url_title="View Results online.",priori ... [TRUNCATED]

Rd file 'send_push.Rd':
  \usage lines wider than 90 characters:
     send_push(user, message, title = "", device = "", url = "", url_title = "", priority = FALSE, timestamp = Sys.time())
  \examples lines wider than 100 characters:
     send_push(userkey,message="finished.",title="World Simulation",url="http://www.myRresults.com/",url_title="View Results online.",priori ... [TRUNCATED]

These lines will be truncated in the PDF manual.
.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.
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.
Dependence on R version ‘3.4.3’ not with patchlevel 0
Malformed Description field: should contain one or more complete sentences.
Non-standard file/directory found at top level:
  ‘tmp.R’
Found the following hidden files and directories:
  .Rapp.history
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
File ‘NPsimex/R/onload.R’:
  .onLoad calls:
    packageStartupMessage("NPsimex 0.2-1 loaded")

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

lambda.select: no visible global function definition for ‘bw.nrd0’
lambda.select: no visible global function definition for ‘bw.nrd’
lambda.select: no visible global function definition for ‘bw.ucv’
lambda.select: no visible global function definition for ‘bw.bcv’
lambda.select: no visible global function definition for ‘bw.SJ’
plot.NPsimex: no visible global function definition for ‘plot.default’
simex.H.density : simex1.est: no visible global function definition for
  ‘lm’
simex.density : simex1.est: no visible global function definition for
  ‘lm’
span.H.select: no visible global function definition for ‘density’
span.H.select : conden : <anonymous>: no visible global function
  definition for ‘dnorm’
span.select: no visible global function definition for ‘density’
span.select : conden : <anonymous>: no visible global function
  definition for ‘dnorm’
Undefined global functions or variables:
  bw.SJ bw.bcv bw.nrd bw.nrd0 bw.ucv density dnorm lm plot.default
Consider adding
  importFrom("graphics", "plot.default")
  importFrom("stats", "bw.SJ", "bw.bcv", "bw.nrd", "bw.nrd0", "bw.ucv",
             "density", "dnorm", "lm")
to your NAMESPACE file.
prepare_Rd: lambda.select.Rd:19-20: Dropping empty section \details
prepare_Rd: lambda.select.Rd:21-22: Dropping empty section \value
prepare_Rd: simex.H.density.Rd:28-29: Dropping empty section \details
prepare_Rd: simex.density.Rd:28-29: Dropping empty section \details
prepare_Rd: span.H.select.Rd:28-29: Dropping empty section \details
prepare_Rd: span.H.select.Rd:30-31: Dropping empty section \value
prepare_Rd: span.select.Rd:27-28: Dropping empty section \details
prepare_Rd: span.select.Rd:29-30: Dropping empty section \value
Rd file 'simex.H.density.Rd':
  \examples lines wider than 100 characters:
     set.seed(123); X <- c(rnorm(N/2, mean=-2), rnorm(N/2,mean=2)); U <- rnorm(N,sd=1); msigma <- runif(N,min=0.3,max=0.5)

Rd file 'span.H.select.Rd':
  \usage lines wider than 90 characters:
      span.H.select(W, msigma, span=c(2,4,6,8,10,12,25), approx=FALSE, from=min(W), to=max(W), n.user=128, n.lambda=50, lambda="SJ", bw="SJ" ... [TRUNCATED]
  \examples lines wider than 100 characters:
     set.seed(123); X <- c(rnorm(N/2, mean=-2), rnorm(N/2,mean=2)); U <- rnorm(N,sd=1); msigma <- runif(N,min=0.3,max=0.5)
     X.simex <- simex.H.density(W, msigma=msigma, adjust=1, n.lambda=50, span=spans$span[order(spans$ISE)[1]])
     # X.simex <- simex.H.density(W, msigma=msigma, adjust=1, n.lambda=50, span=spans$span[order(spans$ISE)[1]])

Rd file 'span.select.Rd':
  \usage lines wider than 90 characters:
      span.select(W, msigma, span=c(2,4,6,8,10,12,25), from=min(W), to=max(W), n.user=128, n.lambda=50, lambda="SJ", bw="SJ", adjust=1, na.r ... [TRUNCATED]
  \examples lines wider than 100 characters:
     X.simex <- simex.density(W, msigma=msigma, adjust=1, n.lambda=50, span=spans$span[order(spans$ISE)[1]])

These lines will be truncated in the PDF manual.
nps.test: no visible global function definition for ‘qnorm’
nps.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
'library' or 'require' call to ‘parallel’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
npst: no visible global function definition for ‘mclapply’
Undefined global functions or variables:
  mclapply
Package in Depends field not imported from: ‘mco’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
boundedPolyMutation: no visible global function definition for ‘runif’
boundedSBXover: no visible global function definition for ‘runif’
nsga2R : <anonymous>: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
.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.
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.

Found the following assignments to the global environment:
File ‘nws/R/workerLoop.R’:
  assign("SleighName", displayName, globalenv())
  assign("SleighNws", nws, globalenv())
  assign("SleighUserNws", userNws, globalenv())
  assign("SleighRank", rank, globalenv())
  assign("SleighWorkerCount", workerCount, globalenv())
Rd file 'nwsVariable-methods.Rd':
  \usage lines wider than 90 characters:
     nwsVariable(.Object, xName, mode=c('fifo','lifo','multi','single'),env=parent.frame(),force=FALSE,quietly=FALSE)

These lines will be truncated in the PDF 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.
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').
Rd file 'Enum-class.Rd':
  \examples lines wider than 100 characters:
     PointSizeSingleEnum.gen <- setGlyphEnum("PointSize", levels = c("1", "2", "5", "10"), contains = "GlyphEnum")

These lines will be truncated in the PDF manual.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Signal.gen: no visible global function definition for ‘new’
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
obliclus: no visible global function definition for ‘rnorm’
obliclus: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  kmeans rnorm
Consider adding
  importFrom("stats", "kmeans", "rnorm")
to your NAMESPACE file.
File ‘obliclus/libs/obliclus.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘random_cluster_C.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘random_cluster_C.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘ROCR’ ‘e1071’ ‘mda’ ‘pls’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
log_wrapper: no visible global function definition for ‘glm’
log_wrapper: no visible global function definition for ‘binomial’
log_wrapper: no visible global function definition for ‘coef’
log_wrapper: no visible global function definition for ‘anova’
obliqueRF.default: no visible binding for global variable ‘predict’
obliqueRF.default: no visible global function definition for
  ‘prediction’
obliqueRF.default: no visible global function definition for
  ‘performance’
pls_wrapper: no visible global function definition for ‘kernelpls.fit’
pls_wrapper: no visible global function definition for ‘coef’
ridge_slow_wrapper: no visible global function definition for
  ‘gen.ridge’
ridge_slow_wrapper: no visible global function definition for ‘predict’
ridge_svd_wrapper: no visible global function definition for
  ‘gen.ridge’
rnd_wrapper: no visible global function definition for ‘rnorm’
svm_wrapper: no visible global function definition for ‘svm’
svm_wrapper: no visible global function definition for ‘predict’
Undefined global functions or variables:
  anova binomial coef gen.ridge glm kernelpls.fit performance predict
  prediction rnorm svm
Consider adding
  importFrom("stats", "anova", "binomial", "coef", "glm", "predict",
             "rnorm")
to your NAMESPACE file.
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.
Rd file 'obsSensCCC.Rd':
  \usage lines wider than 90 characters:
     obsSensCCC(model, which = 2, g0 = c(2, 6, 10), g1, p0 = seq(0, 1, 0.2), p1 = p0, logOdds = FALSE, method = c("approx", "sim"))
     obsSensCCN(model, which = 2, gamma = round(seq(0, 2 * bstar, length = 6), 4), delta = seq(0, 3, 0.5), logOdds = FALSE, method = c("appr ... [TRUNCATED]
     obsSensCNN(model, which = 2, gamma = round(seq(0, 2 * bstar, length = 6), 4), rho = c(0, 0.5, 0.75, 0.85, 0.9, 0.95, 0.98, 0.99), sdx,  ... [TRUNCATED]
     obsSensNCC(model, which = 2, g0 = c(2, 6, 10), g1, p0 = seq(0, 1, 0.2), p1 = p0, log = TRUE, method = c("approx", "sim"))
     obsSensNCN(model, which = 2, gamma = round(seq(0, 3, length = 6), 4), delta = seq(0, 3, 0.5), log = TRUE, method = c("approx", "sim"))
     6), 4), rho = c(0, 0.5, 0.75, 0.85, 0.9, 0.95, 0.98, 0.99), sdx, log = TRUE, method = c("approx", "sim"))
     obsSensSCC(model, which = 2, g0 = c(2, 6, 10), g1, p0 = seq(0, 1, 0.2), p1 = p0, logHaz = FALSE, method = c("approx", "sim"))
     obsSensSCN(model, which = 2, gamma = round(seq(0, 3, length = 6), 4), delta = seq(0, 3, 0.5), logHaz = FALSE, method = c("approx", "sim ... [TRUNCATED]
     obsSensSNN(model, which = 2, gamma = round(seq(0, 3, length = 6), 4), rho = c(0, 0.5, 0.75, 0.85, 0.9, 0.95, 0.98, 0.99), sdx, logHaz = ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Dependence on R version ‘3.4.1’ not with patchlevel 0
Found the following hidden files and directories:
  .Rapp.history
  data/.Rapp.history
  data/.Rhistory
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘RCurl’ ‘maps’
A package should be listed in only one of these fields.
mapvar: no visible global function definition for ‘data’
mapvar: no visible binding for global variable ‘state.fips’
mapvar: no visible global function definition for ‘rgb’
mapvar: no visible global function definition for ‘rect’
mapvar: no visible global function definition for ‘text’
rowScrape: no visible global function definition for ‘tail’
rowScrape: no visible global function definition for ‘head’
scrapeTable: no visible binding for global variable ‘tail’
Undefined global functions or variables:
  data head rect rgb state.fips tail text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "rect", "text")
  importFrom("utils", "data", "head", "tail")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘OIdata/R/mapvar.R’:
  data(state.fips)
See section ‘Good practice’ in ‘?data’.
avgokmts: no visible global function definition for ‘aggregate’
downloadstn: no visible global function definition for ‘read.csv’
nearstn: no visible binding for global variable ‘okstations’
nearstn: no visible binding for global variable ‘Commissioned’
nearstn: no visible binding for global variable ‘Decommissioned’
okcurobs: no visible global function definition for ‘read.csv’
okmts: no visible binding for global variable ‘okstations’
okmts: no visible binding for global variable ‘TIME’
retrievemts: no visible global function definition for ‘read.csv’
totalprecip: no visible binding for global variable ‘TIME’
totalprecip: no visible global function definition for ‘aggregate’
vincenty: no visible global function definition for ‘runif’
Undefined global functions or variables:
  Commissioned Decommissioned TIME aggregate okstations read.csv runif
Consider adding
  importFrom("stats", "aggregate", "runif")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
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.
GNU make is a SystemRequirements.
Found an obsolete/platform-specific call in the following function:
  ‘comp.freq’
Found the platform-specific device:
  ‘x11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
MLparameters: no visible global function definition for ‘optim’
comp.freq: no visible global function definition for ‘x11’
comp.freq: no visible global function definition for ‘par’
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.
Rd file 'oncomodel-package.Rd':
  \examples lines wider than 100 characters:
       #plot.phylog(y.phyl, cnodes =1,  clabel.n=0.6, f=0.75, sub="Oncogenetic tree of given aberrations")

These lines will be truncated in the PDF manual.
generate.data: no visible global function definition for ‘rbinom’
least.common.ancestor: no visible global function definition for
  ‘na.omit’
oncotree.fit : estimate.error.rates: no visible global function
  definition for ‘optim’
plot.boottree: no visible global function definition for ‘par’
plot.boottree: no visible global function definition for
  ‘dev.interactive’
plot.boottree: no visible global function definition for ‘mtext’
plot.oncotree: no visible global function definition for ‘par’
plot.oncotree: no visible global function definition for ‘xinch’
plot.oncotree: no visible global function definition for ‘yinch’
plot.oncotree: no visible global function definition for ‘lines’
plot.oncotree: no visible global function definition for ‘rect’
plot.oncotree: no visible global function definition for ‘strwidth’
plot.oncotree: no visible global function definition for ‘strheight’
plot.oncotree: no visible global function definition for ‘text’
Undefined global functions or variables:
  dev.interactive lines mtext na.omit optim par rbinom rect strheight
  strwidth text xinch yinch
Consider adding
  importFrom("grDevices", "dev.interactive")
  importFrom("graphics", "lines", "mtext", "par", "rect", "strheight",
             "strwidth", "text", "xinch", "yinch")
  importFrom("stats", "na.omit", "optim", "rbinom")
to your NAMESPACE file.
ci.prop: no visible global function definition for ‘qf’
ci.prop: no visible global function definition for ‘qnorm’
ePCP: no visible global function definition for ‘qnorm’
sevennum: no visible global function definition for ‘na.omit’
sevennum: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  na.omit qf qnorm quantile
Consider adding
  importFrom("stats", "na.omit", "qf", "qnorm", "quantile")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Dependence on R version ‘3.4.1’ not with patchlevel 0
Package suggested but not available for checking: ‘openNLPmodels.en’
Df2SpLinesDf: no visible global function definition for ‘slot’
PlotTraj: no visible global function definition for ‘par’
PlotTraj: no visible global function definition for ‘grid’
PlotTraj: no visible global function definition for ‘box’
PlotTrajFreq: no visible global function definition for ‘par’
PlotTrajFreq: no visible global function definition for ‘grid’
PlotTrajFreq: no visible global function definition for
  ‘colorRampPalette’
PlotTrajFreq: no visible global function definition for ‘legend’
PlotTrajFreq: no visible binding for global variable ‘title’
PlotTrajFreq: no visible global function definition for ‘dev.off’
ReadFiles: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  box colorRampPalette dev.off grid legend par read.table slot title
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off")
  importFrom("graphics", "box", "grid", "legend", "par", "title")
  importFrom("methods", "slot")
  importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package suggested but not available for checking: ‘gurobi’
prepare_Rd: distance.Rd:21-22: Dropping empty section \details
prepare_Rd: distance.Rd:32-33: Dropping empty section \note
prepare_Rd: filter.Rd:26-27: Dropping empty section \details
prepare_Rd: filter.Rd:28-29: Dropping empty section \value
prepare_Rd: filter.Rd:36-37: Dropping empty section \note
prepare_Rd: findP.Rd:21-22: Dropping empty section \details
prepare_Rd: findP.Rd:34-35: Dropping empty section \note
prepare_Rd: ops-package.Rd:30-31: Dropping empty section \seealso
Package in Depends field not imported from: ‘MASS’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
nlsolve: no visible global function definition for ‘optim’
nlsolve: no visible global function definition for ‘runif’
optAUC: no visible global function definition for ‘var’
Undefined global functions or variables:
  optim runif var
Consider adding
  importFrom("stats", "optim", "runif", "var")
to your NAMESPACE file.
Rd file 'optAUC-package.Rd':
  \examples lines wider than 100 characters:
     Y1Y2<-mvrnorm(n, c(y1.mean,y2.mean), matrix(c(y1.sd^2,rho*y1.sd*y2.sd, rho*y1.sd*y2.sd, y2.sd^2),2,2))
     # two markers in the model, the AUC from GCV is smaller than just first marker in the model, because the second marker is noise
     # the AUC from ACV (apearent estimate by substituting the estimated beta into the model) is larger than previous model, because overfit ... [TRUNCATED]

Rd file 'optAUC.Rd':
  \examples lines wider than 100 characters:
     Y1Y2<-mvrnorm(n, c(y1.mean,y2.mean), matrix(c(y1.sd^2,rho*y1.sd*y2.sd, rho*y1.sd*y2.sd, y2.sd^2),2,2))
     # two markers in the model, the AUC from GCV is smaller than just first marker in the model, because the second marker is noise
     # the AUC from ACV (apearent estimate by substituting the estimated beta into the model) is larger than previous model, because overfit ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Malformed Description field: should contain one or more complete sentences.
avg2Lower: no visible global function definition for ‘optimize’
classificationError.data.frame: no visible binding for global variable
  ‘na.omit’
classificationError.data.frame: no visible global function definition
  for ‘terms’
classificationError.data.frame: no visible binding for global variable
  ‘predict’
classpredict.lda: no visible global function definition for ‘predict’
simData: no visible global function definition for ‘rnorm’
simData: no visible global function definition for ‘runif’
simData: no visible global function definition for ‘var’
tnormAvg: no visible global function definition for ‘dnorm’
tnormAvg: no visible global function definition for ‘pnorm’
yapprox: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx dnorm na.omit optimize pnorm predict rnorm runif terms var
Consider adding
  importFrom("stats", "approx", "dnorm", "na.omit", "optimize", "pnorm",
             "predict", "rnorm", "runif", "terms", "var")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Package which this enhances but not available for checking: ‘gurobi’
print.optimbase: no visible global function definition for ‘str’
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Rd file 'TestStage.Rd':
  \examples lines wider than 100 characters:
     object1 <- OptimDes(B.init,m.init,alpha,beta,param,x,target="EDA",sf="futility",num.arm=1,num.stage=2)
     mda <- ifelse(l>1,B.init[l-1]+(B.init[l]-B.init[l-1])*(n-sum(m.init[1:(l-1)]))/m.init[l],B.init[l]*(n/m.init[l]))

Rd file 'np.OptimDes.Rd':
  \examples lines wider than 100 characters:
     object14 <- np.OptimDes(B.init,m.init,alpha,beta,param,x,pt=1.1,target="ETSL",sf="futility",num.arm=1,num.stage=2)

These lines will be truncated in the PDF manual.
getMinimumArborescence: no visible global function definition for
  ‘capture.output’
getMinimumCutTree: no visible global function definition for
  ‘capture.output’
getMinimumCutTree: no visible global function definition for ‘par’
getMinimumSpanningTree: no visible global function definition for
  ‘capture.output’
getShortestPathTree: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  capture.output par
Consider adding
  importFrom("graphics", "par")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Agrestiind.CI: no visible global function definition for ‘qnorm’
BPexact.CI: no visible global function definition for ‘uniroot’
BPmidp.CI: no visible global function definition for ‘uniroot’
Cornfieldexact.CI: no visible global function definition for ‘uniroot’
Cornfieldmidp.CI: no visible global function definition for ‘uniroot’
Gart.CI: no visible global function definition for ‘qnorm’
Invsinh.CI: no visible global function definition for ‘qnorm’
Woolf.CI: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm uniroot
Consider adding
  importFrom("stats", "qnorm", "uniroot")
to your NAMESPACE file.
BTLboost: no visible global function definition for ‘as.formula’
design: no visible global function definition for ‘as.formula’
wide2long: no visible global function definition for ‘reshape’
Undefined global functions or variables:
  as.formula reshape
Consider adding
  importFrom("stats", "as.formula", "reshape")
to your NAMESPACE file.
'library' or 'require' call to ‘psych’ which was already attached by Depends.
  Please remove these calls from your code.
Rd file 'dmes.Rd':
  \examples lines wider than 100 characters:
     > #cf. Efron, B. & Tibshirani (1993). An Introduction to the Bootstrap. New York/London: Chapman&Hall.
     > #Ruscio, J. & Mullen, T. (2012). Confidence Intervals for the Probability of Superiority Effect Size Measure and the Area Under a Rec ... [TRUNCATED]

Rd file 'orddom_f.Rd':
  \examples lines wider than 100 characters:
     orddom_f(con_pre,ex_pre,alpha=0.025,decimalpt=",",description="EXP 01: Between groups at time 01")   
     orddom_f(con_post,ex_post,alpha=0.025,decimalpt=",",description="EXP 01: Between groups at time 02") 
     orddom_f(ex_pre,ex_post,alpha=0.025,paired=TRUE,decimalpt=",",description="EXP 01: Within exp 01 to 02") 
     orddom_f(con_pre,con_post,alpha=0.025,paired=TRUE,decimalpt=",",description="EXP 01: Within con 01 to 02") 

These lines will be truncated in the PDF manual.
'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.
genRidge: no visible global function definition for ‘plogis’
ordGene: no visible global function definition for ‘anova’
ordGene: no visible global function definition for ‘lm’
ordSelect: no visible binding for global variable ‘sd’
ordSmooth: no visible binding for global variable ‘sd’
plot.ordPen: no visible global function definition for ‘grey’
plot.ordPen: no visible global function definition for ‘devAskNewPage’
plot.ordPen: no visible global function definition for ‘plot’
plot.ordPen: no visible global function definition for ‘lines’
predict.ordPen: no visible global function definition for ‘plogis’
Undefined global functions or variables:
  anova devAskNewPage grey lines lm plogis plot sd
Consider adding
  importFrom("grDevices", "devAskNewPage", "grey")
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "anova", "lm", "plogis", "sd")
to your NAMESPACE file.
ORICC1: no visible binding for global variable ‘sd’
ORICC1: no visible global function definition for ‘write.table’
ORICC1: no visible global function definition for ‘postscript’
ORICC1: no visible global function definition for ‘jpeg’
ORICC1: no visible global function definition for ‘plot’
ORICC1: no visible global function definition for ‘points’
ORICC1: no visible global function definition for ‘dev.off’
ORICC1: no visible global function definition for ‘par’
ORICC2: no visible binding for global variable ‘sd’
ORICC2: no visible global function definition for ‘write.table’
ORICC2: no visible global function definition for ‘postscript’
ORICC2: no visible global function definition for ‘jpeg’
ORICC2: no visible global function definition for ‘plot’
ORICC2: no visible global function definition for ‘points’
ORICC2: no visible global function definition for ‘dev.off’
ORICC2: no visible global function definition for ‘par’
Undefined global functions or variables:
  dev.off jpeg par plot points postscript sd write.table
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "postscript")
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
boat3d: no visible global function definition for ‘rgl.cur’
boat3d: no visible global function definition for ‘open3d’
boat3d: no visible global function definition for ‘clear3d’
boat3d: no visible global function definition for ‘bg3d’
boat3d: no visible global function definition for ‘rgl.set’
boat3d: no visible global function definition for ‘triangles3d’
boat3d: no visible global function definition for ‘quads3d’
boat3d: no visible global function definition for ‘decorate3d’
boat3d: no visible global function definition for ‘scatterplot3d’
orientlm: no visible global function definition for ‘model.matrix’
orientlm: no visible global function definition for ‘lm’
Undefined global functions or variables:
  bg3d clear3d decorate3d lm model.matrix open3d quads3d rgl.cur
  rgl.set scatterplot3d triangles3d
Consider adding
  importFrom("stats", "lm", "model.matrix")
to your NAMESPACE file.
File ‘OriGen/libs/OriGen.so’:
  Found ‘_gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘_gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘_gfortran_st_read’, possibly from ‘read’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘_gfortran_st_rewind’, possibly from ‘rewind’ (Fortran)
    Object: ‘OriGen.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Package which this enhances but not available for checking: ‘dcemriS4’
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘genefilter’ ‘gtools’ ‘nlme’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
est.lme : <anonymous>: warning in rank(iru, ties = "min"): partial
  argument match of ‘ties’ to ‘ties.method’
est.lme : <anonymous>: no visible global function definition for ‘lme’
est.lme : <anonymous>: no visible global function definition for
  ‘VarCorr’
guo: no visible global function definition for ‘p.adjust’
guo: no visible global function definition for ‘na.omit’
pttest : ptest: no visible global function definition for ‘na.omit’
srt : <anonymous>: no visible global function definition for
  ‘rowttests’
Undefined global functions or variables:
  VarCorr lme na.omit p.adjust rowttests
Consider adding
  importFrom("stats", "na.omit", "p.adjust")
to your NAMESPACE file.
plot.SplineBasis: no visible global function definition for ‘matplot’
plot,SplineBasis-matrix: no visible global function definition for
  ‘matplot’
plot,SplineBasis-missing: no visible global function definition for
  ‘matplot’
Undefined global functions or variables:
  matplot
Consider adding
  importFrom("graphics", "matplot")
to your NAMESPACE file.
'library' or 'require' call to ‘polynom’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘polynom’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
chebyshev.c.polynomials: no visible global function definition for
  ‘polynomial’
chebyshev.s.polynomials: no visible global function definition for
  ‘polynomial’
chebyshev.t.polynomials: no visible global function definition for
  ‘polynomial’
chebyshev.u.polynomials: no visible global function definition for
  ‘polynomial’
gegenbauer.polynomials: no visible global function definition for
  ‘polynomial’
ghermite.h.polynomials: no visible global function definition for
  ‘polynomial’
glaguerre.polynomials: no visible global function definition for
  ‘polynomial’
hermite.h.polynomials: no visible global function definition for
  ‘polynomial’
hermite.he.polynomials: no visible global function definition for
  ‘polynomial’
jacobi.g.polynomials: no visible global function definition for
  ‘polynomial’
jacobi.p.polynomials: no visible global function definition for
  ‘polynomial’
legendre.polynomials: no visible global function definition for
  ‘polynomial’
monic.polynomials: no visible global function definition for
  ‘polynomial’
orthogonal.polynomials: no visible global function definition for
  ‘polynomial’
orthonormal.polynomials: no visible global function definition for
  ‘polynomial’
polynomial.derivatives: no visible global function definition for
  ‘deriv’
polynomial.integrals: no visible global function definition for
  ‘integral’
polynomial.values: no visible global function definition for ‘predict’
schebyshev.t.polynomials: no visible global function definition for
  ‘polynomial’
schebyshev.u.polynomials: no visible global function definition for
  ‘polynomial’
slegendre.polynomials: no visible global function definition for
  ‘polynomial’
Undefined global functions or variables:
  deriv integral polynomial predict
Consider adding
  importFrom("stats", "deriv", "predict")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘igraph’ ‘sp’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
as_igraph : <anonymous>: no visible global function definition for
  ‘distHaversine’
as_igraph: no visible global function definition for ‘graph.edgelist’
as_igraph: no visible global function definition for ‘E’
as_igraph: no visible global function definition for ‘E<-’
as_sp_lines: no visible global function definition for ‘Lines’
as_sp_points: no visible global function definition for
  ‘SpatialPointsDataFrame’
as_sp_polygons: no visible global function definition for ‘Polygons’
as_sp_polygons: no visible global function definition for
  ‘SpatialPolygons’
as_sp_polygons: no visible global function definition for
  ‘SpatialPolygonsDataFrame’
make_SLDF: no visible global function definition for ‘SpatialLines’
make_SLDF: no visible global function definition for
  ‘SpatialLinesDataFrame’
osm_crs: no visible global function definition for ‘CRS’
plot.osmar: no visible global function definition for ‘gray’
plot_nodes: no visible global function definition for ‘points’
plot_nodes: no visible global function definition for ‘plot’
plot_ways: no visible global function definition for ‘plot’
plot_ways: no visible global function definition for ‘lines’
ways_nodes2Line: no visible global function definition for ‘Line’
ways_nodes2Polygon: no visible global function definition for ‘Polygon’
Undefined global functions or variables:
  CRS E E<- Line Lines Polygon Polygons SpatialLines
  SpatialLinesDataFrame SpatialPointsDataFrame SpatialPolygons
  SpatialPolygonsDataFrame distHaversine graph.edgelist gray lines plot
  points
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
Dependence on R version ‘3.4.4’ not with patchlevel 0
Malformed Description field: should contain one or more complete sentences.
odm: no visible binding for global variable ‘sd’
odm : <anonymous>: no visible global function definition for ‘sd’
odm : <anonymous>: no visible global function definition for ‘quantile’
odm: no visible global function definition for ‘prcomp’
quant.const: no visible global function definition for ‘quantile’
quant.const.D: no visible global function definition for ‘reshape’
quant.const.D: no visible global function definition for ‘quantile’
quant.linear.D: no visible global function definition for ‘reshape’
quant.nonlin : FrankModel: no visible global function definition for
  ‘qt’
quant.nonlin : FrankModel: no visible global function definition for
  ‘pt’
quant.nonlin: no visible global function definition for ‘predict’
quant.nonlin.D: no visible global function definition for ‘reshape’
quant.nonlin.D: no visible global function definition for ‘predict’
quant.nonpar.D: no visible global function definition for ‘reshape’
rgrubbs.test: no visible global function definition for ‘sd’
plot,OutlierDM-missing: no visible binding for global variable ‘pch’
summary,OutlierDM: no visible global function definition for ‘head’
Undefined global functions or variables:
  head pch prcomp predict pt qt quantile reshape sd
Consider adding
  importFrom("stats", "prcomp", "predict", "pt", "qt", "quantile",
             "reshape", "sd")
  importFrom("utils", "head")
to your NAMESPACE file.
Electre3_AlphaBetaThresholds: no visible global function definition for
  ‘plot’
Electre3_SimpleThresholds: no visible global function definition for
  ‘plot’
Electre_1: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Dependence on R version ‘3.4.4’ not with patchlevel 0
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.
Missing or unexported objects:
  ‘devtools::use_build_ignore’ ‘devtools::use_travis’
Malformed Description field: should contain one or more complete sentences.
Non-standard files/directories found at top level:
  ‘DESCRIPTION_EX’ ‘divers’ ‘main.R’ ‘testsDev’
[,ClassW: warning in switch(EXP = i, u1 = {: partial argument match of
  ‘EXP’ to ‘EXPR’
[,ClassW: warning in return(x@u1): partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in }, u2 = {: partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in return(x@u2): partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in }, w1 = {: partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in return(x@w1): partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in }): partial argument match of ‘EXP’ to ‘EXPR’
[<-,ClassW: warning in switch(EXP = i, u1 = {: partial argument match
  of ‘EXP’ to ‘EXPR’
[<-,ClassW: warning in x@u1 <- value: partial argument match of ‘EXP’
  to ‘EXPR’
[<-,ClassW: warning in }, u2 = {: partial argument match of ‘EXP’ to
  ‘EXPR’
[<-,ClassW: warning in x@u2 <- value: partial argument match of ‘EXP’
  to ‘EXPR’
[<-,ClassW: warning in }, w1 = {: partial argument match of ‘EXP’ to
  ‘EXPR’
[<-,ClassW: warning in x@w1 <- value: partial argument match of ‘EXP’
  to ‘EXPR’
[<-,ClassW: warning in }): partial argument match of ‘EXP’ to ‘EXPR’
paf: no visible global function definition for ‘as.formula’
paf: no visible global function definition for ‘model.response’
paf: no visible global function definition for ‘model.frame’
paf: no visible global function definition for ‘model.matrix’
plot.paf: no visible global function definition for ‘plot’
plot.paf: no visible global function definition for ‘lines’
Undefined global functions or variables:
  as.formula lines model.frame model.matrix model.response plot
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
CalGIF: no visible binding for global variable ‘PAGIData’
CalGIF2: no visible binding for global variable ‘PAGIData’
PAGI.Main: no visible binding for global variable ‘PAGIData’
PAGI.Main: no visible global function definition for ‘p.adjust’
PAGI.Main: no visible global function definition for ‘pt’
getclass.labels: no visible binding for global variable ‘ExampleData’
getdataset: no visible binding for global variable ‘ExampleData’
Undefined global functions or variables:
  ExampleData PAGIData p.adjust pt
Consider adding
  importFrom("stats", "p.adjust", "pt")
to your NAMESPACE file.
Rd file 'CalGIF.Rd':
  \examples lines wider than 100 characters:
     ###calculate the global influence factor (GIF) by using the random walk with restart (RWR) algorithm###
     #Each element is the GIF score and whose name correspond to gene symbol in the gene expression data. 
     #Each element is the GIF score and whose name correspond to gene symbol in the gene expression data. 

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

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

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

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

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

These lines will be truncated in the PDF manual.
pairsD3: no visible global function definition for ‘gray.colors’
Undefined global functions or variables:
  gray.colors
Consider adding
  importFrom("grDevices", "gray.colors")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘CorShrink’
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘lattice’ ‘vegan’
  Please remove these calls from your code.
Rd file 'syas.Rd':
  \examples lines wider than 100 characters:
     bcrossv.sa(modernq[,1],perq2,a.d,delta=25,method="canberra",quant=0.05,trials=c(5, 0.05),detrend=FALSE)

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

These lines will be truncated in the PDF manual.
GOpredict: no visible global function definition for ‘fisher.test’
KEGGpredict: no visible global function definition for ‘fisher.test’
ProteinCluster: no visible global function definition for ‘ecdf’
ProteinCluster: no visible global function definition for ‘as.hclust’
ProteinCluster: no visible global function definition for
  ‘as.dendrogram’
ProteinCluster : addE: no visible global function definition for
  ‘is.leaf’
ProteinCluster: no visible global function definition for ‘plot’
SignificantSubcluster: no visible global function definition for
  ‘order.dendrogram’
SignificantSubcluster: no visible global function definition for
  ‘fisher.test’
SignificantSubcluster: no visible global function definition for ‘plot’
Undefined global functions or variables:
  as.dendrogram as.hclust ecdf fisher.test is.leaf order.dendrogram
  plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "as.dendrogram", "as.hclust", "ecdf",
             "fisher.test", "is.leaf", "order.dendrogram")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Paneldata.formula: no visible global function definition for
  ‘model.frame’
Paneldata.formula: no visible global function definition for
  ‘model.matrix’
Paneldata.formula: no visible global function definition for
  ‘model.response’
summary.Paneldata: no visible global function definition for ‘coef’
summary.Paneldata: no visible global function definition for ‘pt’
Undefined global functions or variables:
  coef model.frame model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.frame", "model.matrix",
             "model.response", "pt")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from ‘parallelize.dynamic’ for: ‘initialize’

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

Probably some imports need to be declared in the NAMESPACE file.
'library' or 'require' call to ‘package’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘methods’ ‘parallel’ ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
parallelSVM.default: no visible binding for global variable ‘na.omit’
parallelSVM.formula: no visible binding for global variable ‘na.omit’
predict.parallelSVM: no visible binding for global variable ‘predict’
Undefined global functions or variables:
  na.omit predict
Consider adding
  importFrom("stats", "na.omit", "predict")
to your NAMESPACE file.
Package in Depends field not imported from: ‘grid’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.formula.make: no visible global function definition for ‘formula’
regress: no visible global function definition for ‘lm’
regress: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  formula lm model.matrix
Consider adding
  importFrom("stats", "formula", "lm", "model.matrix")
to your NAMESPACE file.
adalasso: no visible global function definition for ‘predict’
lm.ridge.univariate: no visible global function definition for ‘sd’
mylars: no visible global function definition for ‘predict’
mylars: no visible binding for global variable ‘var’
performance.pcor: no visible global function definition for
  ‘ggm.test.edges’
performance.pcor: no visible global function definition for ‘var’
ridge.cv: no visible global function definition for ‘coef’
ridge.cv: no visible global function definition for ‘plot’
Undefined global functions or variables:
  coef ggm.test.edges plot predict sd var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "predict", "sd", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Malformed Title field: should not end in a period.
Calls with DUP:
   .C("aracne", as.double(t(mis)), as.integer(n), as.double(eps), 
       as.double(eta), res = double(n * n), PACKAGE = "parmigene", 
       DUP = FALSE)
   .C("clr", as.double(t(mis)), as.integer(n), res = double(n * 
       n), PACKAGE = "parmigene", DUP = FALSE)
   .C("mrnet", as.double(t(mis)), as.integer(n), res = double(n * 
       n), PACKAGE = "parmigene", DUP = FALSE)
DUP is no longer supported and will be ignored.
File ‘parmigene/libs/parmigene.so’:
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘nnet’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fitOR: no visible global function definition for ‘multinom’
fitOR: no visible global function definition for ‘formula’
fitOR: no visible global function definition for ‘coef’
fitOR: no visible global function definition for ‘optim’
reportOR: no visible global function definition for ‘qnorm’
reportOR: no visible global function definition for ‘pchisq’
reportOR: no visible global function definition for ‘coef’
simData: no visible global function definition for ‘rnorm’
simData: no visible global function definition for ‘runif’
Undefined global functions or variables:
  coef formula multinom optim pchisq qnorm rnorm runif
Consider adding
  importFrom("stats", "coef", "formula", "optim", "pchisq", "qnorm",
             "rnorm", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
partitionMap: no visible global function definition for ‘predict’
partitionMap: no visible global function definition for ‘rnorm’
partitionMap: no visible binding for global variable ‘sd’
partitionMap: no visible global function definition for ‘sd’
partitionMap: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  predict quantile rnorm sd
Consider adding
  importFrom("stats", "predict", "quantile", "rnorm", "sd")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from ‘partsm’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
parviol: no visible global function definition for ‘plot.new’
parviol: no visible global function definition for ‘plot.window’
parviol: no visible global function definition for ‘title’
parviol: no visible global function definition for ‘lines’
parviol: no visible global function definition for ‘text’
parviol: no visible global function definition for ‘rgb’
selecto: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines plot.new plot.window rgb text title
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "plot.new", "plot.window", "text",
             "title")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘ape’ ‘caper’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
conch: no visible global function definition for ‘read.tree’
conch: no visible global function definition for ‘reorder’
conch: no visible global function definition for ‘read.nexus’
conch: no visible global function definition for ‘.compressTipLabel’
conch: no visible global function definition for ‘drop.tip’
conch: no visible global function definition for ‘extract.clade’
conch: no visible global function definition for ‘which.edge’
conch: no visible global function definition for ‘write.tree’
pastis_main: no visible global function definition for ‘combn’
read_input: no visible global function definition for ‘read.tree’
read_input: no visible global function definition for ‘reorder’
read_input: no visible global function definition for ‘read.csv’
read_input: no visible global function definition for ‘read.dna’
Undefined global functions or variables:
  .compressTipLabel combn drop.tip extract.clade read.csv read.dna
  read.nexus read.tree reorder which.edge write.tree
Consider adding
  importFrom("stats", "reorder")
  importFrom("utils", "combn", "read.csv")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘e1071’
  Please remove these calls from your code.
SweaveAll: no visible global function definition for ‘file_test’
texi2dvi: no visible global function definition for ‘file_test’
Undefined global functions or variables:
  file_test
Consider adding
  importFrom("utils", "file_test")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘plspm’ ‘tester’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Checking should be performed on sources prepared by ‘R CMD build’.
GNU make is a SystemRequirements.
Malformed Title field: should not end in a period.
add_noise: no visible global function definition for ‘rnorm’
estimate_risk_dream6 : <anonymous>: no visible global function
  definition for ‘var’
generate_sample: no visible global function definition for ‘rnorm’
generate_sample: no visible global function definition for ‘runif’
sample_function: no visible global function definition for ‘runif’
sample_function : <anonymous>: no visible global function definition
  for ‘var’
sample_function_multi_mod_weight: no visible global function definition
  for ‘runif’
sample_function_multi_mod_weight : <anonymous>: no visible global
  function definition for ‘var’
sample_function_single_mod: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  rnorm runif var
Consider adding
  importFrom("stats", "rnorm", "runif", "var")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from ‘PAWL’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘foreach’ ‘ggplot2’ ‘reshape’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘foreach’ ‘ggplot2’ ‘methods’ ‘mvtnorm’ ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'createAdaptiveRandomWalkProposal.Rd':
  \usage lines wider than 90 characters:
         createAdaptiveRandomWalkProposal(nchains, targetdimension, adaptiveproposal, adaptationrate, sigma_init)

These lines will be truncated in the PDF manual.
Found the following sources/headers with CR or CRLF line endings:
  src/zmqsrc/src/condition_variable.hpp
Some Unix compilers require LF line endings.
'library' or 'require' call to ‘foreach’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
dotplot.pbo: no visible global function definition for ‘reorder’
pbo: no visible global function definition for ‘%dopar%’
pbo: no visible global function definition for ‘foreach’
pbo: no visible global function definition for ‘lm’
xyplot.pbo: no visible global function definition for ‘ecdf’
xyplot.pbo: no visible global function definition for ‘doubleYScale’
xyplot.pbo: no visible global function definition for ‘reorder’
Undefined global functions or variables:
  %dopar% doubleYScale ecdf foreach lm reorder
Consider adding
  importFrom("stats", "ecdf", "lm", "reorder")
to your NAMESPACE file.
a_get_native: no visible global function definition for ‘par’
a_get_relative: no visible global function definition for ‘par’
brackets: no visible global function definition for ‘par’
brackets: no visible global function definition for ‘dist’
brackets: no visible global function definition for ‘lines’
Undefined global functions or variables:
  dist lines par
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "dist")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
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.
PCDReg.wf: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  optimize
Consider adding
  importFrom("stats", "optimize")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘FFTrees’
PdofCSGt.bootstrap5: no visible global function definition for ‘rnorm’
PdofCSGt.bootstrap5: no visible global function definition for ‘rt’
PdofCSt.T1or2: no visible global function definition for ‘combn’
PofCSGt: no visible global function definition for ‘combn’
PofCSLt.bootstrap5: no visible global function definition for ‘rnorm’
PofCSLt.bootstrap5: no visible global function definition for ‘rt’
PofCSt: no visible global function definition for ‘pnorm’
tindep: no visible binding for global variable ‘var’
tindep: no visible global function definition for ‘pt’
Undefined global functions or variables:
  combn pnorm pt rnorm rt var
Consider adding
  importFrom("stats", "pnorm", "pt", "rnorm", "rt", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pdist: no visible global function definition for ‘dist’
pdist: no visible global function definition for ‘new’
Undefined global functions or variables:
  dist new
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dist")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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.
peacf: no visible global function definition for ‘is.ts’
peacf: no visible global function definition for ‘cycle’
peacf: no visible global function definition for ‘ts.intersect’
peacf: no visible global function definition for ‘lag’
peacf: no visible global function definition for ‘ts’
peacf: no visible global function definition for ‘pchisq’
peacf.plot: no visible global function definition for ‘plot’
peacf.plot: no visible global function definition for ‘segments’
peacf.plot: no visible global function definition for ‘title’
pear: no visible global function definition for ‘cycle’
pear: no visible global function definition for ‘pchisq’
peboxplot: no visible global function definition for ‘cycle’
peboxplot: no visible global function definition for ‘boxplot’
peboxplot: no visible global function definition for ‘title’
peplot: no visible global function definition for ‘par’
peplot: no visible global function definition for ‘cycle’
peplot: no visible global function definition for ‘plot’
peplot: no visible global function definition for ‘identify’
peplot: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  boxplot cycle identify is.ts lag mtext par pchisq plot segments title
  ts ts.intersect
Consider adding
  importFrom("graphics", "boxplot", "identify", "mtext", "par", "plot",
             "segments", "title")
  importFrom("stats", "cycle", "is.ts", "lag", "pchisq", "ts",
             "ts.intersect")
to your NAMESPACE file.
The following files should probably not be installed:
  ‘addendum.tex’, ‘slplot.tex’, ‘table1.tex’, ‘table3.tex’

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

These lines will be truncated in the PDF manual.
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘RcppArmadillo’ ‘ggplot2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
AssoTestProc: no visible global function definition for ‘rbinom’
AssoTestProc: no visible global function definition for ‘princomp’
AssoTestProc: no visible global function definition for ‘loadings’
AssoTestProc: no visible global function definition for ‘lm’
CNVtypeAnay: no visible global function definition for ‘cov’
ClusProc: no visible global function definition for ‘princomp’
ClusProc: no visible global function definition for ‘prcomp’
ClusProc0: no visible global function definition for ‘kmeans’
ClusProc0: no visible global function definition for ‘cov’
Inde: no visible global function definition for ‘lm’
Inde: no visible global function definition for ‘var’
STE: no visible global function definition for ‘pchisq’
STIM: no visible global function definition for ‘cor’
STIM: no visible global function definition for ‘pchisq’
plot.clust: no visible global function definition for ‘princomp’
plot.clust: no visible global function definition for ‘loadings’
plot.clust: no visible global function definition for ‘qplot’
plot.clust: no visible global function definition for ‘geom_histogram’
plot.clust: no visible global function definition for ‘aes_string’
plot.clust: no visible global function definition for ‘barplot’
plot.clust: no visible global function definition for ‘title’
plot.clust: no visible global function definition for ‘mtext’
plot.clust: no visible global function definition for ‘text’
Undefined global functions or variables:
  aes_string barplot cor cov geom_histogram kmeans lm loadings mtext
  pchisq prcomp princomp qplot rbinom text title var
Consider adding
  importFrom("graphics", "barplot", "mtext", "text", "title")
  importFrom("stats", "cor", "cov", "kmeans", "lm", "loadings", "pchisq",
             "prcomp", "princomp", "rbinom", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
blup: no visible global function definition for ‘model.matrix’
blup: no visible global function definition for ‘model.frame’
blup: no visible global function definition for ‘read.table’
calcG: no visible global function definition for ‘as’
gblup: no visible global function definition for ‘model.matrix’
gblup: no visible global function definition for ‘model.frame’
Undefined global functions or variables:
  as model.frame model.matrix read.table
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "model.frame", "model.matrix")
  importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
PEMM_fun : find.lambda: no visible global function definition for
  ‘optimize’
PEMM_fun: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov optimize
Consider adding
  importFrom("stats", "cov", "optimize")
to your NAMESPACE file.
create.data: no visible global function definition for ‘rexp’
create.data: no visible global function definition for ‘runif’
create.data: no visible global function definition for ‘rbinom’
opt.splitval: no visible global function definition for ‘na.omit’
opt2D : opt.both: no visible global function definition for ‘optim’
Undefined global functions or variables:
  na.omit optim rbinom rexp runif
Consider adding
  importFrom("stats", "na.omit", "optim", "rbinom", "rexp", "runif")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘CoxBoost’ ‘codetools’ ‘locfit’ ‘penalized’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
complexity.LASSO: no visible global function definition for ‘profL1’
complexity.ipec.CoxBoost: no visible global function definition for
  ‘CoxBoost’
complexity.ipec.CoxBoost: no visible global function definition for
  ‘locfit’
complexity.mincv.CoxBoost: no visible global function definition for
  ‘cv.CoxBoost’
complexity.ripec.CoxBoost: no visible global function definition for
  ‘CoxBoost’
complexity.ripec.CoxBoost: no visible global function definition for
  ‘locfit’
extract: no visible global function definition for ‘findGlobals’
fit.CoxBoost: no visible global function definition for ‘CoxBoost’
fit.LASSO: no visible global function definition for ‘penalized’
Undefined global functions or variables:
  CoxBoost cv.CoxBoost findGlobals locfit penalized profL1
Rd file 'aggregation.brier.Rd':
  \usage lines wider than 90 characters:
     aggregation.brier(full.data=NULL, response, x, model, cplx=NULL,  type=c("apparent", "noinf"), 

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

These lines will be truncated in the PDF manual.
performance.curves.plot: no visible global function definition for
  ‘postscript’
performance.curves.plot: no visible global function definition for
  ‘axis’
performance.curves.plot: no visible global function definition for
  ‘lines’
performance.curves.plot: no visible global function definition for
  ‘legend’
performance.curves.plot: no visible global function definition for
  ‘grid’
performance.curves.plot: no visible global function definition for
  ‘dev.off’
precision.recall.curves.plot: no visible global function definition for
  ‘postscript’
precision.recall.curves.plot: no visible global function definition for
  ‘axis’
precision.recall.curves.plot: no visible global function definition for
  ‘lines’
precision.recall.curves.plot: no visible global function definition for
  ‘legend’
precision.recall.curves.plot: no visible global function definition for
  ‘grid’
precision.recall.curves.plot: no visible global function definition for
  ‘dev.off’
Undefined global functions or variables:
  axis dev.off grid legend lines postscript
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "axis", "grid", "legend", "lines")
to your NAMESPACE file.
Package suggested but not available for checking: ‘dendextendRcpp’
permalgorithm: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Malformed Description field: should contain one or more complete sentences.
ksample.pclt: no visible global function definition for ‘pchisq’
pCI: no visible global function definition for ‘qbeta’
permKS.formula: no visible global function definition for ‘terms’
permTREND.default: no visible global function definition for ‘cor’
permTREND.formula: no visible global function definition for ‘terms’
permTS.formula: no visible global function definition for ‘terms’
trend.pclt: no visible global function definition for ‘pnorm’
twosample.pclt: no visible global function definition for ‘pnorm’
twosample.pclt: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  cor pchisq pnorm qbeta terms
Consider adding
  importFrom("stats", "cor", "pchisq", "pnorm", "qbeta", "terms")
to your NAMESPACE file.
Rd file 'perm-internal.Rd':
  \usage lines wider than 90 characters:
     ksample.exact.mc(scores, group, nmc = 10^4 - 1, seed = 1234321, digits = 12, p.conf.level = 0.99, setSEED = TRUE)
     trend.exact.mc(scores, group, alternative = "two.sided", nmc = 10^3 - 1, seed = 1234321, digits = 12, p.conf.level = 0.99, setSEED = TR ... [TRUNCATED]
     twosample.exact.mc(scores, group, alternative = "two.sided", nmc = 10^4 - 1, seed = 1234321, digits = 12, p.conf.level = 0.99, setSEED  ... [TRUNCATED]

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

These lines will be truncated in the PDF manual.
hasMethod: no visible global function definition for ‘getS3method’
Undefined global functions or variables:
  getS3method
Consider adding
  importFrom("utils", "getS3method")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘MASS’ which was already attached by Depends.
  Please remove these calls from your code.
pGLS: no visible global function definition for ‘model.response’
pGLS: no visible global function definition for ‘model.matrix’
pGLS: no visible global function definition for ‘pt’
Undefined global functions or variables:
  model.matrix model.response pt
Consider adding
  importFrom("stats", "model.matrix", "model.response", "pt")
to your NAMESPACE file.
prepare_Rd: data_fs.Rd:11: Dropping empty section \source
prepare_Rd: var_fs.Rd:12-14: Dropping empty section \references
GNU make is a SystemRequirements.
PharmPow_crossover: no visible global function definition for
  ‘read.table’
PharmPow_crossover: no visible global function definition for
  ‘write.csv’
PharmPow_crossover: no visible global function definition for ‘pdf’
PharmPow_crossover: no visible global function definition for ‘dev.off’
PharmPow_parallel: no visible global function definition for
  ‘read.table’
PharmPow_parallel: no visible global function definition for
  ‘write.csv’
PharmPow_parallel: no visible global function definition for ‘pdf’
PharmPow_parallel: no visible global function definition for ‘dev.off’
fig_PharmPow_crossover: no visible global function definition for
  ‘read.csv’
fig_PharmPow_parallel: no visible global function definition for
  ‘read.csv’
Undefined global functions or variables:
  dev.off pdf read.csv read.table write.csv
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "read.csv", "read.table", "write.csv")
to your NAMESPACE file.
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.
pheno.ddm: no visible global function definition for ‘new’
pheno.flm.fit: no visible binding for global variable ‘na.exclude’
pheno.flm.fit: no visible global function definition for ‘terms’
pheno.flm.fit: no visible global function definition for ‘residuals’
pheno.flm.fit: no visible global function definition for ‘qt’
pheno.lad.fit: no visible binding for global variable ‘na.exclude’
pheno.mlm.fit: no visible binding for global variable ‘na.exclude’
pheno.mlm.fit: no visible global function definition for ‘residuals’
Undefined global functions or variables:
  na.exclude new qt residuals terms
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "na.exclude", "qt", "residuals", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Rd file 'pheno.mlm.fit.Rd':
  \examples lines wider than 100 characters:
             R <- pheno.mlm.fit(DWD)                                                         # parameter estimation
             summary(tr)$coef[2]                                                                     # slope of trend
             summary(tr)$coef[4]                                                                     # standard error of trend

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: ‘OutbreakTools’
Unknown packages ‘surface’, ‘bayou’ in Rd xrefs
Package suggested but not available for checking: ‘INLA’
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.
Dependence on R version ‘3.4.1’ not with patchlevel 0
File which contains pragma(s) suppressing diagnostics:
  ‘src/pijavski.cpp’
plot.pred.int: no visible global function definition for ‘plot.default’
plot.pred.int: no visible global function definition for ‘axis’
plot.pred.int: no visible global function definition for ‘box’
plot.pred.int : cidist: no visible global function definition for
  ‘ecdf’
plot.pred.int : negcidist: no visible global function definition for
  ‘ecdf’
plot.pred.int : pi.col.fun: no visible global function definition for
  ‘gray’
plot.pred.int: no visible global function definition for ‘segments’
plot.pred.int: no visible global function definition for ‘points’
plot.pred.int: no visible global function definition for ‘abline’
pred.int: no visible binding for global variable ‘sd’
prop.test.mult: no visible global function definition for ‘qnorm’
sim.basic: no visible global function definition for ‘rbinom’
sim.basic: no visible global function definition for ‘rnorm’
t.test.mult: no visible global function definition for ‘qt’
Undefined global functions or variables:
  abline axis box ecdf gray plot.default points qnorm qt rbinom rnorm
  sd segments
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "box", "plot.default",
             "points", "segments")
  importFrom("stats", "ecdf", "qnorm", "qt", "rbinom", "rnorm", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: ‘ggsubplot’
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Depends: includes the non-default packages:
  'RGtk2', 'gWidgetsRGtk2', 'cairoDevice', 'lattice', 'rggobi',
  'ggplot2', 'proto'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘RGtk2’ ‘gWidgetsRGtk2’
A package should be listed in only one of these fields.
Package in Depends field not imported from: ‘cairoDevice’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
prepare_Rd: PKgraph.Rd:11-13: Dropping empty section \arguments
prepare_Rd: PKgraph.Rd:17-19: Dropping empty section \examples
prepare_Rd: pkdata.Rd:9-11: Dropping empty section \format
prepare_Rd: pkdata.Rd:14-16: Dropping empty section \examples
prepare_Rd: pkdata2.Rd:9-11: Dropping empty section \format
prepare_Rd: pkdata2.Rd:14-16: Dropping empty section \examples
Rd file 'RSA.Rd':
  \examples lines wider than 100 characters:
     PKI.load.OpenSSH.pubkey("ssh-rsa AAAAB3NzaC1yc2EAAAABIwAAAIEAuvOXqfZ3pJeWeqyQOIXZwmgM1RBqPUmVx3XgntpA+YtOZjKfuoJSpg3LhBuI/wXx8L2QZXNFib ... [TRUNCATED]

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

These lines will be truncated in the PDF manual.
Packages in Depends field not imported from:
  ‘Formula’ ‘sm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
nrmlepln: no visible global function definition for ‘pchisq’
nrmlerasch: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
Package required but not available: ‘ggtern’

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

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

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

These lines will be truncated in the PDF manual.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
llla.bi: no visible global function definition for ‘as.formula’
llla.bi: no visible global function definition for ‘glm’
llla.bi: no visible global function definition for ‘binomial’
llla.bi: no visible binding for global variable ‘logit’
llla.bi: no visible global function definition for ‘vcov’
llla.bi: no visible global function definition for ‘coef’
llla.mc: no visible global function definition for ‘model.matrix’
llla.mc: no visible global function definition for ‘as.formula’
llla.mc: no visible global function definition for ‘coxph’
llla.mc: no visible global function definition for ‘vcov’
llla.mc: no visible global function definition for ‘coef’
llla.mle: no visible global function definition for ‘as.formula’
llla.mle: no visible global function definition for ‘glm’
llla.mle: no visible global function definition for ‘poisson’
llla.mle: no visible global function definition for ‘coef’
llla.mle: no visible global function definition for ‘vcov’
mclgen: no visible global function definition for ‘reshape’
simRasch.1D: no visible global function definition for ‘rnorm’
simRasch.1D: no visible global function definition for ‘runif’
vcov.sandwich.glm: no visible global function definition for
  ‘model.matrix’
vcov.sandwich.glm: no visible global function definition for ‘weights’
vcov.sandwich.glm: no visible global function definition for
  ‘residuals’
vcov.sandwich.glm: no visible global function definition for ‘vcov’
Undefined global functions or variables:
  as.formula binomial coef coxph glm logit model.matrix poisson reshape
  residuals rnorm runif vcov weights
Consider adding
  importFrom("stats", "as.formula", "binomial", "coef", "glm",
             "model.matrix", "poisson", "reshape", "residuals", "rnorm",
             "runif", "vcov", "weights")
to your NAMESPACE file.
print.densityEHpi: no visible global function definition for ‘str’
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
Rd file 'predict.plus.Rd':
  \examples lines wider than 100 characters:
     extracted.values <- predict(object, lam = sort(object$lam.path[1:10],decreasing=TRUE), newx=object$x)

These lines will be truncated in the PDF manual.
Malformed Description field: should contain one or more complete sentences.
.MCM: no visible global function definition for ‘runif’
.MCM: no visible global function definition for ‘rmultinom’
.MCM: no visible global function definition for ‘mahalanobis’
.MCM: no visible global function definition for ‘optimize’
.MCM : f: no visible global function definition for ‘mahalanobis’
.MCM: no visible global function definition for ‘alarm’
.igpark: no visible global function definition for ‘kmeans’
.loglik: no visible global function definition for ‘mahalanobis’
.plot.gpcm: no visible global function definition for ‘plot’
.plot.gpcm: no visible global function definition for ‘lines’
.plot.gpcm: no visible global function definition for ‘legend’
.rwgpar: no visible global function definition for ‘rexp’
.weights: no visible global function definition for ‘mahalanobis’
Undefined global functions or variables:
  alarm kmeans legend lines mahalanobis optimize plot rexp rmultinom
  runif
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "kmeans", "mahalanobis", "optimize", "rexp",
             "rmultinom", "runif")
  importFrom("utils", "alarm")
to your NAMESPACE file.
dbm: no visible global function definition for ‘optim’
dbm: no visible global function definition for ‘new’
destat: no visible global function definition for ‘weighted.mean’
local.knn: no visible global function definition for ‘sd’
local.knn: no visible global function definition for ‘optim’
mdpref: no visible global function definition for ‘sd’
mdpref: no visible global function definition for ‘text’
mdpref: no visible global function definition for ‘lines’
phicom: no visible global function definition for ‘optim’
phicom: no visible global function definition for ‘new’
pl: no visible global function definition for ‘optim’
pl: no visible global function definition for ‘new’
rol: no visible global function definition for ‘nlm’
rol: no visible global function definition for ‘new’
wdbm: no visible global function definition for ‘optim’
wdbm: no visible global function definition for ‘new’
Undefined global functions or variables:
  lines new nlm optim sd text weighted.mean
Consider adding
  importFrom("graphics", "lines", "text")
  importFrom("methods", "new")
  importFrom("stats", "nlm", "optim", "sd", "weighted.mean")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘MASS’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘MASS’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pnmtrem1: no visible global function definition for ‘pnorm’
pnmtrem1: no visible global function definition for ‘dnorm’
pnmtrem1: no visible global function definition for ‘ginv’
pnmtrem1 : fun: no visible global function definition for ‘pnorm’
pnmtrem1 : derf: no visible global function definition for ‘dnorm’
pnmtrem1 : derf: no visible global function definition for ‘pnorm’
pnmtrem1 : fun: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm ginv pnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘TODO.md’
'library' or 'require' call to ‘rgenoud’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
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.
Package which this enhances but not available for checking: ‘gt’
approxMargMLE: no visible global function definition for ‘optim’
approxMargMLECI : ciFunction: no visible global function definition for
  ‘qchisq’
approxMargMLECI: no visible global function definition for ‘uniroot’
margMLE: no visible global function definition for ‘optim’
margMLECI: no visible global function definition for ‘optim’
margMLECI : unNormLikeMinusVal: no visible global function definition
  for ‘qchisq’
margMLECI: no visible global function definition for ‘uniroot’
profMLECI : ciFunction: no visible global function definition for
  ‘qchisq’
profMLECI: no visible global function definition for ‘uniroot’
rtbinom: no visible global function definition for ‘rbinom’
rtpois: no visible global function definition for ‘rpois’
waldCI: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  optim qchisq qnorm rbinom rpois uniroot
Consider adding
  importFrom("stats", "optim", "qchisq", "qnorm", "rbinom", "rpois",
             "uniroot")
to your NAMESPACE file.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Packages in Depends field not imported from:
  ‘combinat’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Est.Depth: no visible global function definition for ‘quantile’
PS.FDR: no visible global function definition for ‘quantile’
Permu.Ind: no visible global function definition for ‘permn’
Permu.Ind: no visible global function definition for ‘hcube’
Trans.Data: no visible global function definition for ‘write.table’
Trans.Data: no visible global function definition for ‘predict’
Trans.Data: no visible global function definition for ‘lm’
Undefined global functions or variables:
  hcube lm permn predict quantile write.table
Consider adding
  importFrom("stats", "lm", "predict", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
rpoistweedie: no visible global function definition for ‘runif’
testOmegaPT: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
prepare_Rd: poistweedie.Rd:51: Dropping empty section \references
prepare_Rd: ppoistweedie.Rd:37: Dropping empty section \references
prepare_Rd: qpoistweedie.Rd:40: Dropping empty section \references
prepare_Rd: rpoistweedie.Rd:36: Dropping empty section \references
prepare_Rd: varpt.Rd:31: Dropping empty section \references
Rd file 'ppoistweedie.Rd':
  \examples lines wider than 100 characters:
     layout.show(1)                                                                                                                          ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Packages in Depends field not imported from:
  ‘MASS’ ‘scatterplot3d’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plot.poLCA: no visible global function definition for ‘layout’
plot.poLCA: no visible global function definition for ‘par’
poLCA: no visible global function definition for ‘model.frame’
poLCA: no visible global function definition for ‘model.response’
poLCA: no visible global function definition for ‘model.matrix’
poLCA: no visible global function definition for ‘runif’
poLCA: no visible global function definition for ‘ginv’
poLCA: no visible global function definition for ‘flush.console’
poLCA.makeplot.dich: no visible global function definition for
  ‘scatterplot3d’
poLCA.makeplot.poly: no visible global function definition for
  ‘scatterplot3d’
poLCA.se: no visible global function definition for ‘ginv’
poLCA.simdata: no visible global function definition for ‘runif’
poLCA.simdata: no visible global function definition for ‘rnorm’
poLCA.table: no visible global function definition for ‘model.frame’
print.poLCA: no visible global function definition for ‘pt’
print.poLCA: no visible global function definition for ‘flush.console’
rmulti: no visible global function definition for ‘runif’
Undefined global functions or variables:
  flush.console ginv layout model.frame model.matrix model.response par
  pt rnorm runif scatterplot3d
Consider adding
  importFrom("graphics", "layout", "par")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "pt", "rnorm", "runif")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Package suggested but not available for checking: ‘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.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘matrixcalc’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘matrixcalc’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
print.mixed.pom: no visible global function definition for ‘pnorm’
print.pom: no visible global function definition for ‘pnorm’
siteocc : get.mod.matrix: no visible binding for global variable
  ‘na.pass’
siteocc : get.mod.matrix: no visible global function definition for
  ‘formula’
siteocc : get.mod.matrix: no visible global function definition for
  ‘model.matrix’
siteocc: no visible global function definition for ‘nlminb’
siteocc: no visible global function definition for
  ‘is.positive.definite’
Undefined global functions or variables:
  formula is.positive.definite model.matrix na.pass nlminb pnorm
Consider adding
  importFrom("stats", "formula", "model.matrix", "na.pass", "nlminb",
             "pnorm")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘extdata’
'library' or 'require' call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Rd file 'popgen.Rd':
  \usage lines wider than 90 characters:
     popgen(datafile, ndigit = 3, freq.overall = T, freq.by.pop = T, genetic.stats = T, pairwise.fst = T)

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: ‘WhopGenome’
asymmetricIntervals: no visible global function definition for ‘stack’
bonferroniIntervals: no visible global function definition for ‘stack’
bonferroniIntervals: no visible global function definition for ‘lm’
bonferroniIntervals: no visible global function definition for
  ‘predict’
bootstrapIntervals: no visible global function definition for ‘stack’
component1a: no visible global function definition for ‘pnorm’
component1b: no visible global function definition for ‘pnorm’
component2: no visible global function definition for ‘dgamma’
eqnForMin: no visible global function definition for ‘pnorm’
eqnForMin: no visible global function definition for ‘integrate’
integrand : <anonymous>: no visible global function definition for
  ‘pnorm’
integrand: no visible global function definition for ‘dnorm’
integrate2: no visible global function definition for ‘integrate’
integrate2a: no visible global function definition for ‘integrate’
integrate2b: no visible global function definition for ‘integrate’
integrate4a: no visible global function definition for ‘integrate’
integrate4b: no visible global function definition for ‘integrate’
optimalCScalar2: no visible global function definition for ‘uniroot’
optimalLambda: no visible global function definition for ‘optimise’
optimalLambdaC: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dgamma dnorm integrate lm optimise pnorm predict stack uniroot
Consider adding
  importFrom("stats", "dgamma", "dnorm", "integrate", "lm", "optimise",
             "pnorm", "predict", "uniroot")
  importFrom("utils", "stack")
to your NAMESPACE file.
'library' or 'require' call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘lattice’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘portfolioSim/R/AllClasses.R’:
  .onLoad calls:
    require(methods)

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

contributionSummaryDf,simResult : <anonymous>: no visible global
  function definition for ‘aggregate’
getSimTrades,stiFromSignal-orderable-portfolio-simData-logical: no
  visible binding for global variable ‘shares’
loadIn,simResult-character-missing: no visible binding for global
  variable ‘master.freq’
loadIn,simResult-character-missing: no visible binding for global
  variable ‘master.errors’
loadIn,simResult-character-missing: no visible binding for global
  variable ‘master.type’
loadIn,simResult-character-missing: no visible binding for global
  variable ‘master.summary.interface’
loadIn,simResultSinglePeriod-character-missing: no visible binding for
  global variable ‘x’
plot,simResult-missing: no visible global function definition for
  ‘xyplot’
runSim,portfolioSim-logical: no visible binding for global variable
  ‘id’
runSim,portfolioSim-logical: no visible global function definition for
  ‘updateSummary’
securityPerfSummaryDf,simResult: no visible global function definition
  for ‘aggregate’
summary,simResult: no visible global function definition for ‘sd’
summary,simResult: no visible global function definition for ‘head’
summary,simResult: no visible global function definition for ‘tail’
Undefined global functions or variables:
  aggregate head id master.errors master.freq master.summary.interface
  master.type sd shares tail updateSummary x xyplot
Consider adding
  importFrom("stats", "aggregate", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
'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.
pps1: no visible global function definition for ‘runif’
ppss: no visible global function definition for ‘runif’
ppswr: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
prepare_Rd: calif.Rd:5-6: Dropping empty section \arguments
prepare_Rd: calif.Rd:8-9: Dropping empty section \examples
prepare_Rd: califcty.Rd:5-6: Dropping empty section \arguments
prepare_Rd: califcty.Rd:8-9: Dropping empty section \examples
prepare_Rd: sizesok.Rd:12-13: Dropping empty section \examples
prepare_Rd: stratumsizes.Rd:11-12: Dropping empty section \examples
Malformed Description field: should contain one or more complete sentences.
LDA.Tree : Find.proj: no visible binding for global variable ‘var’
LDA.Tree : Find.proj: no visible binding for global variable ‘IQR’
LDA.Tree : Find.proj: no visible binding for global variable ‘median’
PDA.Tree : Find.proj: no visible binding for global variable ‘var’
PDA.Tree : Find.proj: no visible binding for global variable ‘median’
PDA.Tree : Find.proj: no visible binding for global variable ‘IQR’
PP.Tree : Find.proj: no visible binding for global variable ‘var’
PP.Tree : Find.proj: no visible binding for global variable ‘median’
PP.Tree : Find.proj: no visible binding for global variable ‘IQR’
PP.optimize.Huber: no visible binding for global variable ‘sd’
PP.optimize.anneal: no visible binding for global variable ‘sd’
PP.optimize.plot: no visible binding for global variable ‘sd’
PP.optimize.plot: no visible global function definition for ‘hist’
PP.optimize.plot: no visible global function definition for ‘text’
PP.optimize.plot: no visible global function definition for ‘par’
PP.optimize.plot: no visible global function definition for ‘plot’
PP.optimize.plot: no visible global function definition for ‘colors’
PP.optimize.plot: no visible global function definition for ‘pairs’
PP.optimize.random: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  IQR colors hist median pairs par plot sd text var
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "hist", "pairs", "par", "plot", "text")
  importFrom("stats", "IQR", "median", "sd", "var")
to your NAMESPACE file.
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
  src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
Malformed Title field: should not end in a period.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  ‘dev’
Malformed Description field: should contain one or more complete sentences.
TT.test : <anonymous>: no visible global function definition for
  ‘t.test’
TT.test: no visible binding for global variable ‘sd’
TT.test: no visible global function definition for ‘setNames’
kirjelda : combo: no visible binding for global variable ‘sd’
kor.tabel: no visible binding for global variable ‘cor.test’
Undefined global functions or variables:
  cor.test sd setNames t.test
Consider adding
  importFrom("stats", "cor.test", "sd", "setNames", "t.test")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
gausspred: no visible global function definition for ‘qt’
mvapred: no visible global function definition for ‘qt’
Undefined global functions or variables:
  qt
Consider adding
  importFrom("stats", "qt")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Non-standard file/directory found at top level:
  ‘DESCRIPTION.bck’
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘predmixcor/R/firstlib.r’:
  .First.lib calls:
    cat("predmixcor loaded\n", "COPY RIGHT: Longhai Li\n", "http://math.usask.ca/~longhai\n",     "Type ?begin.predmixcor for help\n", sep = "")

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

Predict.mix: no visible global function definition for ‘dbinom’
abs_cor: no visible global function definition for ‘cor’
gen.alpha.IGamma: no visible global function definition for ‘qgamma’
gendata.mix: no visible global function definition for ‘runif’
gendata.mix: no visible global function definition for ‘rbeta’
mh1.unif: no visible global function definition for ‘runif’
train_predict_mix: no visible global function definition for ‘dbinom’
training: no visible global function definition for ‘runif’
training: no visible global function definition for ‘dbinom’
Undefined global functions or variables:
  cor dbinom qgamma rbeta runif
Consider adding
  importFrom("stats", "cor", "dbinom", "qgamma", "rbeta", "runif")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Non-standard file/directory found at top level:
  ‘COPYRIGHTS’
Copyright information should be in file inst/COPYRIGHTS
Package suggested but not available for checking: ‘INLA’
basisplot: no visible global function definition for ‘plot’
basisplot: no visible global function definition for ‘abline’
basisplot: no visible global function definition for ‘text’
basisplot: no visible global function definition for ‘par’
plot.prinsimp: no visible global function definition for ‘screeplot’
plot.simpart: no visible global function definition for ‘par’
position_text: no visible global function definition for ‘par’
position_text: no visible global function definition for ‘strwidth’
simpart.formula: no visible global function definition for ‘terms’
simpart.formula: no visible global function definition for
  ‘model.matrix’
varperc: no visible global function definition for ‘plot’
varperc: no visible global function definition for ‘lines’
varperc: no visible global function definition for ‘text’
varsimp: no visible global function definition for ‘plot’
varsimp: no visible global function definition for ‘points’
varsimp: no visible global function definition for ‘text’
varsimp: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline lines model.matrix par plot points screeplot strwidth terms
  text
Consider adding
  importFrom("graphics", "abline", "lines", "par", "plot", "points",
             "strwidth", "text")
  importFrom("stats", "model.matrix", "screeplot", "terms")
to your NAMESPACE file.
Package suggested but not available for checking: ‘gurobi’
pr.conditional: no visible global function definition for ‘qnorm’
pr.marginal: no visible global function definition for ‘qnorm’
prLogisticDelta: no visible global function definition for ‘glm’
prLogisticDelta: no visible binding for global variable ‘binomial’
Undefined global functions or variables:
  binomial glm qnorm
Consider adding
  importFrom("stats", "binomial", "glm", "qnorm")
to your NAMESPACE file.
.pfda.fstep: no visible global function definition for ‘dist’
.pfda.main: no visible global function definition for ‘plot’
.pfda.mstep: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov dist plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "cov", "dist")
to your NAMESPACE file.
prepare_Rd: ProbForecastGOP-package.Rd:42-43: Dropping empty section \seealso
Rd file 'Emp.variog.Rd':
  \usage lines wider than 90 characters:
     Emp.variog(day, obs, forecast, id, coord1, coord2, cut.points=NULL, max.dist=NULL, nbins=300)

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

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

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

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

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

These lines will be truncated in the PDF manual.
Running examples in ‘processanimateR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: renderer_leaflet
> ### Title: Render as graph on a geographical map
> ### Aliases: renderer_leaflet
> 
> ### ** Examples
> 
> data(example_log)
> 
> # Animate the example process with activities placed in some locations
> animate_process(example_log,
+   renderer = renderer_leaflet(
+     node_coordinates = data.frame(
+        act = c("A", "B", "C", "D", "Start", "End"),
+        lat = c(63.443680, 63.426925, 63.409207, 63.422336, 63.450950, 63.419706),
+        lng = c(10.383625, 10.396972, 10.406418, 10.432119, 10.383368, 10.252347),
+        stringsAsFactors = FALSE),
+     edge_coordinates = data.frame(
+        act_from = c("B"),
+        act_to = c("C"),
+        lat = c(63.419207),
+        lng = c(10.386418),
+        stringsAsFactors = FALSE),
+     options = list(center = c(63.412273, 10.399590), zoom = 12)),
+   duration = 5, repeat_count = Inf)
Error in renderer(processmap, width, height) : 
  Missing coordinates for activitiesARTIFICIAL_ENDMissing coordinates for activitiesARTIFICIAL_START
Calls: animate_process -> renderer
Execution halted
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.
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  ‘splines’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
IndividualPROC: no visible global function definition for ‘survfit’
IndividualPROC: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile survfit
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Package suggested but not available for checking: ‘SDMTools’
addpi: no visible global function definition for ‘lines’
genPerms: no visible global function definition for ‘combn’
getVar: no visible global function definition for ‘glm’
getVar: no visible global function definition for ‘binomial’
getVar: no visible global function definition for ‘var’
pba: no visible global function definition for ‘glm’
pba: no visible global function definition for ‘binomial’
pba: no visible global function definition for ‘predict’
pba: no visible global function definition for ‘rbinom’
pcr: no visible global function definition for ‘quantile’
plotpi: no visible global function definition for ‘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.
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.
Non-standard file/directory found at top level:
  ‘doc’
Extract_plant_grapevine_function: no visible global function definition
  for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Package suggested but not available for checking: ‘rdt’
Package suggested but not available for checking: ‘rdt’
Package in Depends field not imported from: ‘rpart’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
mahalanobisComposite: no visible global function definition for
  ‘princomp’
prepareComposite: no visible global function definition for ‘cov’
winsorizor : f: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  cov princomp quantile
Consider adding
  importFrom("stats", "cov", "princomp", "quantile")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
candidate.overlap: no visible global function definition for
  ‘write.table’
fisher: no visible global function definition for ‘fisher.test’
fisher.iteration: no visible global function definition for
  ‘download.file’
fisher.iteration: no visible global function definition for
  ‘read.table’
pSI.list: no visible global function definition for ‘write.table’
specificity.index: no visible global function definition for ‘png’
specificity.index: no visible global function definition for ‘par’
specificity.index: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off download.file fisher.test par png read.table write.table
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "par")
  importFrom("stats", "fisher.test")
  importFrom("utils", "download.file", "read.table", "write.table")
to your NAMESPACE file.
'library' or 'require' call to ‘numDeriv’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
test.problem : g: no visible global function definition for ‘grad’
test.problem: no visible global function definition for ‘new’
psoptim,test.problem-missing-missing-missing-missing: no visible global
  function definition for ‘new’
show,test.result: no visible global function definition for ‘show’
show,test.result: no visible global function definition for ‘sd’
Undefined global functions or variables:
  grad new sd show
Consider adding
  importFrom("methods", "new", "show")
  importFrom("stats", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
pspearman: no visible global function definition for ‘pt’
spearman.test: no visible global function definition for
  ‘complete.cases’
spearman.test: no visible global function definition for ‘cor’
Undefined global functions or variables:
  complete.cases cor pt
Consider adding
  importFrom("stats", "complete.cases", "cor", "pt")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘orig’
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  ‘EffectsRelBaseline’ ‘boot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
catEffectBootAdaptor: no visible binding for global variable ‘sumSqCat’
compExclusionFraction: no visible global function definition for
  ‘rpois’
compExclusionFraction: no visible global function definition for
  ‘t.test’
compExclusionFraction: no visible global function definition for ‘glm’
compExclusionFraction: no visible global function definition for
  ‘anova’
compPowerCatSelectivity: no visible binding for global variable
  ‘fRatioStat’
compPowerGeneralRespDetection: no visible binding for global variable
  ‘sumSqCat’
compPowerRespDetection: no visible binding for global variable
  ‘sumSqCat’
compRejectionFraction: no visible global function definition for
  ‘rpois’
compRejectionFraction: no visible global function definition for
  ‘t.test’
compRejectionFraction: no visible global function definition for ‘glm’
compRejectionFraction: no visible global function definition for
  ‘anova’
simCatResp: no visible global function definition for ‘rpois’
simNormCatResp: no visible global function definition for ‘rnorm’
testCatEffectBoot: no visible global function definition for ‘boot’
Undefined global functions or variables:
  anova boot fRatioStat glm rnorm rpois sumSqCat t.test
Consider adding
  importFrom("stats", "anova", "glm", "rnorm", "rpois", "t.test")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘multilevel’ ‘nlme’
A package should be listed in only one of these fields.
Non-standard file/directory found at top level:
  ‘README.txt’
'library' or 'require' calls to packages already attached by Depends:
  ‘multilevel’ ‘nlme’
  Please remove these calls from your code.
Malformed Description field: should contain one or more complete sentences.
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.
GNU make is a SystemRequirements.
PurBayes: no visible global function definition for ‘update’
PurBayes: no visible global function definition for ‘sd’
plot.PurBayes: no visible global function definition for ‘plot’
plot.PurBayes: no visible global function definition for ‘quantile’
plot.PurBayes: no visible global function definition for ‘lines’
summary.PurBayes : <anonymous>: no visible global function definition
  for ‘quantile’
Undefined global functions or variables:
  lines plot quantile sd update
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "quantile", "sd", "update")
to your NAMESPACE file.
CandidateBio.getBio : <anonymous>: no visible global function
  definition for ‘na.omit’
Committee.getCommittee : <anonymous>: no visible global function
  definition for ‘na.omit’
getAllBios: no visible global function definition for ‘txtProgressBar’
getAllBios: no visible global function definition for
  ‘setTxtProgressBar’
getAllLocalOfficials: no visible global function definition for
  ‘txtProgressBar’
getAllLocalOfficials: no visible global function definition for
  ‘setTxtProgressBar’
getAllVotes: no visible global function definition for ‘txtProgressBar’
getAllVotes: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  na.omit setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
.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').
csQCAbinTest: no visible global function definition for ‘p.adjust’
fsQCApermTest: no visible global function definition for ‘p.adjust’
mvQCAbinTest: no visible global function definition for ‘p.adjust’
p.threshold.adjust: no visible global function definition for
  ‘p.adjust’
plot.fsQCApt: no visible global function definition for ‘dev.cur’
plot.fsQCApt: no visible global function definition for ‘dev.new’
plot.fsQCApt: no visible global function definition for ‘par’
plot.fsQCApt: no visible global function definition for ‘plot’
plot.fsQCApt: no visible global function definition for ‘density’
plot.fsQCApt: no visible global function definition for ‘axis’
plot.fsQCApt: no visible global function definition for ‘polygon’
plot.fsQCApt: no visible global function definition for ‘points’
plot.fsQCApt: no visible global function definition for ‘hist’
summary.csQCAbt: no visible global function definition for
  ‘printCoefmat’
summary.fsQCApt: no visible global function definition for
  ‘printCoefmat’
summary.mvQCAbt: no visible global function definition for
  ‘printCoefmat’
Undefined global functions or variables:
  axis density dev.cur dev.new hist p.adjust par plot points polygon
  printCoefmat
Consider adding
  importFrom("grDevices", "dev.cur", "dev.new")
  importFrom("graphics", "axis", "hist", "par", "plot", "points",
             "polygon")
  importFrom("stats", "density", "p.adjust", "printCoefmat")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
chooseMDoubleBootstrap: no visible global function definition for
  ‘model.matrix’
chooseMDoubleBootstrap: no visible global function definition for
  ‘as.formula’
chooseMDoubleBootstrap: no visible global function definition for
  ‘model.frame’
chooseMDoubleBootstrap: no visible global function definition for ‘lm’
chooseMDoubleBootstrap: no visible global function definition for
  ‘coef’
chooseMDoubleBootstrap: no visible global function definition for
  ‘quantile’
chooseMDoubleBootstrap: no visible global function definition for
  ‘qnorm’
getModel: no visible global function definition for ‘lm’
getModel: no visible global function definition for ‘model.matrix’
getModel: no visible global function definition for ‘as.formula’
getModel: no visible global function definition for ‘model.frame’
getModel: no visible global function definition for ‘model.response’
getModel: no visible global function definition for ‘coef’
getModel: no visible global function definition for ‘qnorm’
qLearn: no visible global function definition for ‘model.matrix’
qLearn: no visible global function definition for ‘as.formula’
qLearn: no visible global function definition for ‘model.frame’
qLearn: no visible global function definition for ‘coef’
qLearn: no visible global function definition for ‘lm’
qLearn: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  as.formula coef lm model.frame model.matrix model.response qnorm
  quantile
Consider adding
  importFrom("stats", "as.formula", "coef", "lm", "model.frame",
             "model.matrix", "model.response", "qnorm", "quantile")
to your NAMESPACE file.
GNU make is a SystemRequirements.
pcAxisCubeMake: no visible global function definition for ‘aggregate’
pcAxisCubeToCSV: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  aggregate write.csv
Consider adding
  importFrom("stats", "aggregate")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘compileMetaObject’
File ‘qtbase/libs/qtbase.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘Rf_EncodeInteger’,
    ‘Rf_EncodeLogical’, ‘Rf_EncodeReal’, ‘Rf_formatInteger’,
    ‘Rf_formatLogical’, ‘Rf_formatReal’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘qtl2’
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.
Note: information on .o files is not available
'library' or 'require' call to ‘Rmpfr’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
adjacencyMatrix: no visible global function definition for ‘as’
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
quadp: no visible global function definition for ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
alphaf: no visible global function definition for ‘pchisq’
alphaf: no visible global function definition for ‘dbinom’
conout: no visible global function definition for ‘sd’
ibgaout: no visible global function definition for ‘qnorm’
ibgaout: no visible global function definition for ‘pnorm’
plot.qualint: no visible global function definition for ‘qnorm’
powerval: no visible global function definition for ‘rnorm’
powerval: no visible global function definition for ‘qnorm’
powerval: no visible global function definition for ‘pnorm’
print.expplot: no visible global function definition for ‘gray’
print.expplot: no visible binding for global variable ‘coef’
print.outplot: no visible global function definition for ‘gray’
print.outplot: no visible binding for global variable ‘coef’
qualint: no visible global function definition for ‘qnorm’
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.
Found the following calls to attach():
File ‘quantmod/R/attachSymbols.R’:
  attach(NULL, pos = pos, name = DB$name)
  attach(NULL, pos = pos, name = DB$name)
See section ‘Good practice’ in ‘?attach’.
Non-standard file/directory found at top level:
  ‘README.txt’
Rd file 'graph.mod.Rd':
  \usage lines wider than 90 characters:
     graph.mod(ssmod, x, y, data, title = "", xlab = "Centered X", ylab = "Raw Y", ylimit = 1.5, ...)

These lines will be truncated in the PDF manual.
Found the following sources/headers with CR or CRLF line endings:
  inst/include/BackTest.h
Some Unix compilers require LF line endings.
Package suggested but not available for checking: ‘fastshp’
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
File ‘QUIC/libs/QUIC.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘QUIC.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘QUIC.o’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
mutualCoherence : .setOneMutualP: no visible global function definition
  for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
conf2d.default: no visible global function definition for ‘polygon’
conf2d_int: no visible global function definition for ‘contourLines’
Undefined global functions or variables:
  contourLines polygon
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "polygon")
to your NAMESPACE file.
'library' or 'require' call to ‘rgdal’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘matrixStats’ ‘rgdal’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following calls to attach():
File ‘R2OpenBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
Found the following calls to attach():
File ‘R2WinBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘rgl’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘lattice’ ‘leaps’ ‘rgl’ ‘s20x’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Malformed Description field: should contain one or more complete sentences.
getsonde: no visible global function definition for ‘read.table’
plotsonde: no visible global function definition for ‘par’
plotwind: no visible global function definition for ‘plot’
plotwind: no visible global function definition for ‘mtext’
plotwind: no visible global function definition for ‘abline’
skewt.axis: no visible global function definition for ‘par’
skewt.axis: no visible global function definition for ‘plot’
skewt.axis: no visible global function definition for ‘axis’
skewt.axis: no visible global function definition for ‘mtext’
skewt.axis: no visible global function definition for ‘segments’
skewt.axis: no visible global function definition for ‘text’
skewt.axis: no visible global function definition for ‘lines’
skewt.lines: no visible global function definition for ‘lines’
skewt.points: no visible global function definition for ‘points’
station.symbol: no visible global function definition for ‘sd’
station.symbol: no visible global function definition for ‘par’
station.symbol: no visible global function definition for ‘lines’
station.symbol: no visible global function definition for ‘polygon’
station.symbol: no visible global function definition for ‘text’
station.symbol: no visible global function definition for ‘segments’
Undefined global functions or variables:
  abline axis lines mtext par plot points polygon read.table sd
  segments text
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "mtext", "par",
             "plot", "points", "polygon", "segments", "text")
  importFrom("stats", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Rd file 'MDMnMod.Rd':
  \usage lines wider than 90 characters:
     MDMnMod(MDMn.form, data, ID, dist="MDMn", scale.covar=FALSE, est.var=TRUE, calc.resid=TRUE, trace=TRUE)
  \examples lines wider than 100 characters:
     model.nij <- MDMnMod(nij.form, data=n.data, ID=n.data$i, dist="MDMn", scale.covar=TRUE, est.var=FALSE, calc.resid=TRUE, trace=TRUE)

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

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

These lines will be truncated in the PDF manual.
RnDif.het: no visible global function definition for ‘runif’
RnDif.hom: no visible global function definition for ‘runif’
RnDifAdv.hom: no visible global function definition for ‘runif’
SoilAdv.hom: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Found the following sources/headers not terminated with a newline:
  inst/include/ramcmc.h
Some compilers warn on such files.
Malformed Description field: should contain one or more complete sentences.
Non-standard file/directory found at top level:
  ‘COPYRIGHTS’
Copyright information should be in file inst/COPYRIGHTS
Malformed Description field: should contain one or more complete sentences.
.disableThreads: no visible global function definition for
  ‘stopCluster’
.enableThreads: no visible global function definition for ‘detectCores’
.enableThreads: no visible global function definition for
  ‘makePSOCKcluster’
.enableThreads: no visible global function definition for
  ‘clusterExport’
.enableThreads: no visible global function definition for ‘clusterCall’
.forwardSelection: no visible binding for global variable ‘var’
.forwardSelection: no visible global function definition for ‘glm’
.forwardSelection: no visible global function definition for ‘formula’
.forwardSelection: no visible global function definition for ‘binomial’
.forwardSelection: no visible global function definition for ‘lm’
.forwardSelection: no visible global function definition for ‘predict’
.predict.internal: no visible global function definition for ‘predict’
randomGLM: no visible binding for global variable ‘cor’
randomGLM: no visible binding for global variable ‘sd’
randomGLM: no visible global function definition for ‘var’
thinRandomGLM: no visible global function definition for ‘glm’
thinRandomGLM: no visible global function definition for ‘binomial’
thinRandomGLM: no visible global function definition for ‘lm’
Undefined global functions or variables:
  binomial clusterCall clusterExport cor detectCores formula glm lm
  makePSOCKcluster predict sd stopCluster var
Consider adding
  importFrom("stats", "binomial", "cor", "formula", "glm", "lm",
             "predict", "sd", "var")
to your NAMESPACE file.

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

Rd file 'randomGLM.Rd':
  \usage lines wider than 90 characters:
       # Multi-level classification options - only apply to classification with multi-level response
  \examples lines wider than 100 characters:
     RGLM = randomGLM(xTrain, yTrain, xTest, classify=FALSE, nCandidateCovariates=ncol(xTrain), nBags=10, 

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

These lines will be truncated in the PDF manual.
anovaF: no visible global function definition for ‘anova’
anovaF: no visible global function definition for ‘lm’
randInterval: no visible global function definition for ‘quantile’
randInterval : <anonymous>: no visible global function definition for
  ‘quantile’
randPlot: no visible global function definition for ‘par’
randPlot: no visible global function definition for ‘hist’
randPlot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline anova hist lm par quantile
Consider adding
  importFrom("graphics", "abline", "hist", "par")
  importFrom("stats", "anova", "lm", "quantile")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
bartels.rank.test: no visible global function definition for ‘na.omit’
bartels.rank.test: no visible global function definition for ‘pbeta’
bartels.rank.test: no visible global function definition for ‘pnorm’
cox.stuart.test: no visible global function definition for ‘pbinom’
difference.sign.test: no visible global function definition for
  ‘na.omit’
difference.sign.test: no visible global function definition for ‘pnorm’
rank.test: no visible global function definition for ‘na.omit’
rank.test: no visible global function definition for ‘pnorm’
rruns: no visible global function definition for ‘runif’
runs.test: no visible global function definition for ‘median’
runs.test: no visible global function definition for ‘na.omit’
runs.test: no visible global function definition for ‘points’
runs.test: no visible global function definition for ‘abline’
runs.test: no visible global function definition for ‘gray’
runs.test: no visible global function definition for ‘pnorm’
turning.point.test: no visible global function definition for ‘embed’
turning.point.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline embed gray median na.omit pbeta pbinom pnorm points runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "points")
  importFrom("stats", "embed", "median", "na.omit", "pbeta", "pbinom",
             "pnorm", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
rank.L2R: no visible global function definition for ‘kmeans’
rank.L2R: no visible global function definition for ‘pnorm’
rank.LN: no visible global function definition for ‘kmeans’
rank.LN: no visible global function definition for ‘pnorm’
rank.gs: no visible global function definition for ‘qnorm’
rank.wald: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  kmeans pnorm qnorm
Consider adding
  importFrom("stats", "kmeans", "pnorm", "qnorm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘BSgenome.Hsapiens.UCSC.hg19’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
  src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
Package in Depends field not imported from: ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
freq: no visible global function definition for ‘xtabs’
freq: no visible binding for global variable ‘na.pass’
freq: no visible global function definition for ‘melt’
freq: no visible global function definition for ‘complete.cases’
freq: no visible global function definition for ‘tail’
kurtosis: no visible global function definition for ‘na.omit’
label: no visible global function definition for ‘tail’
name: no visible global function definition for ‘tail’
nvalid : <anonymous>: no visible global function definition for
  ‘na.omit’
rp.desc: no visible global function definition for ‘melt.data.frame’
rp.desc: no visible global function definition for ‘cast’
rp.desc: no visible global function definition for ‘na.omit’
rp.desc : <anonymous>: no visible global function definition for ‘tail’
rp.desc : <anonymous>: no visible global function definition for ‘head’
rp.freq: no visible global function definition for ‘xtabs’
rp.freq: no visible binding for global variable ‘na.pass’
rp.freq: no visible global function definition for ‘melt’
rp.freq: no visible global function definition for ‘complete.cases’
rp.freq: no visible global function definition for ‘tail’
rp.label: no visible global function definition for ‘tail’
rp.name: no visible global function definition for ‘tail’
rp.outlier : lundcrit: no visible global function definition for ‘qf’
rp.outlier: no visible global function definition for ‘lm’
rp.outlier: no visible global function definition for ‘rstandard’
rp.valid : <anonymous>: no visible global function definition for
  ‘na.omit’
skewness: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  cast complete.cases head lm melt melt.data.frame na.omit na.pass qf
  rstandard tail xtabs
Consider adding
  importFrom("stats", "complete.cases", "lm", "na.omit", "na.pass", "qf",
             "rstandard", "xtabs")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
fnRAP: no visible global function definition for ‘chisq.test’
fnRAP: no visible global function definition for ‘combn’
Undefined global functions or variables:
  chisq.test combn
Consider adding
  importFrom("stats", "chisq.test")
  importFrom("utils", "combn")
to your NAMESPACE file.
Package suggested but not available for checking: ‘gurobi’
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.
rateratio.test: no visible global function definition for
  ‘complete.cases’
rateratio.test: no visible global function definition for ‘pbinom’
rateratio.test : p.L: no visible global function definition for ‘qbeta’
rateratio.test : p.U: no visible global function definition for ‘qbeta’
Undefined global functions or variables:
  complete.cases pbinom qbeta
Consider adding
  importFrom("stats", "complete.cases", "pbinom", "qbeta")
to your NAMESPACE file.
concordance: no visible global function definition for ‘quantile’
concordance : Normal: no visible global function definition for ‘qnorm’
concordance : Normal: no visible global function definition for ‘pnorm’
concordance : MC: no visible global function definition for ‘rmultinom’
concordance : MC: no visible global function definition for ‘quantile’
concordance: no visible global function definition for ‘qnorm’
concordance: no visible global function definition for ‘pnorm’
concordance : Chisq: no visible global function definition for ‘qchisq’
concordance : Chisq: no visible global function definition for ‘pchisq’
concordance : Normal2: no visible global function definition for
  ‘qnorm’
concordance : Normal2: no visible global function definition for
  ‘pnorm’
concordance : MC2: no visible global function definition for
  ‘rmultinom’
concordance : MC2: no visible global function definition for ‘quantile’
wlin.conc: no visible global function definition for ‘quantile’
wlin.conc : MC: no visible global function definition for ‘rmultinom’
wlin.conc : MC: no visible global function definition for ‘quantile’
wquad.conc: no visible global function definition for ‘quantile’
wquad.conc : MC: no visible global function definition for ‘rmultinom’
wquad.conc : MC: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  pchisq pnorm qchisq qnorm quantile rmultinom
Consider adding
  importFrom("stats", "pchisq", "pnorm", "qchisq", "qnorm", "quantile",
             "rmultinom")
to your NAMESPACE file.
.GCD: no visible global function definition for ‘as.polynomial’
.LCM: no visible global function definition for ‘as.polynomial’
.is_zero_polynomial: no visible global function definition for ‘coef’
.poly2expr: no visible global function definition for ‘coef’
integral.rationalfun: no visible global function definition for ‘coef’
integraterf.transcendent: no visible global function definition for
  ‘coef’
rationalfun: no visible global function definition for ‘polynomial’
rationalfun.poly: no visible global function definition for
  ‘polynomial’
rationalfun.poly: no visible global function definition for
  ‘is.polynomial’
rfun: no visible global function definition for ‘polynomial’
rfun.poly: no visible global function definition for ‘polynomial’
rfun.poly: no visible global function definition for ‘is.polynomial’
simplify: no visible global function definition for ‘coef’
simplify: no visible global function definition for ‘polynomial’
Undefined global functions or variables:
  as.polynomial coef is.polynomial polynomial
Consider adding
  importFrom("stats", "coef")
to your NAMESPACE file.
.avisApiBusAvanzada: no visible global function definition for
  ‘read.csv’
.avisRenderMapAdmin: no visible global function definition for ‘points’
.avisRenderMapAdmin: no visible global function definition for ‘rect’
.avisRenderMapPhysical: no visible global function definition for
  ‘points’
avisMap: no visible global function definition for ‘par’
avisMap: no visible global function definition for ‘layout’
Undefined global functions or variables:
  layout par points read.csv rect
Consider adding
  importFrom("graphics", "layout", "par", "points", "rect")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
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.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rblpapi.Rcheck/00install.out’ for details.
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.
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.
RC.read.table: no visible global function definition for ‘type.convert’
Undefined global functions or variables:
  type.convert
Consider adding
  importFrom("utils", "type.convert")
to your NAMESPACE file.
Found the following sources/headers not terminated with a newline:
  inst/include/cereal/types/memory.hpp
Some compilers warn on such files.
Malformed Description field: should contain one or more complete sentences.
.onAttach: no visible global function definition for
  ‘packageDescription’
rselect.list: no visible global function definition for ‘select.list’
Undefined global functions or variables:
  packageDescription select.list
Consider adding
  importFrom("utils", "packageDescription", "select.list")
to your NAMESPACE file.
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', 'rqubic',
  'BicARE', 's4vd', 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
enterTableMHTest : onOK: no visible global function definition for
  ‘na.omit’
startStop: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Namespace with empty importFrom: ‘tcltk’
'library' or 'require' calls to packages already attached by Depends:
  ‘depthTools’ ‘tcltk’
  Please remove these calls from your code.
computeMBD : OnOutput: no visible global function definition for
  ‘tkbutton’
computeMBD: no visible global function definition for ‘tkbutton’
computeMBD : OnPlot: no visible global function definition for
  ‘tkcanvas’
computeMBD : OnPlot: no visible global function definition for
  ‘tkbutton’
computeTmean: no visible global function definition for ‘tkcanvas’
computeTmean: no visible global function definition for ‘tkbutton’
computeTmean : onOK: no visible global function definition for ‘par’
plotCentralCurves: no visible global function definition for ‘tkcanvas’
plotCentralCurves: no visible global function definition for ‘tkbutton’
plotCentralCurves : onOK: no visible global function definition for
  ‘par’
Undefined global functions or variables:
  par tkbutton tkcanvas
Consider adding
  importFrom("graphics", "par")
to your NAMESPACE file.
'library' or 'require' call to ‘FrF2.catlg128’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
managedata: no visible binding for global variable ‘data’
Undefined global functions or variables:
  data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘abind’ ‘e1071’ ‘qcc’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  ‘ENmisc’ ‘Hmisc’ ‘Rcmdr’ ‘vcd’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.onAttach: no visible global function definition for ‘getRcmdr’
.onAttach: no visible global function definition for ‘closeCommander’
.onAttach: no visible global function definition for ‘Commander’
mosaicMenuItem: no visible global function definition for
  ‘mosaicSelectDialog’
mosaicMenuItem: no visible global function definition for ‘Message’
Undefined global functions or variables:
  Commander Message closeCommander getRcmdr mosaicSelectDialog
Malformed Description field: should contain one or more complete sentences.
BOXWP: no visible binding for global variable ‘top’
BOXWP: no visible binding for global variable ‘buttonsFrame’
HIST: no visible binding for global variable ‘top’
HIST: no visible binding for global variable ‘buttonsFrame’
QQN: no visible binding for global variable ‘top’
QQN: no visible binding for global variable ‘buttonsFrame’
Undefined global functions or variables:
  buttonsFrame top
Namespaces with empty importFrom:
  ‘stats’ ‘tcltk’
Malformed Description field: should contain one or more complete sentences.
fncLRpROC: no visible global function definition for ‘palette’
fncLRpROC : onOK : convert: no visible global function definition for
  ‘col2rgb’
fncLRpROC : onOK : convert: no visible global function definition for
  ‘rgb’
fncPairedpROC: no visible global function definition for ‘palette’
fncPairedpROC : onOK : convert: no visible global function definition
  for ‘col2rgb’
fncPairedpROC : onOK : convert: no visible global function definition
  for ‘rgb’
fncUnpairedpROC: no visible global function definition for ‘palette’
fncUnpairedpROC : onOK : convert: no visible global function definition
  for ‘col2rgb’
fncUnpairedpROC : onOK : convert: no visible global function definition
  for ‘rgb’
fncvpROC: no visible global function definition for ‘palette’
fncvpROC : onOK : convert: no visible global function definition for
  ‘col2rgb’
fncvpROC : onOK : convert: no visible global function definition for
  ‘rgb’
Undefined global functions or variables:
  col2rgb palette rgb
Consider adding
  importFrom("grDevices", "col2rgb", "palette", "rgb")
to your NAMESPACE file.
SampleSizes: no visible global function definition for ‘xtabs’
SampleSizes: no visible global function definition for ‘weighted.mean’
SampleSizes: no visible global function definition for ‘reshape’
stage1Sample.fn: no visible global function definition for ‘runif’
stage2Sample.fn: no visible global function definition for ‘runif’
strata.options : onOK: no visible global function definition for
  ‘packageDescription’
Undefined global functions or variables:
  packageDescription reshape runif weighted.mean xtabs
Consider adding
  importFrom("stats", "reshape", "runif", "weighted.mean", "xtabs")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
'library' or 'require' call to ‘SLC’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘SLC’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rcmdr.steeptestDij : onOK: no visible binding for global variable
  ‘replications’
Rcmdr.steeptestPij : onOK: no visible binding for global variable
  ‘replications’
Undefined global functions or variables:
  replications
Consider adding
  importFrom("stats", "replications")
to your NAMESPACE file.
Package suggested but not available for checking: ‘ROpenOffice’
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.
Found the following sources/headers not terminated with a newline:
  inst/include/Rcpp/traits/static_max_int.h
Some compilers warn on such files.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RcppAPT.Rcheck/00install.out’ for details.
Gauss: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Found the following sources/headers not terminated with a newline:
  inst/include/pflineart.h
Some compilers warn on such files.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following sources/headers with CR or CRLF line endings:
  inst/include/rCRM.h
  inst/include/rCRM_RcppExports.h
Some Unix compilers require LF line endings.
Running examples in ‘RCrypto-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CoinMarketCap_Ticker
> ### Title: 'Coinmarketcap' Select Ticker Symbol
> ### Aliases: CoinMarketCap_Ticker
> 
> ### ** Examples
> 
> MyData <- CoinMarketCap_Ticker(currency = "CAD",ticker = "ETH")
Error in symbol %in% c(ticker) : object 'symbol' not found
Calls: CoinMarketCap_Ticker ... as.data.frame -> filter -> filter.tbl_df -> filter_impl -> %in%
Execution halted
GNU make is a SystemRequirements.
Packages in Depends field not imported from:
  ‘MASS’ ‘Matrix’ ‘lattice’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CUR: no visible global function definition for ‘runif’
CUR: no visible global function definition for ‘new’
plotLeverage,CURobj: no visible global function definition for ‘plot’
plotLeverage,CURobj: no visible global function definition for ‘points’
plotLeverage,CURobj: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline new plot points runif
Consider adding
  importFrom("graphics", "abline", "plot", "points")
  importFrom("methods", "new")
  importFrom("stats", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package suggested but not available for checking: ‘rddtools’
Unknown package ‘rddtools’ in Rd xrefs
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > # library(AER)
  > # library(sandwich)
  > # library(lmtest)
  > # library(Formula)
  > library(rddapp)
  > library(rdd)
  Loading required package: sandwich
  Loading required package: lmtest
  Loading required package: zoo
  
  Attaching package: 'zoo'
  
  The following objects are masked from 'package:base':
  
      as.Date, as.Date.numeric
  
  Loading required package: AER
  Loading required package: car
  Loading required package: carData
  Loading required package: survival
  Loading required package: Formula
  > library(rddtools)
  Error in library(rddtools) : there is no package called 'rddtools'
  Execution halted
distimage: no visible binding for global variable ‘terrain.colors’
distimage: no visible global function definition for ‘filled.contour’
distimage: no visible global function definition for ‘title’
distimage: no visible global function definition for ‘axis’
distimage: no visible global function definition for ‘lines’
drawkpc: no visible global function definition for ‘plot’
drawkpc: no visible global function definition for ‘segments’
drawkpc: no visible global function definition for ‘lines’
modelimage: no visible binding for global variable ‘topo.colors’
modelimage: no visible global function definition for ‘filled.contour’
modelimage: no visible global function definition for ‘title’
modelimage: no visible global function definition for ‘axis’
modelimage: no visible global function definition for ‘lines’
sincdata: no visible global function definition for ‘runif’
sincdata: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  axis filled.contour lines plot rnorm runif segments terrain.colors
  title topo.colors
Consider adding
  importFrom("grDevices", "terrain.colors", "topo.colors")
  importFrom("graphics", "axis", "filled.contour", "lines", "plot",
             "segments", "title")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
sumry_categorical: no visible global function definition for ‘freq’
sumry_continous: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  freq quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
mve_single_cvxr: no visible global function definition for ‘Semidef’
Undefined global functions or variables:
  Semidef
'library' or 'require' call to ‘synchronicity’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
ip2coordinates: no visible global function definition for ‘URLencode’
street2coordinates: no visible global function definition for
  ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
Found the following significant warnings:
  compile.cc:292:69: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class re2::Prog::Inst’; use assignment or value-initialization instead [-Wclass-memaccess]
  regexp.cc:343:33: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
  regexp.cc:344:32: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/re2r.Rcheck/00install.out’ for details.
GNU make is a SystemRequirements.
Files which contain pragma(s) suppressing diagnostics:
  ‘inst/include/re2/prog.h’ ‘inst/include/re2/re2.h’
  ‘inst/include/re2/regexp.h’ ‘src/dfa.cc’ ‘src/onepass.cc’
GNU make is a SystemRequirements.
Non-standard file/directory found at top level:
  ‘devel’
'library' or 'require' calls to packages already attached by Depends:
  ‘leaps’ ‘mgcv’
  Please remove these calls from your code.
xy: warning in assign(xname, X, env = .GlobalEnv): partial argument
  match of ‘env’ to ‘envir’
xy: warning in assign(yname, y, env = .GlobalEnv): partial argument
  match of ‘env’ to ‘envir’
bestmods: no visible global function definition for ‘abline’
bestmods: no visible global function definition for ‘axis’
bestmods: no visible global function definition for ‘lines’
cic: no visible global function definition for ‘lsfit’
cic: no visible global function definition for ‘var’
cvic: no visible global function definition for ‘lsfit’
cvic: no visible global function definition for ‘lm’
eic: no visible global function definition for ‘lsfit’
eic: no visible global function definition for ‘lm’
ic.min: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘var’
xy: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline axis lines lm lsfit rnorm var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "lm", "lsfit", "rnorm", "var")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘reams/R/xy.R’:
  assign(xname, X, env = .GlobalEnv)
  assign(yname, y, env = .GlobalEnv)
prepare_Rd: bestmods.Rd:47-49: Dropping empty section \note
prepare_Rd: bestmods.Rd:43-44: Dropping empty section \references
prepare_Rd: cic.Rd:24-26: Dropping empty section \details
prepare_Rd: cic.Rd:40-42: Dropping empty section \note
prepare_Rd: cvic.Rd:49-51: Dropping empty section \note
prepare_Rd: eic.Rd:31-33: Dropping empty section \details
prepare_Rd: eic.Rd:50-52: Dropping empty section \note
prepare_Rd: eic.Rd:56-58: Dropping empty section \seealso
prepare_Rd: ic.min.Rd:22-24: Dropping empty section \details
prepare_Rd: ic.min.Rd:47-49: Dropping empty section \note
prepare_Rd: ic.min.Rd:53-55: Dropping empty section \seealso
prepare_Rd: reams-package.Rd:16-17: Dropping empty section \references
prepare_Rd: reams-package.Rd:19-20: Dropping empty section \seealso
prepare_Rd: reams-package.Rd:21-22: Dropping empty section \examples
prepare_Rd: scoremods.Rd:26-28: Dropping empty section \details
prepare_Rd: scoremods.Rd:43-45: Dropping empty section \note
prepare_Rd: xy.Rd:46-48: Dropping empty section \note
prepare_Rd: xy.Rd:52: Dropping empty section \seealso
ReCiPa: no visible global function definition for ‘count.fields’
ReCiPa: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  count.fields read.table
Consider adding
  importFrom("utils", "count.fields", "read.table")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
AutoCorrelationLRtest: no visible global function definition for
  ‘logLik’
AutoCorrelationLRtest: no visible global function definition for
  ‘pchisq’
REEMtree: no visible global function definition for ‘terms’
REEMtree: no visible binding for global variable ‘SubsetVector’
REEMtree: no visible global function definition for ‘predict’
REEMtree: no visible global function definition for ‘logLik’
fitted.REEMtree: no visible global function definition for ‘fitted’
plot.REEMtree: no visible global function definition for ‘plot’
predict.REEMtree: no visible global function definition for ‘predict’
residuals.REEMtree: no visible global function definition for
  ‘residuals’
Undefined global functions or variables:
  SubsetVector fitted logLik pchisq plot predict residuals terms
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "fitted", "logLik", "pchisq", "predict",
             "residuals", "terms")
to your NAMESPACE file.
Rd file 'REEMtree.Rd':
  \usage lines wider than 90 characters:
                     ErrorTolerance=0.001, MaxIterations=1000, verbose=FALSE, tree.control=rpart.control(), 
                     lme.control=lmeControl(returnObject=TRUE), method="REML", correlation=NULL)

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

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

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

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

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

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

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
cook.outliers: no visible global function definition for ‘lm’
cook.outliers: no visible global function definition for
  ‘cooks.distance’
nonparRI: no visible global function definition for ‘quantile’
plot.interval: no visible global function definition for ‘par’
plot.interval: no visible global function definition for ‘plot.new’
plot.interval: no visible global function definition for ‘plot.window’
plot.interval: no visible global function definition for ‘segments’
plot.interval: no visible global function definition for ‘axis’
plot.interval: no visible global function definition for ‘title’
plot.interval: no visible global function definition for ‘legend’
plot.interval: no visible global function definition for ‘box’
plot.interval: no visible global function definition for ‘text’
robust: no visible global function definition for ‘qt’
singleRefLimit: no visible global function definition for ‘qnorm’
singleRefLimit: no visible global function definition for
  ‘shapiro.test’
singleRefLimit: no visible global function definition for ‘ks.test’
Undefined global functions or variables:
  axis box cooks.distance ks.test legend lm par plot.new plot.window
  qnorm qt quantile segments shapiro.test text title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "par", "plot.new",
             "plot.window", "segments", "text", "title")
  importFrom("stats", "cooks.distance", "ks.test", "lm", "qnorm", "qt",
             "quantile", "shapiro.test")
to your NAMESPACE file.
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.
Malformed Description field: should contain one or more complete sentences.
Non-standard files/directories found at top level:
  ‘prebuild.sh’ ‘regtest-Ex.R’
Warning in fun(libname, pkgname) :
  package regtest is under development and still may change considerably

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

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

These lines will be truncated in the PDF manual.
'library' or 'require' call to ‘lars’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘lars’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
relaxo: no visible global function definition for ‘lars’
Undefined global functions or variables:
  lars
Rd file 'cvrelaxo.Rd':
  \usage lines wider than 90 characters:
     cvrelaxo(X, Y, K = 5, phi = seq(0, 1, length = 10), max.steps = min( 2* length(Y), 2 * ncol(X)), fast = TRUE, keep.data = TRUE, warn=TR ... [TRUNCATED]

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

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

These lines will be truncated in the PDF manual.
print.summary.rem: no visible global function definition for
  ‘printCoefmat’
print.summary.rem: no visible global function definition for ‘pnorm’
print.summary.rem: no visible binding for global variable ‘quantile’
print.summary.rem: no visible global function definition for ‘pchisq’
print.summary.rem.dyad: no visible global function definition for
  ‘printCoefmat’
print.summary.rem.dyad: no visible global function definition for
  ‘pnorm’
print.summary.rem.dyad: no visible global function definition for
  ‘pchisq’
rem: no visible global function definition for ‘rnorm’
rem: no visible global function definition for ‘dnorm’
rem: no visible global function definition for ‘runif’
rem: no visible global function definition for ‘rchisq’
rem: no visible global function definition for ‘cov’
rem.dyad: no visible global function definition for ‘rnorm’
rem.dyad: no visible global function definition for ‘optim’
rem.dyad: no visible global function definition for ‘rchisq’
rem.dyad: no visible global function definition for ‘quantile’
rem.dyad: no visible global function definition for ‘sd’
rem.dyad: no visible global function definition for ‘var’
rem.dyad.lprior: no visible global function definition for ‘dnorm’
rem.dyad.lprior: no visible global function definition for ‘dt’
Undefined global functions or variables:
  cov dnorm dt optim pchisq pnorm printCoefmat quantile rchisq rnorm
  runif sd var
Consider adding
  importFrom("stats", "cov", "dnorm", "dt", "optim", "pchisq", "pnorm",
             "printCoefmat", "quantile", "rchisq", "rnorm", "runif",
             "sd", "var")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
CapDistSlope: no visible global function definition for ‘coef’
CapDistSlope: no visible global function definition for ‘lm’
EnergyEntropyDecomp: no visible global function definition for ‘legend’
FernholzDecomp: no visible global function definition for ‘legend’
Invest: no visible global function definition for ‘par’
Invest: no visible global function definition for ‘legend’
SimMarketModel: no visible global function definition for ‘rnorm’
plot.capdist: no visible global function definition for ‘plot’
plot.capdist: no visible global function definition for ‘abline’
plot.capdist: no visible global function definition for ‘lm’
plot.toymkt: no visible global function definition for ‘par’
plot.toymkt: no visible global function definition for ‘plot’
plot.toymkt: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline coef legend lm par plot rnorm
Consider adding
  importFrom("graphics", "abline", "legend", "par", "plot")
  importFrom("stats", "coef", "lm", "rnorm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
RearrangeData: no visible global function definition for ‘rainbow’
RearrangeData: no visible global function definition for ‘hclust’
RearrangeData: no visible global function definition for
  ‘as.dendrogram’
RearrangeData: no visible global function definition for ‘heatmap’
RearrangeData: no visible global function definition for ‘pdf’
RearrangeData: no visible global function definition for
  ‘colorRampPalette’
RearrangeData: no visible global function definition for ‘legend’
RearrangeData: no visible global function definition for ‘dev.off’
RearrangeJoseph: no visible global function definition for
  ‘write.table’
RearrangeJoseph: no visible global function definition for
  ‘as.dendrogram’
RearrangeJoseph: no visible global function definition for
  ‘order.dendrogram’
colorDendClass : colLab: no visible global function definition for
  ‘is.leaf’
colorDendClass: no visible global function definition for ‘dendrapply’
colorDendClass: no visible global function definition for ‘plot’
testData1: no visible global function definition for ‘runif’
testData1: no visible global function definition for ‘image’
testData2: no visible global function definition for ‘runif’
testData2: no visible global function definition for ‘image’
Undefined global functions or variables:
  as.dendrogram colorRampPalette dendrapply dev.off hclust heatmap
  image is.leaf legend order.dendrogram pdf plot rainbow runif
  write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf",
             "rainbow")
  importFrom("graphics", "image", "legend", "plot")
  importFrom("stats", "as.dendrogram", "dendrapply", "hclust", "heatmap",
             "is.leaf", "order.dendrogram", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  ‘MASS’ ‘nlme’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GlobTestMissing: no visible global function definition for ‘lme’
GlobTestMissing: no visible global function definition for ‘anova’
TestStatSP: no visible global function definition for ‘pf’
TestStatSimple: no visible global function definition for ‘ginv’
TestStatSimple: no visible global function definition for ‘pf’
Undefined global functions or variables:
  anova ginv lme pf
Consider adding
  importFrom("stats", "anova", "pf")
to your NAMESPACE file.
delete: no visible global function definition for ‘menu’
doc_temp: no visible global function definition for ‘menu’
html5: no visible global function definition for ‘na.omit’
install_pandoc: no visible global function definition for
  ‘download.file’
new_report: no visible global function definition for ‘tail’
new_report: no visible global function definition for ‘head’
new_report: no visible global function definition for ‘menu’
presentation: no visible global function definition for ‘head’
presentation: no visible global function definition for ‘tail’
presentation: no visible global function definition for ‘menu’
repo2github: no visible global function definition for ‘download.file’
repo2github: no visible global function definition for ‘unzip’
reveal.js: no visible global function definition for ‘na.omit’
update_bib: no visible global function definition for ‘tail’
update_bib: no visible global function definition for ‘menu’
Undefined global functions or variables:
  download.file head menu na.omit tail unzip
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "download.file", "head", "menu", "tail", "unzip")
to your NAMESPACE file.
MBoxtest: no visible global function definition for ‘var’
jrparams: no visible global function definition for ‘prcomp’
jrparams: no visible global function definition for ‘predict’
jrparams: no visible global function definition for ‘qchisq’
jrparams: no visible global function definition for ‘qf’
Undefined global functions or variables:
  prcomp predict qchisq qf var
Consider adding
  importFrom("stats", "prcomp", "predict", "qchisq", "qf", "var")
to your NAMESPACE file.
Rd file 'jrparams.Rd':
  \usage lines wider than 90 characters:
     jrparams(BLOCK.1, BLOCK.2, ncomp = min(c(dim(BLOCK.1), dim(BLOCK.2))), Cscrit=0.6, Rscrit=0.6)

These lines will be truncated in the PDF manual.
call.eqs: no visible global function definition for ‘write.table’
read.eqs: no visible global function definition for ‘read.fwf’
Undefined global functions or variables:
  read.fwf write.table
Consider adding
  importFrom("utils", "read.fwf", "write.table")
to your NAMESPACE file.
Rd file 'call.eqs.rd':
  \examples lines wider than 100 characters:
     ##res <- call.eqs(EQSpgm = "C:/Program Files/EQS61/WINEQS.EXE", EQSmodel = "c:/eqs61/examples/manul7.eqs", serial = "1234")

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

These lines will be truncated in the PDF manual.
.resampleMakeFunction: no visible global function definition for ‘is’
.resampleSetSeed: no visible global function definition for ‘runif’
CI.bca: no visible global function definition for ‘is’
CI.bca: no visible global function definition for ‘qnorm’
CI.bca: no visible global function definition for ‘pnorm’
CI.t: no visible global function definition for ‘qt’
ExpandProbs: no visible global function definition for ‘pnorm’
ExpandProbs: no visible global function definition for ‘qt’
colVars : f: no visible global function definition for ‘var’
colVars: no visible global function definition for ‘var’
hist.resample: no visible global function definition for ‘density’
hist.resample: no visible global function definition for ‘lines’
hist.resample: no visible global function definition for ‘points’
hist.resample: no visible global function definition for ‘approx’
hist.resample: no visible global function definition for ‘segments’
resample: no visible global function definition for ‘is’
samp.bootknife: no visible global function definition for ‘runif’
samp.bootstrap: no visible global function definition for ‘runif’
Undefined global functions or variables:
  approx density is lines pnorm points qnorm qt runif segments var
Consider adding
  importFrom("graphics", "lines", "points", "segments")
  importFrom("methods", "is")
  importFrom("stats", "approx", "density", "pnorm", "qnorm", "qt",
             "runif", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package suggested but not available for checking: ‘prospectr’
Running examples in ‘resemble-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fDiss
> ### Title: Euclidean, Mahalanobis and cosine dissimilarity measurements
> ### Aliases: fDiss
> 
> ### ** Examples
> 
> require(prospectr)
Loading required package: prospectr
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘prospectr’
> 
> data(NIRsoil)
Warning in data(NIRsoil) : data set ‘NIRsoil’ not found
> 
> Xu <- NIRsoil$spc[!as.logical(NIRsoil$train),]
Error: object 'NIRsoil' not found
Execution halted
Malformed Title field: should not end in a period.
Non-standard file/directory found at top level:
  ‘load.r’
Packages in Depends field not imported from:
  ‘gWidgets’ ‘gWidgetsRGtk2’ ‘plyr’ ‘reshape2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
reshapeGUI: no visible global function definition for ‘gwindow’
reshapeGUI: no visible global function definition for ‘gnotebook’
reshapeGUI: no visible global function definition for ‘size<-’
reshapeGUI: no visible global function definition for ‘ggroup’
reshapeGUI: no visible global function definition for ‘gtable’
reshapeGUI: no visible global function definition for ‘addSpring’
reshapeGUI: no visible global function definition for ‘gbutton’
reshapeGUI: no visible global function definition for ‘glabel’
reshapeGUI: no visible global function definition for ‘gedit’
reshapeGUI: no visible global function definition for ‘gcheckbox’
reshapeGUI: no visible global function definition for ‘gdf’
reshapeGUI: no visible global function definition for ‘visible<-’
reshapeGUI: no visible global function definition for
  ‘addHandlerClicked’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘gmessage’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘svalue’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘svalue<-’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘delete’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘add’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘gdf’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘visible<-’
reshapeGUI: no visible global function definition for
  ‘addHandlerChanged’
updateMeltCodeBox: no visible global function definition for ‘svalue<-’
Undefined global functions or variables:
  add addHandlerChanged addHandlerClicked addSpring delete gbutton
  gcheckbox gdf gedit ggroup glabel gmessage gnotebook gtable gwindow
  size<- svalue svalue<- visible<-
GUI_template : onHelp: no visible global function definition for ‘help’
Undefined global functions or variables:
  help
Consider adding
  importFrom("utils", "help")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Warning: no function found corresponding to methods exports from ‘retimes’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dexgauss: no visible global function definition for ‘pnorm’
loglik: no visible global function definition for ‘pnorm’
mexgauss: no visible global function definition for ‘sd’
rexgauss: no visible global function definition for ‘rnorm’
rexgauss: no visible global function definition for ‘rexp’
timefit: no visible global function definition for ‘optim’
timefit: no visible global function definition for ‘sd’
timefit: no visible global function definition for ‘par’
timefit: no visible global function definition for ‘hist’
timefit: no visible global function definition for ‘density’
timefit: no visible global function definition for ‘curve’
timefit: no visible global function definition for ‘new’
plot,timefit: no visible global function definition for ‘density’
plot,timefit: no visible global function definition for ‘par’
plot,timefit: no visible global function definition for ‘curve’
Undefined global functions or variables:
  curve density hist new optim par pnorm rexp rnorm sd
Consider adding
  importFrom("graphics", "curve", "hist", "par")
  importFrom("methods", "new")
  importFrom("stats", "density", "optim", "pnorm", "rexp", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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.
FDSNGetTimeSeries: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
fs_author_ids : <anonymous>: no visible global function definition for
  ‘select.list’
fs_download : <anonymous>: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file select.list
Consider adding
  importFrom("utils", "download.file", "select.list")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
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
.testLTS: no visible binding for global variable ‘stackloss’
Undefined global functions or variables:
  stackloss
Consider adding
  importFrom("datasets", "stackloss")
to your NAMESPACE file.
gabriel.plot: no visible global function definition for ‘barplot’
gabriel.plot: no visible global function definition for ‘arrows’
rgabriel: no visible binding for global variable ‘sd’
rgabriel : psmm_x: no visible global function definition for ‘pnorm’
rgabriel : psmm: no visible global function definition for ‘integrate’
rgabriel : qsmm: no visible global function definition for ‘qnorm’
rgabriel : qsmm: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  arrows barplot integrate pnorm qnorm sd uniroot
Consider adding
  importFrom("graphics", "arrows", "barplot")
  importFrom("stats", "integrate", "pnorm", "qnorm", "sd", "uniroot")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Package in Depends field not imported from: ‘gsl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gammaIntegral: no visible global function definition for ‘integrate’
gammaIntegral : <anonymous>: no visible global function definition for
  ‘hyperg_1F1’
gammaMLE: no visible global function definition for ‘weighted.mean’
gammaMME: no visible binding for global variable ‘sd’
gammaMME: no visible binding for global variable ‘var’
Undefined global functions or variables:
  hyperg_1F1 integrate sd var weighted.mean
Consider adding
  importFrom("stats", "integrate", "sd", "var", "weighted.mean")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
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
Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred.
  Output from running autoreconf:
  aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in'
Packages suggested but not available for checking:
  'playwith', 'pmg', 'SVGAnnotation'
Found the following significant warnings:
  Note: possible error in 'coord_trans(xtrans = "exp", ': unused arguments (xtrans = "exp", ytrans = "exp") 
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RGraphics.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’.
figure5.11: possible error in coord_trans(xtrans = "exp", ytrans =
  "exp"): unused arguments (xtrans = "exp", ytrans = "exp")
Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred.
  Output from running autoreconf:
  aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in'
File ‘RGtk2/libs/RGtk2.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_new_custom_connection’,
    ‘Rf_EncodeInteger’, ‘Rf_EncodeLogical’, ‘Rf_EncodeReal’,
    ‘Rf_formatInteger’, ‘Rf_formatLogical’, ‘Rf_formatReal’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.quick_fetch: no visible global function definition for ‘POST’
.quick_fetch: no visible global function definition for ‘add_headers’
.quick_fetch: no visible global function definition for
  ‘stop_for_status’
.quick_fetch: no visible global function definition for ‘content’
fetch_healthdata: no visible binding for global variable ‘resources’
fetch_healthdata : <anonymous>: no visible binding for global variable
  ‘filters’
Undefined global functions or variables:
  POST add_headers content filters resources stop_for_status
GNU make is a SystemRequirements.
Packages in Depends field not imported from:
  ‘RCurl’ ‘XML’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ECL: no visible global function definition for ‘new’
ECLDataset: no visible global function definition for ‘new’
ECLDedUp: no visible global function definition for ‘new’
ECLDistribute: no visible global function definition for ‘new’
ECLIterate: no visible global function definition for ‘new’
ECLJoin: no visible global function definition for ‘new’
ECLOutput: no visible global function definition for ‘new’
ECLProject: no visible global function definition for ‘new’
ECLRecord: no visible global function definition for ‘new’
ECLRollUp: no visible global function definition for ‘new’
ECLSort: no visible global function definition for ‘new’
ECLTOPN: no visible global function definition for ‘new’
ECLTable: no visible global function definition for ‘new’
ECLTransform: no visible global function definition for ‘new’
eclDirectCall: no visible global function definition for ‘postForm’
parseResults: no visible global function definition for ‘xmlRoot’
parseResults: no visible global function definition for ‘xmlTreeParse’
parseResults: no visible global function definition for ‘getNodeSet’
parseResults: no visible global function definition for ‘xmlGetAttr’
parseResults: no visible global function definition for ‘xmlValue’
parseResults: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  getNodeSet new postForm write.table xmlGetAttr xmlRoot xmlTreeParse
  xmlValue
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
RHT.2samp : my.HotellingT2 : my.InvCov2: no visible global function
  definition for ‘cov’
RHT.2samp : get.lambda : get.para: no visible global function
  definition for ‘optimize’
RHT.2samp : get.lambda : gg: no visible global function definition for
  ‘qchisq’
RHT.2samp : get.lambda : ggl: no visible global function definition for
  ‘qnorm’
RHT.2samp : <anonymous>: no visible global function definition for
  ‘cov’
RHT.fun : my.HotellingT : my.InvCov: no visible global function
  definition for ‘cov’
RHT.fun : get.lambda : get.para: no visible global function definition
  for ‘optimize’
RHT.fun : get.lambda : gg: no visible global function definition for
  ‘qchisq’
RHT.fun : get.lambda : ggl: no visible global function definition for
  ‘qnorm’
RHT.fun : <anonymous>: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov optimize qchisq qnorm
Consider adding
  importFrom("stats", "cov", "optimize", "qchisq", "qnorm")
to your NAMESPACE file.
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.
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.
plot.ijzip: no visible global function definition for ‘plot’
plot.ijzip : <anonymous>: no visible global function definition for
  ‘plot’
plot.ijzip: no visible global function definition for ‘axis’
read.ijzip: no visible global function definition for ‘unzip’
Undefined global functions or variables:
  axis plot unzip
Consider adding
  importFrom("graphics", "axis", "plot")
  importFrom("utils", "unzip")
to your NAMESPACE file.
File ‘RInside/libs/RInside.so’:
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLdo1’, ‘R_ReplDLLinit’,
    ‘R_RunExitFinalizers’, ‘R_SetParams’, ‘R_SignalHandlers’,
    ‘R_TempDir’, ‘Rf_endEmbeddedR’, ‘Rf_initEmbeddedR’

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

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

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

These lines will be truncated in the PDF manual.
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.
Packages in Depends field not imported from:
  ‘compiler’ ‘signal’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
NumConv: no visible global function definition for ‘pchip’
NumConv: no visible global function definition for ‘cmpfun’
NumDeconv: no visible global function definition for ‘pchip’
NumDeconv : error_function: no visible global function definition for
  ‘pchip’
NumDeconv: no visible global function definition for ‘cmpfun’
NumDeconv: no visible global function definition for ‘optim’
RivivcA: no visible global function definition for ‘lm’
Undefined global functions or variables:
  cmpfun lm optim pchip
Consider adding
  importFrom("stats", "lm", "optim")
to your NAMESPACE file.
Rd file 'NumConv.Rd':
  \usage lines wider than 90 characters:
     NumConv(impulse.matrix, input.matrix, conv.timescale = NULL, explicit.interpolation = 1000)

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
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.
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.
GNU make is a SystemRequirements.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following Makefile(s) without a final LF:
  src/Makevars.in
Some ‘make’ programs ignore lines not ending in LF.
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
  src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_LIBS but not in PKG_CXXFLAGS
  src/Makevars: it is not portable to include SHLIB_OPENMP_*' macros in PKG_CPPFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
PKG_CPPFLAGS is used for both C and C++ code so it is not portable to
use it for these macros.
Package in Depends field not imported from: ‘msm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘EMSRb_internal’ ‘EM_internal’ ‘PD_internal’
EMSRb_internal: no visible global function definition for ‘qnorm’
EM_internal: no visible global function definition for ‘dnorm’
EM_internal: no visible global function definition for ‘pnorm’
PD_internal: no visible global function definition for ‘qtnorm’
PD_internal: no visible global function definition for ‘sd’
Undefined global functions or variables:
  dnorm pnorm qnorm qtnorm sd
Consider adding
  importFrom("stats", "dnorm", "pnorm", "qnorm", "sd")
to your NAMESPACE file.
Rd file 'EMSRb_internal.Rd':
  \usage lines wider than 90 characters:
     EMSRb_internal(Fare = Fare, Mean = Mean, Var = Var, p_up = numeric(length(Fare)), cap = cap)

These lines will be truncated in the PDF manual.
ma.filter: no visible global function definition for ‘par’
ma.filter: no visible global function definition for ‘lines’
ma.filter: no visible global function definition for ‘abline’
qn: no visible global function definition for ‘lm’
qn: no visible global function definition for ‘var’
qn: no visible global function definition for ‘resid’
ss.filter: no visible global function definition for ‘smooth.spline’
ss.filter: no visible global function definition for ‘par’
ss.filter: no visible global function definition for ‘lines’
ss.filter: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline lines lm par resid smooth.spline var
Consider adding
  importFrom("graphics", "abline", "lines", "par")
  importFrom("stats", "lm", "resid", "smooth.spline", "var")
to your NAMESPACE file.
GNU make is a SystemRequirements.
CI: no visible global function definition for ‘sd’
CI: no visible global function definition for ‘qt’
L: no visible global function definition for ‘sd’
L: no visible global function definition for ‘residuals’
Qa: no visible global function definition for ‘logLik’
Qb: no visible global function definition for ‘residuals’
Qc: no visible global function definition for ‘residuals’
Qc: no visible global function definition for ‘logLik’
STDERR: no visible global function definition for ‘sd’
group.UCL: no visible global function definition for ‘aggregate’
lr.glover: no visible binding for global variable ‘logLik’
lr.glover: no visible binding for global variable ‘update’
lr.glover : nobs0: no visible binding for global variable ‘nobs’
lr.glover : nobs0 : nobs2: no visible global function definition for
  ‘residuals’
lr.glover : tlab: no visible global function definition for ‘terms’
lr.glover : name: no visible global function definition for ‘formula’
lr.glover : modelUpdate: no visible global function definition for
  ‘as.formula’
lr.glover: no visible global function definition for ‘model.frame’
lr.glover: no visible binding for global variable ‘AIC’
lr.glover: no visible binding for global variable ‘BIC’
summarySE : <anonymous>: no visible global function definition for ‘sd’
summarySE: no visible global function definition for ‘qt’
Undefined global functions or variables:
  AIC BIC aggregate as.formula formula logLik model.frame nobs qt
  residuals sd terms update
Consider adding
  importFrom("stats", "AIC", "BIC", "aggregate", "as.formula", "formula",
             "logLik", "model.frame", "nobs", "qt", "residuals", "sd",
             "terms", "update")
to your NAMESPACE file.
Combi: no visible global function definition for ‘new’
barplotMixCluster: no visible global function definition for ‘is’
barplotMixCluster: no visible global function definition for ‘par’
barplotMixCluster: no visible global function definition for ‘lines’
barplotMixCluster: no visible global function definition for ‘text’
barplotMixCluster: no visible global function definition for ‘title’
barplotMixCluster: no visible global function definition for ‘mtext’
histMixCluster: no visible global function definition for ‘is’
histMixCluster: no visible global function definition for ‘par’
histMixCluster: no visible global function definition for ‘dnorm’
histMixCluster: no visible global function definition for ‘lines’
mixmodEntPlot: no visible global function definition for ‘par’
mixmodEntPlot: no visible global function definition for ‘lines’
mixmodEntPlot: no visible global function definition for ‘axis’
mixmodEntPlot: no visible global function definition for ‘title’
mixmodEntPlot: no visible binding for global variable ‘par’
plot,MixmodCombi: no visible global function definition for ‘par’
plot,MixmodCombi: no visible global function definition for ‘plot.new’
plot,MixmodCombi: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis dnorm is lines mtext new par plot.new text title
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "par", "plot.new",
             "text", "title")
  importFrom("methods", "is", "new")
  importFrom("stats", "dnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.pLGP_qvec: no visible global function definition for ‘ppois’
.qLGP_pvec: no visible global function definition for ‘qpois’
.rLGP.failsafe: no visible global function definition for ‘runif’
.subdmg: no visible global function definition for ‘dbinom’
dnegbin: no visible global function definition for ‘dnbinom’
pLGP: no visible global function definition for ‘ppois’
qLGP: no visible global function definition for ‘qpois’
rLGP: no visible global function definition for ‘rpois’
rLGP: no visible global function definition for ‘rnorm’
rLGP: no visible global function definition for ‘runif’
rbinegbin: no visible global function definition for ‘rnbinom’
rmanaclash: no visible global function definition for ‘rbinom’
rmanaclash: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dbinom dnbinom ppois qpois rbinom rnbinom rnorm rpois runif
Consider adding
  importFrom("stats", "dbinom", "dnbinom", "ppois", "qpois", "rbinom",
             "rnbinom", "rnorm", "rpois", "runif")
to your NAMESPACE file.
Found the following calls to attach():
File ‘Rmosek/R/builder.R’:
  attach(builderenv, pos, name, warn.conflicts)
See section ‘Good practice’ in ‘?attach’.
rms.pval: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
dWishartSpike: no visible global function definition for ‘dnorm’
pWishartSpike: no visible global function definition for ‘pnorm’
qWishartSpike: no visible global function definition for ‘qnorm’
rWishartSpike: no visible global function definition for ‘qnorm’
rmp: no visible global function definition for ‘runif’
rtw: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dnorm pnorm qnorm runif
Consider adding
  importFrom("stats", "dnorm", "pnorm", "qnorm", "runif")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls in package code:
  ‘DESeq’ ‘seqinr’ ‘topGO’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: ‘rnaturalearthhires’
Malformed Title field: should not end in a period.
Package suggested but not available for checking: ‘XMLRPC’
well19937.validate: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Nnls.trimW : fun1: no visible global function definition for ‘runif’
initM: no visible global function definition for ‘runif’
rnmf: no visible global function definition for ‘txtProgressBar’
rnmf: no visible global function definition for ‘setTxtProgressBar’
see: no visible global function definition for ‘heat.colors’
see: no visible global function definition for ‘colorRampPalette’
see: no visible global function definition for ‘grey’
see: no visible global function definition for ‘par’
see: no visible global function definition for ‘image’
see: no visible global function definition for ‘mtext’
simtum: no visible global function definition for ‘runif’
simtum: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  colorRampPalette grey heat.colors image mtext par rnorm runif
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey", "heat.colors")
  importFrom("graphics", "image", "mtext", "par")
  importFrom("stats", "rnorm", "runif")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘robustbase’ ‘sfsmisc’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.BuildPartial: no visible global function definition for ‘as.formula’
.BuildPartial: no visible global function definition for ‘residuals’
.PairwiseCorrelation : .Standardize : <anonymous>: no visible global
  function definition for ‘na.omit’
.PairwiseCorrelation : .Standardize: no visible binding for global
  variable ‘median’
.PairwiseCorrelation: no visible global function definition for
  ‘complete.cases’
.yw: no visible global function definition for ‘toeplitz’
FastQn: no visible global function definition for ‘median’
FastQn: no visible global function definition for ‘mad’
fqn: no visible global function definition for ‘median’
fqn: no visible global function definition for ‘mad’
psdcor: no visible global function definition for ‘posdefify’
psdcor: no visible global function definition for ‘nearcor’
robar: no visible global function definition for ‘frequency’
robcor: no visible global function definition for ‘covMcd’
s_FastQn: no visible global function definition for ‘median’
Undefined global functions or variables:
  as.formula complete.cases covMcd frequency mad median na.omit nearcor
  posdefify residuals toeplitz
Consider adding
  importFrom("stats", "as.formula", "complete.cases", "frequency", "mad",
             "median", "na.omit", "residuals", "toeplitz")
to your NAMESPACE file.
RobRSVD: no visible global function definition for ‘median’
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘RcppArmadillo’ ‘mgcv’ ‘robustbase’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GIC: no visible global function definition for ‘integrate’
QM.poisson: no visible global function definition for ‘ppois’
QM.poisson: no visible global function definition for ‘dpois’
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.
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.
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  ‘penalized’ ‘splines’ ‘survival’ ‘survivalROC’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
boot.ROC: no visible global function definition for ‘qnorm’
boot.ROC: no visible global function definition for ‘penalized’
boot.ROC: no visible global function definition for ‘coefficients’
boot.ROC: no visible global function definition for ‘sd’
boot.ROC: no visible global function definition for ‘optL1’
boot.ROCt: no visible global function definition for ‘qnorm’
boot.ROCt: no visible global function definition for ‘penalized’
boot.ROCt: no visible global function definition for ‘Surv’
boot.ROCt: no visible global function definition for ‘coefficients’
boot.ROCt: no visible global function definition for ‘sd’
boot.ROCt: no visible global function definition for ‘survivalROC’
boot.ROCt: no visible global function definition for ‘optL1’
Undefined global functions or variables:
  Surv coefficients optL1 penalized qnorm sd survivalROC
Consider adding
  importFrom("stats", "coefficients", "qnorm", "sd")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
NPROCwoGS: no visible global function definition for ‘quantile’
NPROCwoGS : rdirichlet: no visible global function definition for
  ‘rgamma’
NPROCwoGS: no visible global function definition for ‘rbinom’
NPROCwoGS: no visible global function definition for ‘rbeta’
NPROCwoGS: no visible binding for global variable ‘quantile’
Undefined global functions or variables:
  quantile rbeta rbinom rgamma
Consider adding
  importFrom("stats", "quantile", "rbeta", "rbinom", "rgamma")
to your NAMESPACE file.
prepare_Rd: score.Rd:20-22: Dropping empty section \details
prepare_Rd: score.Rd:23-25: Dropping empty section \source
prepare_Rd: score.Rd:26-28: Dropping empty section \references
Rd file 'NPROCwoGS.Rd':
  \examples lines wider than 100 characters:
     AUC<- sum((ROC.est$T.Se[1,-1]+ROC.est$T.Se[1,-(ncutoff+2)])*(ROC.est$T.Sp[1,-1]-ROC.est$T.Sp[1,-(ncutoff+2)])/2)
     plot(1-ROC.est$T.Sp[1,],ROC.est$T.Se[1,],"l", xlab="1-Specificities",ylab="Sensitivities", main=paste("AUC=", format(AUC, digits=4),

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

These lines will be truncated in the PDF manual.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘RODBC’
A package should be listed in only one of these fields.
'library' or 'require' call to ‘RODBC’ which was already attached by Depends.
  Please remove these calls from your code.
GNU make is a SystemRequirements.
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.
bestFM: no visible global function definition for ‘data’
gaRoth: no visible global function definition for ‘data’
ros: no visible global function definition for ‘na.omit’
rosunc: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  data na.omit rnorm
Consider adding
  importFrom("stats", "na.omit", "rnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
mfix : m4m: no visible global function definition for ‘median’
rrfa: no visible global function definition for ‘predict’
rrfb: no visible global function definition for ‘predict’
rrfc1: no visible global function definition for ‘predict’
rrfc2: no visible global function definition for ‘predict’
rrfc3: no visible global function definition for ‘predict’
rrfc4: no visible global function definition for ‘predict’
rrfc5 : regdat: no visible global function definition for ‘predict’
rrfc5 : regdat: no visible global function definition for ‘glm’
rrfc5: no visible global function definition for ‘predict’
rrfc6: no visible global function definition for ‘predict’
rrfc7: no visible global function definition for ‘predict’
rrfd: no visible global function definition for ‘predict’
rrfe : rdms: no visible global function definition for ‘rbinom’
rrfe: no visible global function definition for ‘predict’
Undefined global functions or variables:
  glm median predict rbinom
Consider adding
  importFrom("stats", "glm", "median", "predict", "rbinom")
to your NAMESPACE file.
.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.
Rd file 'C.FRNN.FRST.Rd':
  \examples lines wider than 100 characters:
                     type.relation = c("tolerance", "eq.1"), t.implicator = "lukasiewicz")                                                   ... [TRUNCATED]

These lines will be truncated in the PDF manual.
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.
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.
Non-standard file/directory found at top level:
  ‘Read-and-delete-me’
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘survival’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘MASS’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GenerateData: no visible global function definition for ‘mvrnorm’
GetVarImp : FitPenalizedModel: no visible global function definition
  for ‘clogit’
Undefined global functions or variables:
  clogit mvrnorm
Rd file 'GetVarImp.Rd':
  \examples lines wider than 100 characters:
     hist(MyResults, breaks=6, col="orange", xlab="Importance score", ylab="Number of features", main="Histogram of R-PCLR variable importan ... [TRUNCATED]
     ## Sort from most important (highest importance score) to least important feature (lowest importance score)

These lines will be truncated in the PDF manual.
Dependence on R version ‘3.4.2’ not with patchlevel 0
Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred.
  Output from running autoreconf:
  aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in'
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/libpq/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Error(s) in re-building vignettes:
  ...
--- re-building ‘rpredictit-vignette.Rmd’ using rmarkdown
Quitting from lines 54-56 (rpredictit-vignette.Rmd) 
Error: processing vignette 'rpredictit-vignette.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building ‘rpredictit-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
GNU make is a SystemRequirements.
but_last: no visible global function definition for ‘head’
first: no visible global function definition for ‘head’
last: no visible global function definition for ‘tail’
preview_frames: no visible global function definition for ‘str’
print.EprimeFrame: no visible global function definition for ‘str’
print.FrameList: no visible global function definition for ‘str’
Undefined global functions or variables:
  head str tail
Consider adding
  importFrom("utils", "head", "str", "tail")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘rpsychi-Ex.R’
Rd file 'ind.prop.Rd':
  \examples lines wider than 100 characters:
     ind.prop(y~x, data=dat, lev.count=2, ref.ind=1)    #Odds for not relapse is higher in treatment than control condition.
     ind.prop(y~x, data=dat, lev.count=1, ref.ind=1)    #Odds for relapse is lower in treatment than control condition.
     ind.prop(y~x, data=dat, lev.count=2, ref.ind=2)    #Odds for not relapse is lower in control than treatment condition.
     ind.prop(y~x, data=dat, lev.count=1, ref.ind=2)    #Odds for relapse is higher in control than treatment condition.

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

These lines will be truncated in the PDF manual.
Package which this enhances but not available for checking: ‘rjpod’
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.
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.
Package suggested but not available for checking: ‘SDMTools’
stripslash: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
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.
Package suggested but not available for checking: ‘Rcompression’
rsem: no visible global function definition for ‘write.table’
rsem.Ascov: no visible global function definition for ‘qchisq’
rsem.Ascov: no visible global function definition for ‘pchisq’
rsem.emmusig: no visible global function definition for ‘na.omit’
rsem.emmusig: no visible global function definition for ‘qchisq’
rsem.emmusig: no visible global function definition for ‘pchisq’
rsem.fit: no visible global function definition for ‘pchisq’
rsem.fit: no visible global function definition for ‘pf’
rsem.print : print.estimate: no visible global function definition for
  ‘pnorm’
rsem.weight: no visible global function definition for ‘qchisq’
rsem.weight: no visible global function definition for ‘pchisq’
semdiag.call.eqs: no visible global function definition for
  ‘write.table’
semdiag.read.eqs: no visible global function definition for ‘read.fwf’
Undefined global functions or variables:
  na.omit pchisq pf pnorm qchisq read.fwf write.table
Consider adding
  importFrom("stats", "na.omit", "pchisq", "pf", "pnorm", "qchisq")
  importFrom("utils", "read.fwf", "write.table")
to your NAMESPACE file.
Non-standard files/directories found at top level:
  ‘aclocal.m4’ ‘clients’ ‘clients.txt’ ‘version’
GNU make is a SystemRequirements.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
addNoisyCopies: no visible global function definition for ‘rnorm’
eta: no visible global function definition for ‘var’
gaussClassifier: no visible global function definition for ‘runif’
getSigma: no visible global function definition for ‘sd’
getSigma: no visible binding for global variable ‘sd’
sfaClassify: no visible global function definition for ‘rainbow’
sfaClassify: no visible global function definition for ‘par’
sfaClassify: no visible global function definition for ‘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.
Package suggested but not available for checking: ‘INLA’
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.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Malformed Title field: should not end in a period.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Math.Sym: no visible binding for global variable ‘transtab’
jythonStart: no visible global function definition for ‘.jinit’
jythonStart: no visible global function definition for ‘.jnew’
jythonStart: no visible binding for global variable ‘.Jython’
sympy: no visible binding for global variable ‘.Jython’
sympy: no visible global function definition for ‘.jstrVal’
sympyStart: no visible binding for global variable ‘.Jython’
Undefined global functions or variables:
  .Jython .jinit .jnew .jstrVal transtab

Found the following assignments to the global environment:
File ‘rSymPy/R/sympy.R’:
  assign(".Jython", .jnew("org.python.util.PythonInterpreter"), 
    .GlobalEnv)
  assign(".Jython", rJython(modules = system.file("Lib", package = "rSymPy")), 
    .GlobalEnv)
Malformed Title field: should not end in a period.
barplot.rtconnect: no visible global function definition for ‘rainbow’
barplot.rtconnect: no visible global function definition for ‘text’
plot.rtconnect: no visible global function definition for ‘par’
plot.rtconnect: no visible global function definition for ‘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.
Documented arguments not in \usage in documentation object 'show-methods':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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.
Documented arguments not in \usage in documentation object 'RTF':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
  src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Rd file 'Runiversal-package.Rd':
  \examples lines wider than 100 characters:
     #Getting estimates from regression object as Java variables that be directly interpretable by Bean Shell.

These lines will be truncated in the PDF manual.
Malformed Title field: should not end in a period.
HapMendlianCheck: no visible global function definition for
  ‘write.table’
rvPDT.test.sub: no visible global function definition for ‘pnorm’
whap.prehap: no visible global function definition for ‘write.table’
whap.prehap: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  pnorm read.table write.table
Consider adding
  importFrom("stats", "pnorm")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
'library' or 'require' call to ‘pixmap’ which was already attached by Depends.
  Please remove these calls from your code.
rvideopoker: warning in rp.radiogroup(mypanel, var =
  state$penny.nickel.quarter.dollar, initval = 1, values = c(1, 5, 25,
  100), title = "Bet (in Cents)", action = setbet): partial argument
  match of ‘var’ to ‘variable’
rvideopoker: warning in rp.slider(mypanel, var = state$no.of.credits,
  from = 1, to = 5, initval = 1, title = "How many Credits?",
  resolution = 1, action = creditset, showvalue = TRUE): partial
  argument match of ‘var’ to ‘variable’
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC1, action = card1check, title = "Keep Card 1?"): partial
  argument match of ‘var’ to ‘variable’
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC2, action = card2check, title = "Keep Card 2?"): partial
  argument match of ‘var’ to ‘variable’
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC3, action = card3check, title = "Keep Card 3?"): partial
  argument match of ‘var’ to ‘variable’
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC4, action = card4check, title = "Keep Card 4?"): partial
  argument match of ‘var’ to ‘variable’
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC5, action = card5check, title = "Keep Card 5?"): partial
  argument match of ‘var’ to ‘variable’
rvideopoker : plotFrame: no visible global function definition for
  ‘par’
rvideopoker : showBack: no visible global function definition for
  ‘title’
rvideopoker : showCardsInitially: no visible global function definition
  for ‘title’
Undefined global functions or variables:
  par title
Consider adding
  importFrom("graphics", "par", "title")
to your NAMESPACE file.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RVowpalWabbit.Rcheck/00install.out’ for details.
Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred.
  Output from running autoreconf:
  aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in'
  configure.in:22: warning: underquoted definition of AC_PROG_R
  configure.in:22:   run info Automake 'Extending aclocal'
  configure.in:22:   or see https://www.gnu.org/software/automake/manual/automake.html#Extending-aclocal
  configure.in:86: warning: the serial number must appear before any macro definition
  configure.in:362: warning: the serial number must appear before any macro definition
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.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Malformed Title field: should not end in a period.
.dwt: no visible global function definition for ‘median’
.udwt: no visible global function definition for ‘median’
plotSignalTransformation: no visible global function definition for
  ‘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.
Packages suggested but not available for checking:
  'SnakeCharmR', 'installr'
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
calculate.summary: no visible global function definition for ‘sd’
detect.saccades: no visible global function definition for ‘median’
diagnostic.plot: no visible global function definition for ‘dev.new’
diagnostic.plot: no visible global function definition for ‘par’
diagnostic.plot: no visible global function definition for ‘recordPlot’
diagnostic.plot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.new dev.off median par recordPlot sd
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "recordPlot")
  importFrom("graphics", "par")
  importFrom("stats", "median", "sd")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
prepare_Rd: BootsModelTest.Rd:28-29: Dropping empty section \details
prepare_Rd: BootsModelTest.Rd:43: Dropping empty section \note
prepare_Rd: CriticalValues.Rd:38: Dropping empty section \note
prepare_Rd: Pvalues.Rd:24-25: Dropping empty section \details
prepare_Rd: Pvalues.Rd:38: Dropping empty section \note
prepare_Rd: cumsum.test.Rd:16-17: Dropping empty section \details
prepare_Rd: cumsum.test.Rd:28: Dropping empty section \note
fit.saery.AR1: no visible global function definition for ‘qnorm’
fit.saery.MA1: no visible global function definition for ‘qnorm’
fit.saery.indep: no visible global function definition for ‘qnorm’
mse.saery.boot.AR1.typeI: no visible global function definition for
  ‘rnorm’
mse.saery.boot.AR1.typeI: no visible global function definition for
  ‘write.table’
mse.saery.boot.AR1.typeII: no visible global function definition for
  ‘rnorm’
mse.saery.boot.AR1.typeII: no visible global function definition for
  ‘write.table’
mse.saery.boot.MA1.typeI: no visible global function definition for
  ‘rnorm’
mse.saery.boot.MA1.typeI: no visible global function definition for
  ‘write.table’
mse.saery.boot.MA1.typeII: no visible global function definition for
  ‘rnorm’
mse.saery.boot.MA1.typeII: no visible global function definition for
  ‘write.table’
plot.saery: no visible global function definition for ‘devAskNewPage’
plot.saery: no visible global function definition for ‘par’
plot.saery: no visible global function definition for ‘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.
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.
Rd file 'mudiff.acc.Rd':
  \usage lines wider than 90 characters:
     mudiff.acc(len, alpha1, beta1, alpha2, beta2, n01, n02, level = 0.95, equal = TRUE, m = 10000, mcs = 3)

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

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

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

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

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

These lines will be truncated in the PDF manual.
propdiff.acc: no visible global function definition for ‘rbeta’
propdiff.acc: no visible global function definition for ‘rbinom’
propdiff.acc: no visible global function definition for ‘pbeta’
propdiff.alc: no visible global function definition for ‘rbeta’
propdiff.alc: no visible global function definition for ‘rbinom’
propdiff.alc: no visible global function definition for ‘qbeta’
propdiff.freq: no visible global function definition for ‘qnorm’
propdiff.mblacc: no visible global function definition for ‘rbeta’
propdiff.mblacc: no visible global function definition for ‘rbinom’
propdiff.mblacc: no visible global function definition for ‘pbeta’
propdiff.mblalc: no visible global function definition for ‘rbeta’
propdiff.mblalc: no visible global function definition for ‘rbinom’
propdiff.mblalc: no visible global function definition for ‘qbeta’
propdiff.mblmodwoc: no visible global function definition for ‘qchisq’
propdiff.mblmodwoc: no visible global function definition for ‘pbeta’
propdiff.mblwoc: no visible global function definition for ‘pbeta’
propdiff.modwoc: no visible global function definition for ‘qchisq’
propdiff.modwoc: no visible global function definition for ‘pbeta’
propdiff.woc: no visible global function definition for ‘pbeta’
Undefined global functions or variables:
  pbeta qbeta qchisq qnorm rbeta rbinom
Consider adding
  importFrom("stats", "pbeta", "qbeta", "qchisq", "qnorm", "rbeta",
             "rbinom")
to your NAMESPACE file.
GraphBinaryForestPlot: no visible global function definition for
  ‘abline’
GraphBinaryForestPlot: no visible global function definition for ‘text’
GraphContinuousForestPlot: no visible global function definition for
  ‘abline’
GraphContinuousForestPlot: no visible global function definition for
  ‘text’
ImputeBinaryEvents: no visible global function definition for ‘rbinom’
ImputeSMD: no visible global function definition for ‘rnorm’
funnelplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline rbinom rnorm text
Consider adding
  importFrom("graphics", "abline", "text")
  importFrom("stats", "rbinom", "rnorm")
to your NAMESPACE file.
generate.sample.core: no visible global function definition for
  ‘predict’
mdh: no visible global function definition for ‘model.frame’
mdh: no visible binding for global variable ‘na.fail’
mdh: no visible global function definition for ‘.getXlevels’
mdh: no visible global function definition for ‘quantile’
mdh: no visible global function definition for ‘hist’
predict.mdh: no visible global function definition for ‘model.frame’
samur: no visible global function definition for ‘predict’
Undefined global functions or variables:
  .getXlevels hist model.frame na.fail predict quantile
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", ".getXlevels", "model.frame", "na.fail", "predict",
             "quantile")
to your NAMESPACE file.
Package suggested but not available for checking: ‘mixer’
GNU make is a SystemRequirements.
download.sas7bdat.sources : <anonymous>: no visible global function
  definition for ‘download.file’
generate.sas7bdat.source: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
parse.SAScii: no visible binding for global variable ‘end’
parse.SAScii: no visible binding for global variable ‘start’
read.SAScii: no visible global function definition for ‘download.file’
read.SAScii: no visible global function definition for ‘unzip’
read.SAScii: no visible global function definition for ‘read.fwf’
read.SAScii: no visible global function definition for ‘capture.output’
Undefined global functions or variables:
  capture.output download.file end read.fwf start unzip
Consider adding
  importFrom("stats", "end", "start")
  importFrom("utils", "capture.output", "download.file", "read.fwf",
             "unzip")
to your NAMESPACE file.
Rd file 'read.SAScii.Rd':
  \usage lines wider than 90 characters:
     read.SAScii( fn, sas_ri, beginline = 1, buffersize = 50, zipped = F , n = -1 , intervals.to.print = 1000 , lrecl = NULL , skip.decimal. ... [TRUNCATED]
  \examples lines wider than 100 characters:
                     paste( "http://smpbff2.dsd.census.gov/pub/sipp/2004/l04puw" , i , ".zip" , sep = "" )

These lines will be truncated in the PDF manual.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
SASPECT: no visible global function definition for ‘dbinom’
my.SOnePro: missing arguments not allowed in calls to ‘c’
my.ttest: no visible global function definition for ‘var’
Undefined global functions or variables:
  dbinom var
Consider adding
  importFrom("stats", "dbinom", "var")
to your NAMESPACE file.
GNU make is a SystemRequirements.
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.
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.
Malformed Title field: should not end in a period.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
Malformed Description field: should contain one or more complete sentences.
fitSBSA: no visible binding for global variable ‘var’
fitSBSA: no visible global function definition for ‘var’
fitSBSA: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm var
Consider adding
  importFrom("stats", "qnorm", "var")
to your NAMESPACE file.
Packages which this enhances but not available for checking:
  'gurobi', 'pogs'
Missing or unexported objects:
  ‘Rmosek::mosek_lptoprob’ ‘Rmosek::mosek_qptoprob’
Non-standard file/directory found at top level:
  ‘src-java’
GNU make is a SystemRequirements.
ChooseBest: no visible global function definition for ‘head’
GetScores: no visible global function definition for ‘write.table’
ReportTable: no visible binding for global variable ‘sd’
ReportTable: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  head sd write.table
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "head", "write.table")
to your NAMESPACE file.
src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
'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.
Malformed Description field: should contain one or more complete sentences.
prime.factor: no visible global function definition for ‘data’
prime.factor: no visible binding for global variable ‘primlist’
Undefined global functions or variables:
  data primlist
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘schoolmath/R/prime.factor.R’:
  data(primlist)
See section ‘Good practice’ in ‘?data’.
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
License components which are templates and need '+ file LICENSE':
  MIT License
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls to packages already attached by Depends:
  ‘RCurl’ ‘XML’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RCurl’ ‘XML’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
scrape: no visible global function definition for ‘getURLAsynchronous’
scrape: no visible global function definition for ‘runif’
scrape: no visible global function definition for ‘capture.output’
scrape: no visible binding for global variable ‘xmlParse’
scrape: no visible binding for global variable ‘htmlParse’
Undefined global functions or variables:
  capture.output getURLAsynchronous htmlParse runif xmlParse
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Found the following calls to attach():
File ‘scriptests/R/source.pkg.R’:
  attach(NULL, pos = pos, name = paste("pkgcode", pkg.name, sep = ":"))
  attach(envir, pos = pos, name = paste("pkgcode", pkg.name, sep = ":"))
See section ‘Good practice’ in ‘?attach’.
GNU make is a SystemRequirements.
lahiri.design: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
estimateTimeToComputeTargetDefinition: no visible global function
  definition for ‘flush.console’
estimateTimeToComputeTargetDefinition: no visible global function
  definition for ‘combn’
initialize,sdcTargetDefinitionClass: no visible global function
  definition for ‘flush.console’
initialize,sdcTargetDefinitionClass: no visible global function
  definition for ‘combn’
initialize,sdcTargetDefinitionClass: no visible global function
  definition for ‘quantile’
initialize,sdcTargetMatrixClass: no visible global function definition
  for ‘flush.console’
Undefined global functions or variables:
  combn flush.console quantile
Consider adding
  importFrom("stats", "quantile")
  importFrom("utils", "combn", "flush.console")
to your NAMESPACE file.
prepare_Rd: sdd.Rd:46-47: Dropping empty section \seealso
prepare_Rd: sddpack-package.Rd:31-32: Dropping empty section \seealso
prepare_Rd: sddsolve.Rd:29-30: Dropping empty section \references
prepare_Rd: sddsolve.Rd:38-39: Dropping empty section \seealso
prepare_Rd: sddsolve.Rd:40-41: Dropping empty section \examples
Package in Depends field not imported from: ‘lars’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
sealasso: no visible global function definition for ‘lars’
weight.calc: no visible global function definition for ‘lars’
Undefined global functions or variables:
  lars
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'createTree.Rd':
  \usage lines wider than 90 characters:
     createTree(data, treeType = "quad", dataType = "point", columns = if (dataType=="point") 1:2 else 1:4, ...)

These lines will be truncated in the PDF manual.
adx: no visible global function definition for ‘abline’
adx: no visible global function definition for ‘legend’
dx: no visible global function definition for ‘abline’
dx: no visible global function definition for ‘legend’
maxd: no visible global function definition for ‘abline’
maxd: no visible global function definition for ‘legend’
pc: no visible global function definition for ‘rainbow’
pc: no visible global function definition for ‘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.
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  ‘NADA’ ‘lubridate’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
GNU make is a SystemRequirements.
src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
Malformed Description field: should contain one or more complete sentences.
.read.SeerStatTXT: no visible global function definition for
  ‘read.table’
.write.SeerStatTXT: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
prepare_Rd: SEER2RTestdata.Rd:77-78: Dropping empty section \source
Rd file 'SEER2R-package.Rd':
  \examples lines wider than 100 characters:
     #load testing data: there are three data objects, i.e. SEER2RTestData1,SEER2RTestData2,SEER2RTestData3 
     dicinfoused = write.SeerStat(SEER2RTestData2, DICfileName = "testrun1.dic",UseVarLabelsInTxtFile=FALSE);

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

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

These lines will be truncated in the PDF manual.
get.infectiousness: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  qchisq
Consider adding
  importFrom("stats", "qchisq")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
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.
Rd file 'semdiag.Rd':
  \usage lines wider than 90 characters:
     semdiag(x,  EQSmodel, varphi=0.1, EQSdata='data.txt', D='E', delete=integer(0), max_it=1000, EQSprog='C:/Progra~1/EQS61/WINEQS',serial= ... [TRUNCATED]

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

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

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

These lines will be truncated in the PDF manual.
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.
GNU make is a SystemRequirements.
GNU make is a SystemRequirements.
Malformed Title field: should not end in a period.
plotenz : addmark: no visible global function definition for ‘par’
plotenz : addmark: no visible global function definition for ‘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.
Rd file 'plotenz.Rd':
  \usage lines wider than 90 characters:
     plotenz(sequences, enznames, enzdata, side = TRUE, type = c("RFLP", "TRFLP"), Terminal = c("T5", "T3"))

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

Found the following calls to attach():
File ‘session/R/session.R’:
  attach(sub("file:", "", i))
See section ‘Good practice’ in ‘?attach’.
theory.intersections: no visible global function definition for ‘sop’
Undefined global functions or variables:
  sop
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: 'loomR', 'SDMTools'
Package unavailable to check Rd xrefs: ‘loomR’
Unknown package ‘SDMTools’ in Rd xrefs
'library' or 'require' call to ‘graphics’ which was already attached by Depends.
  Please remove these calls from your code.
severity: no visible global function definition for ‘qnorm’
severity: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
L_exp: no visible global function definition for ‘pnorm’
L_hNV: no visible global function definition for ‘pnorm’
L_trunc: no visible global function definition for ‘pnorm’
L_trunc_mufest: no visible global function definition for ‘pnorm’
dgp: no visible global function definition for ‘runif’
dgp: no visible global function definition for ‘rnorm’
eff.sfa: no visible global function definition for ‘predict’
fitted.sfa: no visible global function definition for ‘predict’
predict.sfa: no visible global function definition for ‘coef’
print.sfa: no visible global function definition for ‘coef’
residuals.sfa: no visible global function definition for ‘fitted’
sfa: no visible global function definition for ‘model.frame’
sfa: no visible global function definition for ‘model.response’
sfa.fit: no visible global function definition for ‘lm’
sfa.fit: no visible global function definition for ‘resid’
sfa.fit: no visible global function definition for ‘var’
sfa.fit: no visible global function definition for ‘optim’
summary.sfa: no visible global function definition for ‘logLik’
summary.sfa: no visible global function definition for ‘pchisq’
te.eff.sfa: no visible global function definition for ‘residuals’
te.eff.sfa: no visible global function definition for ‘pnorm’
u.sfa: no visible global function definition for ‘residuals’
u.sfa: no visible global function definition for ‘dnorm’
u.sfa: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  coef dnorm fitted lm logLik model.frame model.response optim pchisq
  pnorm predict resid residuals rnorm runif var
Consider adding
  importFrom("stats", "coef", "dnorm", "fitted", "lm", "logLik",
             "model.frame", "model.response", "optim", "pchisq", "pnorm",
             "predict", "resid", "residuals", "rnorm", "runif", "var")
to your NAMESPACE file.
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.
amse: no visible global function definition for ‘na.omit’
arb: no visible global function definition for ‘na.omit’
rdatagen: no visible global function definition for ‘qnorm’
rdatagen: no visible global function definition for ‘pbinom’
rdatagen: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  na.omit pbinom pnorm qnorm
Consider adding
  importFrom("stats", "na.omit", "pbinom", "pnorm", "qnorm")
to your NAMESPACE file.
UQnormalize.count: no visible binding for global variable ‘quantile’
plotNScores: no visible global function definition for ‘par’
plotNScores: no visible global function definition for ‘hist’
plotNScores: no visible global function definition for ‘title’
plotScores: no visible global function definition for ‘par’
plotScores: no visible global function definition for ‘hist’
plotScores: no visible global function definition for ‘title’
sgRSEA: no visible binding for global variable ‘sd’
sgRSEA: no visible global function definition for ‘p.adjust’
sgRSEA.mean: no visible binding for global variable ‘sd’
sgRSEA.mean: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  hist p.adjust par quantile sd title
Consider adding
  importFrom("graphics", "hist", "par", "title")
  importFrom("stats", "p.adjust", "quantile", "sd")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘foreign’ which was already attached by Depends.
  Please remove these calls from your code.
Package suggested but not available for checking: ‘hydromad’
popify: no visible global function definition for ‘runif’
tipify: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
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.
Depends: includes the non-default packages:
  'hdrcde', 'coda', 'MASS', 'bayesm', 'mnormt', 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  ‘MASS’ ‘bayesm’ ‘coda’ ‘hdrcde’ ‘mnormt’ ‘spatstat’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'siarmcmcdirichletv4.Rd':
  \usage lines wider than 90 characters:
     siarmcmcdirichletv4(data, sources, corrections = 0, concdep = 0, iterations=200000, burnin=50000, howmany=10000, thinby=15, prior = rep ... [TRUNCATED]

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

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

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

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

These lines will be truncated in the PDF manual.
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.
Rd file 'plot.verify.ho.Rd':
  \examples lines wider than 100 characters:
     attack=verify.ho(model=gaussian,filter=filter.PCA,Xlearn=traces[1:128,],Ylearn=key[1:128],Xval=traces[129:256,],Yval=key[129:256],nbreV ... [TRUNCATED]

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

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

These lines will be truncated in the PDF manual.
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.
Sight.Est: no visible global function definition for ‘glm’
Sight.Est: no visible global function definition for ‘binomial’
Sight.Est: no visible global function definition for ‘coef’
Sight.Est: no visible global function definition for ‘terms’
Sight.Est: no visible binding for global variable ‘binomial’
covtheta: no visible global function definition for ‘cov’
print.sightest: no visible global function definition for ‘qnorm’
summary.sightest: no visible global function definition for ‘qnorm’
vardiff: no visible global function definition for ‘vcov’
vardiff: no visible global function definition for ‘coef’
vardiff: no visible global function definition for ‘terms’
varlog.lam: no visible global function definition for ‘vcov’
varlog.lam: no visible global function definition for ‘coef’
varlog.lam: no visible global function definition for ‘terms’
Undefined global functions or variables:
  binomial coef cov glm qnorm terms vcov
Consider adding
  importFrom("stats", "binomial", "coef", "cov", "glm", "qnorm", "terms",
             "vcov")
to your NAMESPACE file.
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.
'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.
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.
GNU make is a SystemRequirements.
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.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  ‘HISTORY’
Non-standard file/directory found at top level:
  ‘COPYRIGHTS’
Copyright information should be in file inst/COPYRIGHTS
Package in Depends field not imported from: ‘mclust’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Simpsons: no visible global function definition for ‘Mclust’
Simpsons: no visible global function definition for ‘lm’
Simpsons: no visible global function definition for ‘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.
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
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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 ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/skeleSim.Rcheck/00install.out’ for details.
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.
GNU make is a SystemRequirements.
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.
GNU make is a SystemRequirements.
File ‘smco/R/smco.R’:
  .onAttach calls:
    cat(paste("This is smco package", version, "\n"))

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

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

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

.MHUpdateFuncGen.PF : MHUpdateFunc: no visible global function
  definition for ‘runif’
MarkovSwitchingFuncGenerator : generateNextStreamsFunc: no visible
  global function definition for ‘runif’
MarkovSwitchingFuncGenerator: no visible global function definition for
  ‘rnorm’
MarkovSwitchingFuncGenerator: no visible global function definition for
  ‘runif’
MarkovSwitchingFuncGenerator : logObsDensFunc: no visible global
  function definition for ‘dnorm’
MarkovSwitchingFuncGenerator : propagateFunc: no visible global
  function definition for ‘dnorm’
MarkovSwitchingFuncGenerator : propagateFunc: no visible global
  function definition for ‘runif’
Undefined global functions or variables:
  dnorm rnorm runif
Consider adding
  importFrom("stats", "dnorm", "rnorm", "runif")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
em: no visible global function definition for ‘coxph’
em: no visible global function definition for ‘optim’
plotpredictsmcure: no visible global function definition for ‘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.
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.
Malformed Description field: should contain one or more complete sentences.
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.
Malformed Description field: should contain one or more complete sentences.
dNMR: no visible global function definition for ‘pnorm’
dNMR: no visible global function definition for ‘dnorm’
pNMR: no visible global function definition for ‘pnorm’
pNMR: no visible global function definition for ‘dnorm’
rMR: no visible global function definition for ‘rnorm’
rMR: no visible global function definition for ‘rchisq’
Undefined global functions or variables:
  dnorm pnorm rchisq rnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm", "rchisq", "rnorm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
SMVar.paired : <anonymous>: no visible global function definition for
  ‘var’
SMVar.paired: no visible global function definition for ‘var’
SMVar.paired: no visible global function definition for ‘pt’
SMVar.paired: no visible global function definition for ‘p.adjust’
SMVar.paired: no visible global function definition for ‘write.table’
SMVar.unpaired : <anonymous>: no visible global function definition for
  ‘var’
SMVar.unpaired: no visible global function definition for ‘var’
SMVar.unpaired: no visible global function definition for ‘pt’
SMVar.unpaired: no visible global function definition for ‘p.adjust’
SMVar.unpaired: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  p.adjust pt var write.table
Consider adding
  importFrom("stats", "p.adjust", "pt", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Rd file 'SMVar.paired.Rd':
  \usage lines wider than 90 characters:
     SMVar.paired(geneNumbers, logratio, fileexport = NULL, minrep = 2, method = "BH", threshold = 0.05)

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

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

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

Probably some imports need to be declared in the NAMESPACE file.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing or unexported object: ‘base::WHAT’
Call with DUP:
   .Fortran("GEODISTV", as.double(lat1), as.double(lon1), as.double(lat2), 
       as.double(lon2), dist = double(nok), as.integer(nok), DUP = DUP, 
       PACKAGE = "SoDA")
DUP is no longer supported and will be ignored.
Packages in Depends field not imported from:
  ‘MASS’ ‘magic’ ‘ppls’ ‘psych’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
get.hnx.B.initialW: no visible global function definition for
  ‘normalize.vector’
get.hnx.B.initialW: no visible global function definition for ‘adiag’
hclust.wrap: no visible global function definition for ‘hclust’
hclust.wrap: no visible global function definition for ‘dist’
hclust.wrap: no visible global function definition for ‘cutree’
my.normdata.gen: no visible global function definition for ‘mvrnorm’
my.normdata.gen: no visible global function definition for ‘rnorm’
odc.clust: no visible binding for global variable ‘kmeans’
odc.cv: no visible global function definition for ‘ginv’
odc.optimallambda2: no visible global function definition for ‘tr’
odc.optimallambda2: no visible global function definition for ‘ginv’
odc.optimallambda2: no visible binding for global variable ‘sd’
sodc.clust: no visible binding for global variable ‘kmeans’
Undefined global functions or variables:
  adiag cutree dist ginv hclust kmeans mvrnorm normalize.vector rnorm
  sd tr
Consider adding
  importFrom("stats", "cutree", "dist", "hclust", "kmeans", "rnorm",
             "sd")
to your NAMESPACE file.
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.
compileDatabase: no visible global function definition for ‘use_data’
Undefined global functions or variables:
  use_data
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.
Warning: no function found corresponding to methods exports from ‘someMTP’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' call to ‘hexbin’ which was already attached by Depends.
  Please remove these calls from your code.
hexbinpie: no visible global function definition for ‘quantile’
hexbinpie: no visible global function definition for ‘polygon’
hexbinpie: no visible global function definition for ‘text’
makehexbinplot: no visible global function definition for ‘rainbow’
makehexbinplot: no visible global function definition for ‘col2rgb’
makehexbinplot: no visible global function definition for ‘edit’
makehexbinplot: no visible global function definition for ‘dev.new’
makehexbinplot: no visible global function definition for ‘plot.new’
makehexbinplot: no visible global function definition for ‘plot.window’
makehexbinplot: no visible global function definition for ‘box’
makehexbinplot: no visible global function definition for ‘axis’
makehexbinplot: no visible global function definition for ‘legend’
som.plot: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  axis box col2rgb dev.new edit legend plot.new plot.window polygon
  quantile rainbow read.table text
Consider adding
  importFrom("grDevices", "col2rgb", "dev.new", "rainbow")
  importFrom("graphics", "axis", "box", "legend", "plot.new",
             "plot.window", "polygon", "text")
  importFrom("stats", "quantile")
  importFrom("utils", "edit", "read.table")
to your NAMESPACE file.
Found the following hidden files and directories:
  .gitignore
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Malformed Title field: should not end in a period.
License components which are templates and need '+ file LICENSE':
  MIT
Non-standard files/directories found at top level:
  ‘README.markdown’ ‘build_package.sh’ ‘upload.sh’
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’

Package which this enhances but not available for checking: ‘RecordLinkage’
License components which are templates and need '+ file LICENSE':
  MIT
Package suggested but not available for checking: ‘r2cytoscape’
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.
Rd file 'space.joint.Rd':
  \examples lines wider than 100 characters:
     #################### view the network corresponding to the parcial correlation matrix in the simulation example
     #plot(temp, vertex.size=3, vertex.frame.color="white",layout=layout.fruchterman.reingold, vertex.label=NA, edge.color=grey(0.5))

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

These lines will be truncated in the PDF manual.
hausman: no visible global function definition for ‘pchisq’
span.formula: no visible global function definition for ‘model.frame’
span.formula: no visible global function definition for ‘model.matrix’
span.formula: no visible global function definition for
  ‘model.response’
spbe: no visible global function definition for ‘cor’
spbe: no visible global function definition for ‘pt’
spfe: no visible global function definition for ‘cor’
spfe: no visible global function definition for ‘pt’
sprandom: no visible global function definition for ‘cor’
sprandom: no visible global function definition for ‘pt’
summary.span: no visible global function definition for ‘printCoefmat’
Undefined global functions or variables:
  cor model.frame model.matrix model.response pchisq printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.frame", "model.matrix",
             "model.response", "pchisq", "printCoefmat", "pt")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘RCurl’ ‘XML’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SPARQL : <anonymous>: no visible global function definition for
  ‘URLencode’
SPARQL: no visible binding for global variable ‘getURL’
SPARQL: no visible global function definition for ‘URLencode’
SPARQL: no visible binding for global variable ‘xmlParse’
SPARQL: no visible global function definition for ‘getNodeSet’
SPARQL: no visible global function definition for ‘xpathApply’
SPARQL: no visible binding for global variable ‘postForm’
get_attr: no visible global function definition for ‘getNodeSet’
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for ‘getNodeSet’
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for ‘xmlDoc’
get_value: no visible global function definition for ‘xmlDoc’
get_value: no visible global function definition for ‘xpathSApply’
get_value: no visible binding for global variable ‘xmlValue’
get_value: no visible global function definition for ‘xpathApply’
get_value: no visible binding for global variable ‘xmlGetAttr’
readCSVstring: no visible global function definition for ‘read.csv’
readTSVstring: no visible global function definition for ‘read.delim’
Undefined global functions or variables:
  URLencode getNodeSet getURL postForm read.csv read.delim xmlDoc
  xmlGetAttr xmlParse xmlValue xpathApply xpathSApply
Consider adding
  importFrom("utils", "URLencode", "read.csv", "read.delim")
to your NAMESPACE file.
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.
Malformed Description field: should contain one or more complete sentences.
Found the following sources/headers with CR or CRLF line endings:
  inst/include/MatrixAddons.h
  inst/include/sparseLTSEigen.h
Some Unix compilers require LF line endings.
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘INLA’
Checking should be performed on sources prepared by ‘R CMD build’.
Found the following sources/headers not terminated with a newline:
  src/calc.c
Some compilers warn on such files.
Package suggested but not available for checking: ‘INLA’
Found the following sources/headers not terminated with a newline:
  inst/include/STCXEM.h
  inst/include/STCXEMnonspatial.h
  inst/include/STCXEMspatial.h
  inst/include/STCdata.h
  inst/include/STCmodel.h
  inst/include/STCparam.h
  inst/include/STCtune.h
Some compilers warn on such files.
GNU make is a SystemRequirements.
src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
Malformed Description field: should contain one or more complete sentences.
GenerateCliquesCovariance: no visible global function definition for
  ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Package suggested but not available for checking: ‘spDataLarge’
Malformed Title field: should not end in a period.
bartlett: no visible global function definition for ‘pchisq’
local.rbfdot: no visible binding for global variable ‘sd’
local.rbfdot: no visible global function definition for ‘dist’
local.rbfdot : <anonymous>: no visible global function definition for
  ‘median’
speccalt: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  dist kmeans median pchisq sd
Consider adding
  importFrom("stats", "dist", "kmeans", "median", "pchisq", "sd")
to your NAMESPACE file.
ChaoBunge: no visible global function definition for ‘qnorm’
ChaoLee1992: no visible global function definition for ‘qnorm’
Pmix: no visible global function definition for ‘dpois’
PmixSCon: no visible global function definition for ‘dbeta’
bootPCG: no visible global function definition for ‘flush.console’
bootPCG: no visible global function definition for ‘quantile’
bootPnpmle: no visible global function definition for ‘flush.console’
bootPnpmle: no visible global function definition for ‘quantile’
bootUnpmle: no visible global function definition for ‘flush.console’
bootUnpmle: no visible global function definition for ‘quantile’
chao1984: no visible global function definition for ‘qnorm’
jackknife: no visible global function definition for ‘dbinom’
jackknife: no visible global function definition for ‘qnorm’
pcg: no visible global function definition for ‘flush.console’
unpmle: no visible global function definition for ‘flush.console’
untrunPmix: no visible global function definition for ‘dpois’
Undefined global functions or variables:
  dbeta dbinom dpois flush.console qnorm quantile
Consider adding
  importFrom("stats", "dbeta", "dbinom", "dpois", "qnorm", "quantile")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
'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.
Malformed Description field: should contain one or more complete sentences.
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of ‘nr’ to ‘nrow’
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of ‘nc’ to ‘ncol’
spe: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Package in Depends field not imported from: ‘rgl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pointsphere: no visible global function definition for ‘runif’
rgl.sphMW: no visible global function definition for ‘plot3d’
rgl.sphcirc: no visible global function definition for ‘rotate3d’
rgl.sphcirc: no visible global function definition for ‘lines3d’
rgl.sphgrid: no visible global function definition for ‘open3d’
rgl.sphgrid: no visible global function definition for ‘plot3d’
rgl.sphgrid: no visible global function definition for ‘lines3d’
rgl.sphgrid: no visible global function definition for ‘text3d’
rgl.sphpoints: no visible global function definition for ‘points3d’
rgl.sphsun: no visible global function definition for ‘plot3d’
rgl.sphtext: no visible global function definition for ‘text3d’
Undefined global functions or variables:
  lines3d open3d plot3d points3d rotate3d runif text3d
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘lars’ ‘parallel’ ‘randomForest’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: ‘mbgraphic’
'library' or 'require' call to ‘quadprog’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘quadprog’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SPIn: no visible global function definition for ‘density’
SPIn: no visible global function definition for ‘quantile’
SPIn: no visible global function definition for ‘solve.QP’
bootSPIn: no visible global function definition for ‘runif’
plot.SPIn: no visible global function definition for ‘hist’
plot.SPIn: no visible global function definition for ‘lines’
plot.SPIn: no visible global function definition for ‘text’
plot.SPIn: no visible global function definition for ‘quantile’
plot.SPIn: no visible global function definition for ‘legend’
Undefined global functions or variables:
  density hist legend lines quantile runif solve.QP text
Consider adding
  importFrom("graphics", "hist", "legend", "lines", "text")
  importFrom("stats", "density", "quantile", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
spi: no visible global function definition for ‘read.table’
spi: no visible global function definition for ‘ecdf’
spi: no visible global function definition for ‘qnorm’
spi: no visible global function definition for ‘colorRampPalette’
spi: no visible global function definition for ‘filled.contour’
spi: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis colorRampPalette ecdf filled.contour qnorm read.table
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "filled.contour")
  importFrom("stats", "ecdf", "qnorm")
  importFrom("utils", "read.table")
to your NAMESPACE file.
prepare_Rd: spi.Rd:117-119: Dropping empty section \note
prepare_Rd: spi.Rd:123-125: Dropping empty section \seealso
Rd file 'spi.Rd':
  \examples lines wider than 100 characters:
     spi(7,"spi.txt",1963,2010,"Standardized Precipitation Index - Rio Grande do Norte State",1,"years","months")

These lines will be truncated in the PDF manual.
Malformed Description field: should contain one or more complete sentences.
R2.global: no visible global function definition for ‘var’
calculer.var.exp: no visible global function definition for ‘var’
creer.noeud: no visible global function definition for ‘var’
ponderer.classe: no visible global function definition for ‘var’
ponderer.classe: no visible global function definition for ‘cov’
spodt: no visible global function definition for ‘model.frame’
spodt.tree: no visible global function definition for ‘plot.new’
spodt.tree: no visible global function definition for ‘par’
spodt.tree: no visible global function definition for ‘plot.window’
spodt.tree: no visible global function definition for ‘text’
spodt.tree: no visible global function definition for ‘segments’
test.spodt: no visible global function definition for ‘model.frame’
test.spodt: no visible global function definition for ‘hist’
test.spodt: no visible global function definition for ‘abline’
tracer.noeud: no visible global function definition for ‘text’
tracer.noeud: no visible global function definition for ‘segments’
Undefined global functions or variables:
  abline cov hist model.frame par plot.new plot.window segments text
  var
Consider adding
  importFrom("graphics", "abline", "hist", "par", "plot.new",
             "plot.window", "segments", "text")
  importFrom("stats", "cov", "model.frame", "var")
to your NAMESPACE file.
Ell.Theta: no visible global function definition for ‘ell.theta’
confid.int.theta: no visible global function definition for ‘qchisq’
confid.int.theta : sim.c: no visible global function definition for
  ‘runif’
confid.int.theta: no visible global function definition for ‘quantile’
dd.est: no visible global function definition for ‘ecdf’
ks.sporm : Simul: no visible global function definition for ‘runif’
ks.stat: no visible global function definition for ‘ecdf’
plotor: no visible global function definition for ‘ecdf’
plotor: no visible global function definition for ‘plot’
test.theta: no visible global function definition for ‘ecdf’
test.theta : sim: no visible global function definition for ‘runif’
Undefined global functions or variables:
  ecdf ell.theta plot qchisq quantile runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "ecdf", "qchisq", "quantile", "runif")
to your NAMESPACE file.
prepare_Rd: H.Binv.Rd:48-50: Dropping empty section \note
prepare_Rd: V.theta.Rd:28-30: Dropping empty section \details
prepare_Rd: V.theta.Rd:43-45: Dropping empty section \note
prepare_Rd: V.theta.Rd:49-51: Dropping empty section \seealso
prepare_Rd: V.theta.Rd:52-53: Dropping empty section \examples
prepare_Rd: confid.int.theta.Rd:62-64: Dropping empty section \note
prepare_Rd: dd.est.Rd:39-41: Dropping empty section \note
prepare_Rd: dd.est.Rd:45-47: Dropping empty section \seealso
prepare_Rd: ell.theta.Rd:60-62: Dropping empty section \note
prepare_Rd: ell.theta.Rd:69-70: Dropping empty section \examples
prepare_Rd: grad.hessinv.Rd:47-49: Dropping empty section \note
prepare_Rd: ks.sporm.Rd:43-45: Dropping empty section \note
prepare_Rd: ks.stat.Rd:39-41: Dropping empty section \note
prepare_Rd: mrle.sporm.Rd:66-68: Dropping empty section \note
prepare_Rd: mrle.sporm.Rd:72-74: Dropping empty section \seealso
prepare_Rd: newton.theta.Rd:47-49: Dropping empty section \note
prepare_Rd: phi.Rd:32-38: Dropping empty section \value
prepare_Rd: phi.Rd:48-50: Dropping empty section \note
prepare_Rd: plotor.Rd:26-32: Dropping empty section \value
prepare_Rd: plotor.Rd:42-44: Dropping empty section \note
prepare_Rd: plotor.Rd:48-50: Dropping empty section \seealso
prepare_Rd: sporm-package.Rd:53-54: Dropping empty section \seealso
prepare_Rd: sporm-package.Rd:55-56: Dropping empty section \examples
prepare_Rd: test.theta.Rd:54-56: Dropping empty section \note
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fetch_NBAPlayerStatistics: no visible global function definition for
  ‘read.table’
Undefined global functions or variables:
  read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following sources/headers with CR or CRLF line endings:
  inst/include/sppmix.h
Some Unix compilers require LF line endings.
Missing or unexported objects:
  ‘rgdal::checkCRSArgs_ng’ ‘rgdal::new_proj_and_gdal’
Rd file 'SlrArd.Rd':
  \usage lines wider than 90 characters:
     SlrArd(T, X, bias = TRUE, method = c("VB", "VBMacKay", "PX-VB"), control = list(), check.lb=TRUE, a0 = 0, b0 = 0, mu0 = 0, xi0 = 1)

These lines will be truncated in the PDF manual.
plot.SPRT: no visible global function definition for ‘par’
plot.SPRT: no visible global function definition for ‘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.
Dependence on R version ‘3.4.1’ not with patchlevel 0
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.
Found the following hidden files and directories:
  .Rapp.history
  inst/script/.Rapp.history
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
File ‘sROC/R/onload.R’:
  .onLoad calls:
    packageStartupMessage("sROC 0.1-2 loaded")

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

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

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

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

These lines will be truncated in the PDF manual.
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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
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.
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
map.world: no visible global function definition for ‘par’
map.world: no visible global function definition for ‘plot.new’
map.world: no visible global function definition for ‘plot.window’
map.world: no visible global function definition for ‘lines’
map.world: no visible global function definition for ‘title’
map.world: no visible global function definition for ‘axis’
map.world: no visible global function definition for ‘box’
plot.smooth.sspline: no visible global function definition for
  ‘predict’
plot.smooth.sspline: no visible global function definition for
  ‘filled.contour’
plot.smooth.sspline: no visible binding for global variable
  ‘terrain.colors’
plot.smooth.sspline: no visible global function definition for ‘title’
plot.smooth.sspline: no visible global function definition for ‘axis’
station: no visible binding for global variable ‘WTdiff’
station: no visible global function definition for ‘points’
Undefined global functions or variables:
  WTdiff axis box filled.contour lines par plot.new plot.window points
  predict terrain.colors title
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "axis", "box", "filled.contour", "lines", "par",
             "plot.new", "plot.window", "points", "title")
  importFrom("stats", "predict")
to your NAMESPACE file.
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.
.expandLevels: no visible global function definition for ‘na.omit’
.ffStack: no visible global function definition for ‘na.omit’
.ffffStack: no visible global function definition for ‘na.omit’
Stack : <anonymous>: no visible global function definition for
  ‘na.omit’
ffStack,ffdf-data.frame: no visible global function definition for
  ‘na.omit’
ffStack,ffdf-ffdf: no visible global function definition for ‘na.omit’
ffStack,ffdf-list: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
genericPlot: no visible global function definition for ‘dev.new’
genericPlot: no visible global function definition for ‘par’
genericPlot: no visible global function definition for ‘rainbow’
genericPlot: no visible global function definition for ‘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.
Non-standard file/directory found at top level:
  ‘Licence’
'library' or 'require' calls to packages already attached by Depends:
  ‘np’ ‘sp’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘np’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
stkde: no visible global function definition for ‘npudensbw’
stkde: no visible global function definition for ‘npudens’
stkde: no visible global function definition for ‘quantile’
stkde: no visible global function definition for ‘heat.colors’
stkde: no visible global function definition for ‘par’
stkde: no visible global function definition for ‘image’
stkde: no visible global function definition for ‘contour’
stkde.base: no visible global function definition for ‘npudensbw’
stkde.base: no visible global function definition for ‘npudens’
stkde.sig: no visible global function definition for ‘SpatialPoints’
stkde.sig: no visible global function definition for ‘spsample’
stkde.sig: no visible global function definition for ‘bbox’
stkde.sig: no visible global function definition for ‘quantile’
stkde.sig: no visible global function definition for ‘heat.colors’
stkde.sig: no visible global function definition for ‘par’
stkde.sig: no visible global function definition for ‘image’
stkde.sig: no visible global function definition for ‘contour’
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.

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

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

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

These lines will be truncated in the PDF manual.
'library' or 'require' call to ‘codetools’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘codetools’ ‘gss’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: ‘starsdata’
Unexported objects imported by ':::' calls:
  ‘s2dverification:::.KnownLatNames’ ‘s2dverification:::.KnownLonNames’
  See the note in ?`:::` about the use of this operator.
Package suggested but not available for checking: ‘asreml’
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.
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.
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.
Documented arguments not in \usage in documentation object 'sticky':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
GNU make is a SystemRequirements.
Rd file 'calc.stoich.coef.Rd':
  \usage lines wider than 90 characters:
     calc.stoich.coef(alpha, name, subst, subst.norm, nu.norm = 1, constraints = list(), eps = 1e-5, verbose = TRUE)

These lines will be truncated in the PDF manual.
Malformed Title field: should not end in a period.
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.
Missing or unexported object: ‘limma::ebayes’
Malformed Title field: should not end in a period.
Package suggested but not available for checking: ‘STRaitRazoR’
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
Warning: no function found corresponding to methods exports from ‘stsm.class’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
stsm.model: no visible global function definition for ‘is.ts’
stsm.model: no visible global function definition for ‘var’
stsm.model: no visible global function definition for ‘frequency’
stsm.model: no visible global function definition for ‘na.omit’
stsm.model: no visible global function definition for ‘fft’
stsm.model: no visible global function definition for ‘new’
stsm.sgf: no visible global function definition for ‘frequency’
char2numeric,stsm: no visible global function definition for
  ‘frequency’
set.cpar,stsm: no visible global function definition for ‘validObject’
set.nopars,stsm: no visible global function definition for
  ‘validObject’
set.pars,stsm: no visible global function definition for ‘validObject’
transPars,stsm: no visible global function definition for ‘var’
Undefined global functions or variables:
  fft frequency is.ts na.omit new validObject var
Consider adding
  importFrom("methods", "new", "validObject")
  importFrom("stats", "fft", "frequency", "is.ts", "na.omit", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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.
'library' or 'require' calls to packages already attached by Depends:
  ‘ROCR’ ‘penalized’
  Please remove these calls from your code.
ELF: no visible global function definition for ‘pt’
ELF: no visible global function definition for ‘qnorm’
ELF: no visible global function definition for ‘lm’
ELF: no visible global function definition for ‘lowess’
ELF: no visible global function definition for ‘dnorm’
ELF: no visible global function definition for ‘approx’
subtype: no visible global function definition for ‘runif’
subtype: no visible global function definition for ‘hclust’
subtype: no visible global function definition for ‘dist’
subtype: no visible global function definition for ‘cutree’
subtype: no visible global function definition for ‘pt’
subtype: no visible global function definition for ‘heatmap’
test_subtype_only: no visible global function definition for ‘pt’
test_subtype_only: no visible global function definition for ‘survdiff’
test_subtype_only: no visible global function definition for ‘survfit’
test_subtype_only: no visible global function definition for ‘title’
ufun: no visible global function definition for ‘dnorm’
ufun: no visible global function definition for ‘lowess’
Undefined global functions or variables:
  approx cutree dist dnorm hclust heatmap lm lowess pt qnorm runif
  survdiff survfit title
Consider adding
  importFrom("graphics", "title")
  importFrom("stats", "approx", "cutree", "dist", "dnorm", "hclust",
             "heatmap", "lm", "lowess", "pt", "qnorm", "runif")
to your NAMESPACE file.
Rd file 'subtype.Rd':
  \usage lines wider than 90 characters:
     subtype(GEset, outcomeLabels, treatment=NULL, Npermutes=10, Nchunks = 25, minClusterSizeB = 20, NclustersASet = 100, FDRpermutation = T ... [TRUNCATED]
  \examples lines wider than 100 characters:
     summary(A,f.out=0)  ### f.out can be used for filtering out uninteresting subtypes. e.g. if f.out=2, we ignore subtypes having N01_0<=2 ... [TRUNCATED]

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

These lines will be truncated in the PDF manual.
'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.
Rd file 'SUE.lm.Rd':
  \examples lines wider than 100 characters:
     ##We analysis the well known stackloss data by using ordinary linear method and the subsampling method. 
     ##proportion of outliers in the data. The subsample size is chosen to be the default size of ns = 11.
     plot(SUE.fitted.values(a2),SUE.residuals(a2),xlab="(b) fitted values",ylab="residuals",ylim=c(-12,12))
     plot(SUE.fitted.values(a3),SUE.residuals(a3),xlab="(c) fitted values",ylab="residuals",ylim=c(-12,12))

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: ‘INLA’
Malformed Description field: should contain one or more complete sentences.
MCMCCV: no visible global function definition for ‘rnorm’
MLCVGauss: no visible global function definition for ‘runif’
MLCVGauss: no visible global function definition for ‘optim’
SimSunderData: no visible global function definition for ‘runif’
SimSunderData: no visible global function definition for ‘dist’
SimSunderData: no visible global function definition for ‘rnorm’
SimSunderData: no visible global function definition for ‘qgamma’
SimSunderData: no visible global function definition for ‘pnorm’
SimSunderData: no visible global function definition for ‘rmultinom’
Undefined global functions or variables:
  dist optim pnorm qgamma rmultinom rnorm runif
Consider adding
  importFrom("stats", "dist", "optim", "pnorm", "qgamma", "rmultinom",
             "rnorm", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
sunter: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
supcluster : itgamma: no visible global function definition for
  ‘rgamma’
supcluster : itgamma: no visible global function definition for
  ‘dgamma’
supcluster : itgamma: no visible global function definition for ‘runif’
supcluster : itbeta: no visible global function definition for ‘rnorm’
supcluster : itbeta: no visible global function definition for ‘runif’
supcluster : itj: no visible global function definition for ‘dmultinom’
supcluster: no visible global function definition for ‘kmeans’
tab1: no visible global function definition for ‘image’
tab1: no visible global function definition for ‘gray’
tab1: no visible global function definition for ‘var’
Undefined global functions or variables:
  dgamma dmultinom gray image kmeans rgamma rnorm runif var
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "image")
  importFrom("stats", "dgamma", "dmultinom", "kmeans", "rgamma", "rnorm",
             "runif", "var")
to your NAMESPACE file.
Call with DUP:
   .C(R_clusterer, E = as.double(E), X = as.double(X), W = as.double(W), 
       P = as.double(P), y = as.double(y), prob = as.double(prob), 
       theta = as.double(theta), lambda = as.double(lambda * n), 
       n = as.integer(n), g = as.integer(g), m = as.integer(m), 
       p = as.integer(p), critflag = as.integer(critflag), penflag = as.integer(penflag), 
       blockflag = as.integer(blockflag), valiflag = as.integer(valiflag), 
       traceflag = as.integer(trace), genliste = integer(lSize), 
       kriterium = double(lSize), DUP = FALSE)
DUP is no longer supported and will be ignored.
HCLtree: no visible global function definition for ‘hclust’
HCLtree: no visible global function definition for ‘as.dist’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘matplot’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘matlines’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘axis’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘box’
plotProfilesWithinBicluster: no visible global function definition for
  ‘matplot’
plotProfilesWithinBicluster: no visible global function definition for
  ‘title’
plotProfilesWithinBicluster: no visible global function definition for
  ‘axis’
plotProfilesWithinBicluster: no visible global function definition for
  ‘par’
plotProfilesWithinBicluster: no visible global function definition for
  ‘box’
plotProfilesWithinBicluster: no visible global function definition for
  ‘matlines’
plotProfilesWithinBicluster: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  as.dist axis box hclust legend matlines matplot par title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "matlines", "matplot",
             "par", "title")
  importFrom("stats", "as.dist", "hclust")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘boa’ ‘coda’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
superdiag: no visible global function definition for ‘as.mcmc.list’
superdiag: no visible global function definition for ‘as.mcmc’
superdiag: no visible global function definition for ‘runif’
superdiag: no visible global function definition for ‘geweke.diag’
superdiag: no visible global function definition for ‘heidel.diag’
superdiag: no visible global function definition for ‘raftery.diag’
superdiag: no visible global function definition for ‘gelman.diag’
Undefined global functions or variables:
  as.mcmc as.mcmc.list gelman.diag geweke.diag heidel.diag raftery.diag
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
'library' or 'require' call to ‘gam’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
TrainSuperMDS: no visible global function definition for ‘rnorm’
TrainSuperMDSOnce: no visible global function definition for ‘cmdscale’
TrainSuperMDSOnce: no visible global function definition for ‘quantile’
distmat: no visible global function definition for ‘dist’
Undefined global functions or variables:
  cmdscale dist quantile rnorm
Consider adding
  importFrom("stats", "cmdscale", "dist", "quantile", "rnorm")
to your NAMESPACE file.
'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.
Dependence on R version ‘3.4.4’ not with patchlevel 0
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 in Depends field not imported from: ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Est.PH: no visible global function definition for ‘coxph’
Inf.Cval: no visible global function definition for ‘rexp’
Inf.Cval: no visible global function definition for ‘var’
Inf.Cval.Delta: no visible global function definition for ‘rexp’
Inf.Cval.Delta: no visible global function definition for ‘var’
cvC: no visible global function definition for ‘coxph’
cvC: no visible global function definition for ‘weighted.mean’
Undefined global functions or variables:
  coxph rexp var weighted.mean
Consider adding
  importFrom("stats", "rexp", "var", "weighted.mean")
to your NAMESPACE file.
pearson: no visible global function definition for ‘cor’
plot.survcorr: no visible global function definition for ‘pnorm’
plot.survcorr: no visible global function definition for ‘par’
plot.survcorr: no visible global function definition for ‘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.
Package suggested but not available for checking: ‘INLA’
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'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’
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.
Rd file 'IDI.INF.GRAPH.Rd':
  \usage lines wider than 90 characters:
     IDI.INF.GRAPH(x, main = NULL, xlab = NULL, ylab = NULL, cex.main = NULL, cex.lab = NULL, ...)

Rd file 'IDI.INF.Rd':
  \usage lines wider than 90 characters:
     IDI.INF(indata, covs0, covs1, t0, npert = 300, npert.rand = NULL, seed1 = NULL, alpha = 0.05)

These lines will be truncated in the PDF manual.
Malformed Description field: should contain one or more complete sentences.
Running examples in ‘survsup-Ex.R’ failed
The error most likely occurred in:

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

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

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

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

Error: Vignette re-building failed.
Execution halted
Malformed Title field: should not end in a period.
fitModel: no visible global function definition for ‘var’
fitModel: no visible global function definition for ‘cov’
svpls: no visible global function definition for ‘pt’
Undefined global functions or variables:
  cov pt var
Consider adding
  importFrom("stats", "cov", "pt", "var")
to your NAMESPACE file.
Calls with DUP:
   .C("myInversion", Senv$diag, Senv$env, Senv$xenv, Senv$N, Senv$Nenv, 
       Senv$Nplus1, DUP = FALSE, PACKAGE = "svcm")
   .C("myTrace", Senv$diag, Senv$env, Senv$xenv, Senv$N, Senv$Nenv, 
       Senv$Nplus1, BBenv$diag, BBenv$env, BBenv$xenv, BBenv$N, 
       BBenv$Nenv, BBenv$Nplus1, ED = ED, DUP = FALSE, PACKAGE = "svcm")
   .C("dsC2env", N, A@x, as.integer(A@i), as.integer(A@p), diagvec = diagvec, 
       env = env, xenv = as.integer(xenv), DUP = FALSE)
DUP is no longer supported and will be ignored.
Malformed Description field: should contain one or more complete sentences.
dlgMessage.tcltkGUI: no visible global function definition for ‘alarm’
Undefined global functions or variables:
  alarm
Consider adding
  importFrom("utils", "alarm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘lattice’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
svd3dplot: no visible global function definition for ‘wireframe’
svd3dplot: no visible global function definition for ‘levelplot’
Undefined global functions or variables:
  levelplot wireframe
Malformed Description field: should contain one or more complete sentences.
startHttpServer : <anonymous> : Rjsonp: no visible global function
  definition for ‘localeToCharset’
Undefined global functions or variables:
  localeToCharset
Consider adding
  importFrom("utils", "localeToCharset")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
.onAttach : svBrowser: no visible global function definition for
  ‘browseURL’
.onAttach: no visible global function definition for ‘loadhistory’
Undefined global functions or variables:
  browseURL loadhistory
Consider adding
  importFrom("utils", "browseURL", "loadhistory")
to your NAMESPACE file.
File ‘svmpath/libs/svmpath.so’:
  Found ‘_gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘_gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘_gfortran_st_read’, possibly from ‘read’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi30spec.o’, ‘mi35mps.o’,
      ‘mi36mps.o’, ‘mi40bfil.o’
  Found ‘_gfortran_st_rewind’, possibly from ‘rewind’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi10unix.o’, ‘mi35mps.o’, ‘mi40bfil.o’
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
processSocket: no visible global function definition for ‘URLdecode’
Undefined global functions or variables:
  URLdecode
Consider adding
  importFrom("utils", "URLdecode")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘XML’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.formatResult : capture.str: no visible global function definition for
  ‘str’
createLog: no visible global function definition for ‘sessionInfo’
protocol_junit.svSuiteData: no visible global function definition for
  ‘xmlNode’
protocol_junit.svSuiteData: no visible global function definition for
  ‘addChildren’
protocol_junit.svSuiteData: no visible global function definition for
  ‘saveXML’
protocol_junit.svTestData: no visible global function definition for
  ‘xmlNode’
protocol_junit.svTestData: no visible global function definition for
  ‘addChildren’
Undefined global functions or variables:
  addChildren saveXML sessionInfo str xmlNode
Consider adding
  importFrom("utils", "sessionInfo", "str")
to your NAMESPACE file.
svycox.calibrate: no visible global function definition for ‘quantile’
svycox.calibrate: no visible binding for global variable ‘median’
svycox.calibrate: no visible global function definition for
  ‘as.formula’
svycox.calibrate: no visible global function definition for ‘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.
Package suggested but not available for checking: ‘swephRdata’
Packages in Depends field not imported from:
  ‘MASS’ ‘fda’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fj_pl: no visible global function definition for ‘getbasismatrix’
fj_pl: no visible global function definition for ‘create.bspline.basis’
fj_pl: no visible global function definition for ‘getbasispenalty’
forward_backward.quantities : <anonymous>: no visible global function
  definition for ‘dnorm’
function_cases1AND2: no visible global function definition for ‘dnorm’
function_cases3AND4: no visible global function definition for ‘dnorm’
pij_iid: no visible global function definition for ‘dnorm’
pilj: no visible global function definition for ‘dnorm’
updateLambda: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  create.bspline.basis dnorm getbasismatrix getbasispenalty optimize
Consider adding
  importFrom("stats", "dnorm", "optimize")
to your NAMESPACE file.
Packages suggested but not available for checking: 'sylly.de', 'sylly.es'
symbol: no visible global function definition for ‘plot.new’
symbol: no visible global function definition for ‘plot.window’
symbol: no visible global function definition for ‘axis’
symbol: no visible global function definition for ‘box’
symbol: no visible global function definition for ‘title’
symbol: no visible global function definition for ‘rainbow’
symbol: no visible global function definition for ‘hsv’
symbol: no visible global function definition for ‘rect’
symbol: no visible global function definition for ‘polygon’
symbol: no visible global function definition for ‘lines’
symbol: no visible global function definition for ‘text’
Undefined global functions or variables:
  axis box hsv lines plot.new plot.window polygon rainbow rect text
  title
Consider adding
  importFrom("grDevices", "hsv", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "polygon", "rect", "text", "title")
to your NAMESPACE file.
Rd file 'symbol.Rd':
  \usage lines wider than 90 characters:
     symbol(df, type="star", colin=NULL, colout=NULL, colin2=NA, colout2=1, ssize=NULL, labels=0, labelsize=0.6,
            scheme=1, sortby=0, descending=FALSE, coorx=NULL, coory=NULL, lty=1, main=NULL, sub=NULL, xlab=NULL, ylab=NULL,
            add=FALSE, xlim=NULL, ylim=NULL, facew=0.5, faceh=0.5, eyes=0.5, eyed=0.5, mouthw=0.5, mouthc=0.5, brows=0.5,
            browp=0.5, nosel=0.5, nosew=0.5, ears=0.5, pupils=0.5, body=0.5, limb1=0.5, limb2=0.5, limb3=0.5, limb4=0.5, defcol=NA)

These lines will be truncated in the PDF manual.
Package in Depends field not imported from: ‘fields’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cwt_fw: no visible global function definition for ‘fft’
cwt_iw: no visible global function definition for ‘fft’
est_riskshrink_thresh: no visible global function definition for
  ‘median’
Undefined global functions or variables:
  fft median
Consider adding
  importFrom("stats", "fft", "median")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘doc’
'library' or 'require' calls to packages already attached by Depends:
  ‘tcltk’ ‘tkrplot’
  Please remove these calls from your code.
Rd file 'SyNet-package.rd':
  \examples lines wider than 100 characters:
       # Run NAM method on the previously inferred sympatry network                                           

Rd file 'acshgral.rd':
  \examples lines wider than 100 characters:
       #Display relationships into a parenthetical notation. You can track the indices of the species in the

Rd file 'gridinfer.rd':
  \examples lines wider than 100 characters:
       #are nested inside it. In a network analysis this kind of element will behave as intermediary node.  

Rd file 'reweight.rd':
  \examples lines wider than 100 characters:
       plot(unlist(ej),unlist(reweight(ej)), xlab = "Input matrix", ylab = "Reweighted matrix", main = "First reweighting")

These lines will be truncated in the PDF manual.
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.
.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.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘grid’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘perturb’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘grid’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cellgram: no visible global function definition for ‘grid.rect’
cellgram: no visible global function definition for ‘gpar’
cellgram: no visible global function definition for ‘grid.segments’
cellgram: no visible global function definition for ‘grid.circle’
cellgram: no visible global function definition for ‘grid.polygon’
cellgram: no visible global function definition for ‘grid.text’
cellgram: no visible global function definition for ‘unit’
compare: no visible global function definition for ‘sd’
tableplot.colldiag: no visible global function definition for
  ‘colldiag’
tableplot.colldiag: no visible global function definition for ‘xtabs’
tableplot.default: no visible global function definition for
  ‘grid.newpage’
tableplot.default: no visible global function definition for
  ‘grid.layout’
tableplot.default: no visible global function definition for ‘unit’
tableplot.default: no visible global function definition for
  ‘pushViewport’
tableplot.default: no visible global function definition for ‘viewport’
tableplot.default: no visible global function definition for
  ‘grid.text’
tableplot.default: no visible global function definition for
  ‘upViewport’
tableplot.default: no visible global function definition for ‘gpar’
tableplot.default: no visible global function definition for
  ‘grid.rect’
tableplot.default: no visible global function definition for
  ‘popViewport’
Undefined global functions or variables:
  colldiag gpar grid.circle grid.layout grid.newpage grid.polygon
  grid.rect grid.segments grid.text popViewport pushViewport sd unit
  upViewport viewport xtabs
Consider adding
  importFrom("stats", "sd", "xtabs")
to your NAMESPACE file.
Rd file 'Linehan.Rd':
  \examples lines wider than 100 characters:
             cell.specs=list(list(0,"grey50",1,1,"red",1,"white","grey90",2,.7,"black",FALSE,"black",99)),
             cell.specs=list(list(0,c("black","blue"),1,1,c("black","blue"),1,"white","grey80",2,.7,"black",FALSE,"black",99))

Rd file 'cellgram.Rd':
  \usage lines wider than 90 characters:
     cellgram(cell, shape = 0, shape.col = "black", shape.lty = 1, shape.neg = 0, shape.col.neg = "red", shape.lty.neg = 1, cell.fill = "whi ... [TRUNCATED]

Rd file 'congruence.array.Rd':
  \usage lines wider than 90 characters:
     congruence.array(X, FUN = congruence.coef, stat.name = "phi", round = FALSE, scale = 1, ref = "last")

Rd file 'make.specs0.Rd':
  \usage lines wider than 90 characters:
     make.specs0(n = NULL, as.data.frame = FALSE, shape = 0, shape.col = "black", shape.lty = 1, shape.neg = 0, shape.col.neg = "red", shape ... [TRUNCATED]
     cell.fill = "white", back.fill = "white", label = 0, label.size = 0.7, label.col = "black", ref.lines = FALSE, ref.col = "gray80",  sca ... [TRUNCATED]

Rd file 'tableplot.Rd':
  \usage lines wider than 90 characters:
             v.parts = 0, h.parts = 0, gap = 2, text.m = 0, empty.text.size = 0.8, empty.text.col = "grey30", 
             title = NULL, table.label = TRUE, label.size = 0.8, side.rot = 0, left.space = 10, top.space = 10+10*(!is.null(title)), ...)
  \examples lines wider than 100 characters:
             cell.specs = list(list(0,"grey50",1,0,"red",1,"white","grey80",1,0.7,"black",FALSE,"black",93)),

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: ‘pmatch’
Malformed Description field: should contain one or more complete sentences.
'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.
Documented arguments not in \usage in documentation object 'bytable':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘tashudata’
Packages suggested but not available for checking: 'MonetDBLite', 'duckdb'
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.
Malformed Description field: should contain one or more complete sentences.
Documented arguments not in \usage in documentation object 'cosine.sharing':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
cluster_cutoff_at_first_empty_bin: no visible global function
  definition for ‘hist’
mapper1D: no visible global function definition for ‘dist’
mapper1D: no visible global function definition for ‘as.dist’
mapper1D: no visible global function definition for ‘hclust’
mapper1D: no visible global function definition for ‘cutree’
mapper2D: no visible global function definition for ‘dist’
mapper2D: no visible global function definition for ‘as.dist’
mapper2D: no visible global function definition for ‘hclust’
mapper2D: no visible global function definition for ‘cutree’
Undefined global functions or variables:
  as.dist cutree dist hclust hist
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "as.dist", "cutree", "dist", "hclust")
to your NAMESPACE file.
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.
Package suggested but not available for checking: ‘R2wd’
Calls with DUP:
   .C(tensoraCmulhelper, dimx = as.integer(c(outerx, inner, para)), 
       as.integer(c(inner, outery, para)), as.integer(c(outerx, 
           outery, para)), as.complex(X[xtidx]), as.complex(Y[ytidx]), 
       erg = complex(outerx * outery * para), NAOK = TRUE, DUP = FALSE)
   .C(tensoramulhelper, dimx = as.integer(c(outerx, inner, para)), 
       as.integer(c(inner, outery, para)), as.integer(c(outerx, 
           outery, para)), as.numeric(X[xtidx]), as.numeric(Y[ytidx]), 
       erg = numeric(outerx * outery * para), NAOK = TRUE, DUP = FALSE)
DUP is no longer supported and will be ignored.
S3 methods shown with full name in documentation object 'mean.tensor':
  ‘mean.tensor’

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
TER.deesc.1.B : A1.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.1.B : A1.f: no visible binding for global variable ‘ID’
TER.deesc.1.B : A2.n.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.1.B : A2.n.f: no visible binding for global variable ‘ID’
TER.deesc.1.B: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.1.B: no visible binding for global variable ‘ID’
TER.deesc.A.B : A1.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : A1.f: no visible binding for global variable ‘ID’
TER.deesc.A.B : A3.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : A3.f: no visible binding for global variable ‘ID’
TER.deesc.A.B : A2.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : A2.f: no visible binding for global variable ‘ID’
TER.deesc.A.B : B1.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : B1.f: no visible binding for global variable ‘ID’
TER.deesc.A.B: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B: no visible binding for global variable ‘ID’
Undefined global functions or variables:
  ID
Package suggested but not available for checking: ‘gurobi’
Package suggested but not available for checking: ‘btergm’

Package which this enhances but not available for checking: ‘xergm’
phyper_right: no visible global function definition for ‘dhyper’
progression: no visible global function definition for ‘density’
progression: no visible global function definition for ‘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.
transfer: no visible global function definition for ‘rgamma’
transfer: no visible global function definition for ‘rnorm’
transfer: no visible global function definition for ‘rnbinom’
transfer: no visible global function definition for ‘rpois’
transfer: no visible global function definition for ‘rbinom’
transfer: no visible global function definition for ‘runif’
plot,transfer: no visible global function definition for ‘barplot’
plot,transfer: no visible global function definition for ‘axis’
plot,transfer: no visible global function definition for ‘par’
plot,transfer: no visible global function definition for ‘hist’
Undefined global functions or variables:
  axis barplot hist par rbinom rgamma rnbinom rnorm rpois runif
Consider adding
  importFrom("graphics", "axis", "barplot", "hist", "par")
  importFrom("stats", "rbinom", "rgamma", "rnbinom", "rnorm", "rpois",
             "runif")
to your NAMESPACE file.
ParseTrueFX: no visible global function definition for ‘read.csv’
TrueFXRef: no visible global function definition for ‘download.file’
TrueFXRef: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL download.file read.csv
Consider adding
  importFrom("utils", "browseURL", "download.file", "read.csv")
to your NAMESPACE file.
Package unavailable to check Rd xrefs: ‘dada2’
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.
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.
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.
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').
Malformed Description field: should contain one or more complete sentences.
'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
'library' or 'require' calls in package code:
  ‘ggplot2’ ‘plyr’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Matrix’ ‘lubridate’ ‘timeDate’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
is.Bizday: no visible global function definition for ‘isWeekday’
plotCalendarHeatmap: no visible global function definition for ‘ddply’
plotCalendarHeatmap: no visible global function definition for ‘.’
plotCalendarHeatmap: no visible binding for global variable ‘year’
plotCalendarHeatmap: no visible binding for global variable ‘month’
plotCalendarHeatmap: no visible binding for global variable ‘week’
plotCalendarHeatmap: no visible global function definition for ‘ggplot’
plotCalendarHeatmap: no visible global function definition for ‘aes’
plotCalendarHeatmap: no visible binding for global variable ‘monthweek’
plotCalendarHeatmap: no visible binding for global variable ‘weekday’
plotCalendarHeatmap: no visible global function definition for
  ‘geom_tile’
plotCalendarHeatmap: no visible global function definition for
  ‘facet_grid’
plotCalendarHeatmap: no visible global function definition for
  ‘scale_fill_gradientn’
projectDate: no visible global function definition for ‘holidayNYSE’
projectDate: no visible global function definition for
  ‘sparse.model.matrix’
Undefined global functions or variables:
  . aes ddply facet_grid geom_tile ggplot holidayNYSE isWeekday month
  monthweek scale_fill_gradientn sparse.model.matrix week weekday year
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘boot’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘boot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
boot_autocov: no visible global function definition for ‘is.ts’
boot_autocov: no visible global function definition for ‘tsboot’
boot_autocov: no visible global function definition for ‘quantile’
boot_autocov: no visible global function definition for ‘par’
boot_autocov: no visible global function definition for ‘frequency’
boot_autocov: no visible global function definition for ‘polygon’
boot_autocov: no visible global function definition for ‘lines’
boot_autocov: no visible global function definition for ‘abline’
boot_autocov: no visible global function definition for ‘acf’
boot_spec: no visible global function definition for ‘is.ts’
boot_spec: no visible global function definition for ‘tsboot’
boot_spec: no visible global function definition for ‘spec.pgram’
boot_spec: no visible global function definition for ‘quantile’
boot_spec: no visible global function definition for ‘polygon’
boot_spec: no visible global function definition for ‘lines’
redraw: no visible global function definition for ‘spec.pgram’
statistic: no visible global function definition for ‘acf’
Undefined global functions or variables:
  abline acf frequency is.ts lines par polygon quantile spec.pgram
  tsboot
Consider adding
  importFrom("graphics", "abline", "lines", "par", "polygon")
  importFrom("stats", "acf", "frequency", "is.ts", "quantile",
             "spec.pgram")
to your NAMESPACE file.
author.search: no visible binding for global variable ‘na.omit’
reference.list: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
drawGraph: no visible global function definition for ‘pdf’
drawGraph: no visible global function definition for ‘par’
drawGraph: no visible global function definition for ‘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.
Non-standard files/directories found at top level:
  ‘DESCRIPTION.orig’ ‘README.rst’
tipom.car: no visible global function definition for ‘abline’
tipom.car: no visible global function definition for ‘axis’
tipom.heat: no visible global function definition for ‘image’
tipom.heat: no visible global function definition for ‘gray’
tipom.lw: no visible global function definition for ‘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.
Non-standard file/directory found at top level:
  ‘CONTENTS’
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘boot’ ‘lattice’ ‘splines’ ‘tcltk’
  Please remove these calls from your code.
ls.tree: no visible global function definition for ‘lm’
ls.tree: no visible global function definition for ‘coef’
Undefined global functions or variables:
  coef lm
Consider adding
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
Found an obsolete/platform-specific call in the following function:
  ‘.my.tkdev’
Found the platform-specific device:
  ‘X11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
FLXmclust.Density: no visible global function definition for ‘dmvnorm’
FLXmclust.Estimate: no visible global function definition for ‘flexmix’
FLXmclust.Estimate: no visible global function definition for
  ‘FLXmclust’
coefmclust: no visible global function definition for ‘parameters’
flexmix.Density: no visible global function definition for
  ‘model.matrix’
flexmix.Density: no visible global function definition for
  ‘model.response’
flexmix.Density: no visible global function definition for
  ‘model.frame’
flexmix.Density: no visible global function definition for ‘dnorm’
flexmix.Density: no visible global function definition for ‘dpois’
flexmix.Density: no visible global function definition for ‘dbinom’
flexmix.Estimate: no visible global function definition for ‘flexmix’
flexmix.Estimate: no visible global function definition for ‘FLXglm’
tleplot,TLE-data.frame: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  FLXglm FLXmclust dbinom dmvnorm dnorm dpois flexmix legend
  model.frame model.matrix model.response parameters
Consider adding
  importFrom("graphics", "legend")
  importFrom("stats", "dbinom", "dnorm", "dpois", "model.frame",
             "model.matrix", "model.response")
to your NAMESPACE file.
'library' or 'require' call to ‘mvtnorm’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
EMN: no visible global function definition for ‘dmvnorm’
EMN: no visible global function definition for ‘pmvnorm’
EMT: no visible global function definition for ‘GenzBretz’
EMT: no visible global function definition for ‘dmvt’
EMT: no visible global function definition for ‘pmvt’
MomemNT: no visible global function definition for ‘pnorm’
MomemNT: no visible global function definition for ‘dnorm’
MomemNT: no visible global function definition for ‘pmvnorm’
MomemNT: no visible global function definition for ‘dmvnorm’
TT.moment: no visible global function definition for ‘GenzBretz’
TT.moment: no visible global function definition for ‘pmvt’
TT.moment: no visible global function definition for ‘dt’
TT.moment: no visible global function definition for ‘pt’
TT.moment: no visible global function definition for ‘dmvt’
cdfNI: no visible global function definition for ‘pnorm’
cdfNI: no visible global function definition for ‘pt’
inits: no visible global function definition for ‘lm’
Undefined global functions or variables:
  GenzBretz dmvnorm dmvt dnorm dt lm pmvnorm pmvt pnorm pt
Consider adding
  importFrom("stats", "dnorm", "dt", "lm", "pnorm", "pt")
to your NAMESPACE file.
Rd file 'UTIdata.Rd':
  \examples lines wider than 100 characters:
     x = cbind((UTIdata$Fup==0)+0, (UTIdata$Fup==1)+0, (UTIdata$Fup==3)+0, (UTIdata$Fup==6)+0, (UTIdata$Fup==9)+0, (UTIdata$Fup==12)+0, (UTI ... [TRUNCATED]

These lines will be truncated in the PDF manual.
search_collection: no visible global function definition for
  ‘URLencode’
search_company: no visible global function definition for ‘URLencode’
search_keyword: no visible global function definition for ‘URLencode’
search_list: no visible global function definition for ‘URLencode’
search_movie: no visible global function definition for ‘URLencode’
search_multi: no visible global function definition for ‘URLencode’
search_person: no visible global function definition for ‘URLencode’
search_tv: no visible global function definition for ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
extractContentDOM: no visible global function definition for
  ‘capture.output’
extractHTMLStrip: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  capture.output
Consider adding
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'Rcampdf', 'tm.lexicon.GeneralInquirer'
Dependence on R version ‘3.4.1’ not with patchlevel 0
Package suggested but not available for checking: ‘corpus.JSS.papers’
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.
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.
Rd file 'ci.plot.Rd':
  \usage lines wider than 90 characters:
     ci.plot(x, y, se, level = 0.95, ylim = NULL, newplot = TRUE, fun = gaussian()$linkinv, dfun = gaussian()$mu.eta, ...)

These lines will be truncated in the PDF manual.
File ‘tpr/libs/tpr.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following calls to attach():
File ‘track/R/track.attach.R’:
  attach(what = NULL, pos = pos, name = name)
See section ‘Good practice’ in ‘?attach’.
Malformed Title field: should not end in a period.
Package suggested but not available for checking: ‘taxidata’
Malformed Description field: should contain one or more complete sentences.
microsoftTranslate: no visible global function definition for
  ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
rtrapezoid: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Build_JTree: no visible global function definition for ‘flush.console’
Run_JTree: no visible global function definition for ‘cov2cor’
Undefined global functions or variables:
  cov2cor flush.console
Consider adding
  importFrom("stats", "cov2cor")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
LikAge: no visible global function definition for ‘read.table’
bd.ME.optim: no visible global function definition for ‘optim’
bd.ME.optim.rho: no visible global function definition for ‘optim’
bd.ME.optim.rho.all: no visible global function definition for ‘optim’
bd.MEyule.optim: no visible global function definition for ‘optimize’
bd.MEyule.optim: no visible global function definition for ‘optim’
bd.age.optim.matlab: no visible global function definition for
  ‘read.table’
bd.groups.conf: no visible global function definition for ‘uniroot’
bd.shifts.plot: no visible global function definition for ‘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.
GNU make is a SystemRequirements.
Package required but not available: ‘ggtern’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
cinbag: no visible global function definition for ‘var’
trimTrees: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict var
Consider adding
  importFrom("stats", "predict", "var")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘gtools’ ‘mgcv’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘gtools’ ‘mgcv’ ‘msm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HtoGp: no visible global function definition for ‘odd’
HtoGp: no visible global function definition for ‘even’
plot.pirls.gam: no visible global function definition for ‘par’
plot.pirls.gam: no visible global function definition for ‘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.
Malformed Title field: should not end in a period.
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.
tfDetails: no visible global function definition for ‘start’
tfDetails: no visible global function definition for ‘end’
Undefined global functions or variables:
  end start
Consider adding
  importFrom("stats", "end", "start")
to your NAMESPACE file.
Qhat: no visible global function definition for ‘pnorm’
plrt: no visible global function definition for ‘uniroot’
plrt: no visible global function definition for ‘optimize’
simulatedata: no visible global function definition for ‘rnorm’
tsc.test: no visible global function definition for ‘shapiro.test’
tsc.test: no visible global function definition for ‘p.adjust’
tsc.test: no visible global function definition for ‘glm’
tsc.test : f: no visible global function definition for ‘pnorm’
tsc.test: no visible global function definition for ‘uniroot’
tsc.test: no visible global function definition for ‘optimize’
variance: no visible global function definition for ‘density’
variance: no visible global function definition for ‘ecdf’
Undefined global functions or variables:
  density ecdf glm optimize p.adjust pnorm rnorm shapiro.test uniroot
Consider adding
  importFrom("stats", "density", "ecdf", "glm", "optimize", "p.adjust",
             "pnorm", "rnorm", "shapiro.test", "uniroot")
to your NAMESPACE file.
Dependence on R version ‘3.4.2’ not with patchlevel 0
vintageMap: no visible global function definition for ‘read.table’
TSget,character-TSfameLocalConnection: no visible global function
  definition for ‘as.ts’
TSget,character-TSfameLocalConnection: no visible global function
  definition for ‘zoo’
TSget,character-TSfameLocalConnection: no visible global function
  definition for ‘frequency’
TSget,character-TSfameServerConnection: no visible global function
  definition for ‘as.ts’
TSget,character-TSfameServerConnection: no visible global function
  definition for ‘zoo’
TSget,character-TSfameServerConnection: no visible global function
  definition for ‘frequency’
Undefined global functions or variables:
  as.ts frequency read.table zoo
Consider adding
  importFrom("stats", "as.ts", "frequency")
  importFrom("utils", "read.table")
to your NAMESPACE file.
DstandardizedLoadings.TSFmodel: no visible global function definition
  for ‘cov’
FAfitStats.TSFmodel: no visible global function definition for ‘cov’
FAfitStats.default: no visible global function definition for ‘cor’
FAfitStats.default: no visible global function definition for
  ‘factanal’
FAfitStats.default: no visible global function definition for ‘pchisq’
FAmodelFitStats: no visible global function definition for ‘pchisq’
checkResiduals.TSFmodel: no visible global function definition for
  ‘cov’
distribution.factorsEstEval: no visible global function definition for
  ‘par’
distribution.factorsEstEval: no visible binding for global variable
  ‘par’
distribution.factorsEstEval: no visible global function definition for
  ‘density’
distribution.factorsEstEval: no visible global function definition for
  ‘matplot’
distribution.factorsEstEval: no visible global function definition for
  ‘title’
summary.TSFmodel: no visible global function definition for ‘start’
summary.TSFmodel: no visible global function definition for ‘end’
Undefined global functions or variables:
  cor cov density end factanal matplot par pchisq start title
Consider adding
  importFrom("graphics", "matplot", "par", "title")
  importFrom("stats", "cor", "cov", "density", "end", "factanal",
             "pchisq", "start")
to your NAMESPACE file.
Func.SAX: no visible global function definition for ‘sd’
Func.SAX: no visible global function definition for ‘qnorm’
Func.matrix: no visible global function definition for ‘qnorm’
Func.motif: no visible global function definition for ‘sd’
Func.motif: no visible global function definition for ‘na.omit’
Func.motif: no visible global function definition for ‘combn’
Func.motif.multivariate: no visible global function definition for
  ‘txtProgressBar’
Func.motif.multivariate: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  combn na.omit qnorm sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit", "qnorm", "sd")
  importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/tsmp.Rcheck/00install.out’ for details.
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.
TT.GS : TT.GS.sp: no visible global function definition for ‘qt’
TT.GS : TT.GS.sp: no visible global function definition for ‘runif’
TT.GS : TT.GS.sp: no visible global function definition for ‘pt’
TT.moment: no visible global function definition for ‘dt’
TT.moment: no visible global function definition for ‘pt’
Undefined global functions or variables:
  dt pt qt runif
Consider adding
  importFrom("stats", "dt", "pt", "qt", "runif")
to your NAMESPACE file.
.saveDevice: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off
Consider adding
  importFrom("grDevices", "dev.off")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
ttwa: no visible global function definition for ‘aggregate’
ttwa: no visible global function definition for ‘txtProgressBar’
ttwa: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  aggregate setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "aggregate")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
http.connection: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
turf: no visible global function definition for ‘read.table’
turf: no visible global function definition for ‘flush.console’
turf.combos: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn flush.console read.table
Consider adding
  importFrom("utils", "combn", "flush.console", "read.table")
to your NAMESPACE file.
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
TwoCop: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
txtacf: no visible binding for global variable ‘na.fail’
txtacf: no visible global function definition for ‘acf’
txtboxplot : <anonymous>: no visible global function definition for
  ‘boxplot.stats’
txtboxplot: no visible global function definition for ‘boxplot.stats’
txtdensity: no visible global function definition for ‘density’
Undefined global functions or variables:
  acf boxplot.stats density na.fail
Consider adding
  importFrom("grDevices", "boxplot.stats")
  importFrom("stats", "acf", "density", "na.fail")
to your NAMESPACE file.
Crm: no visible global function definition for ‘integrate’
Crm : <anonymous>: no visible global function definition for
  ‘integrate’
Crm: no visible global function definition for ‘optimize’
ail1: no visible global function definition for ‘uniroot’
ail2 : fu : <anonymous>: no visible global function definition for
  ‘integrate’
ail2: no visible global function definition for ‘uniroot’
aip : fu : <anonymous>: no visible global function definition for
  ‘integrate’
aip: no visible global function definition for ‘uniroot’
ait1: no visible global function definition for ‘uniroot’
ait2 : fu : <anonymous>: no visible global function definition for
  ‘integrate’
ait2: no visible global function definition for ‘uniroot’
sim3p3: no visible global function definition for ‘rbinom’
simCrm: no visible global function definition for ‘rbinom’
simCrm: no visible global function definition for ‘palette’
simCrm: no visible global function definition for ‘gray’
simCrm: no visible global function definition for ‘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.
rmd2pdf: no visible global function definition for ‘tail’
rnw2pdf: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
GNU make is a SystemRequirements.
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.
Dependence on R version ‘3.4.4’ not with patchlevel 0
dudewicz.unif.test: no visible global function definition for ‘runif’
frosini.unif.test: no visible global function definition for ‘runif’
hegazy.unif.test: no visible global function definition for ‘runif’
kolmogorov.unif.test: no visible global function definition for ‘runif’
kuiper.unif.test: no visible global function definition for ‘runif’
neyman.unif.test: no visible global function definition for ‘runif’
quesenberry.unif.test: no visible global function definition for
  ‘runif’
sarkadi.unif.test: no visible global function definition for ‘runif’
sherman.unif.test: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
cumcount: no visible global function definition for ‘setNames’
uniqtag: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘USAboundariesData’
readSEER: no visible global function definition for ‘read.fwf’
Undefined global functions or variables:
  read.fwf
Consider adding
  importFrom("utils", "read.fwf")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘UScensus2000cdp/R/zzz.R’:
  .First.lib calls:
    cat(paste("'", ehelp[4], "'\n", "Version ", ehelp[2], " created on ",     ehelp[3], ".\n", sep = ""))
    cat(paste(substring(ehelp[3], first = 16), "\n", "Version ",     substring(ehelp[4], first = 16), " created on ", substring(ehelp[5],         first = 16), ".\n", sep = ""))
    cat(paste("copyright (c) 2009, Zack W. Almquist, University of California-Irvine\n",     sep = ""))
    cat("For citation information, type citation(\"UScensus2000cdp\").\n")
    cat("Type help(package=\"UScensus2000cdp\") to get started.\n")

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

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.
Found the following hidden files and directories:
  data/.Rhistory
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘rgdal’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘foreign’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'MSA.Rd':
  \usage lines wider than 90 characters:
     MSA(msafips = NULL, msaname = NULL, state=NULL , statefips=FALSE, level = c("tract", "blk", "blkgrp"), proj = NULL)

Rd file 'areaPoly.Rd':
  \examples lines wider than 100 characters:
     choropleth(oregon.county10,"den00",color = list(fun = "rainbow", attr = list(4)),main="2010 US Counties \n Oregon",type="plot",border=" ... [TRUNCATED]

Rd file 'choropleth.Rd':
  \usage lines wider than 90 characters:
     choropleth(sp, dem = "P0010001", cuts = list("quantile", seq(0, 1, 0.25)), color = list(fun = "hsv", attr = list(h = c(0.4, 0.5, 0.6, 0 ... [TRUNCATED]
  \examples lines wider than 100 characters:
     choropleth(oregon.county10,"P0010001",color = list(fun = "rainbow", attr = list(4)),main="2010 Counties \n Oregon",type="plot",border=" ... [TRUNCATED]
     choropleth(oregon.county10,"P0010001",main="2010 Counties \n Oregon",border="transparent",type="spplot")

Rd file 'choropleth.plot.Rd':
  \usage lines wider than 90 characters:
     choropleth.plot(sp, dem = "P0010001", cuts = list("quantile", seq(0, 1, 0.25)), color = list(fun = "hsv", attr = list(h = c(0.4, 0.5, 0 ... [TRUNCATED]

Rd file 'choropleth.spplot.Rd':
  \usage lines wider than 90 characters:
     choropleth.spplot(sp, dem = "P0010001", cuts = list("quantile", seq(0, 1, 0.25)), color = list(fun = "hsv", attr = list(h = c(0.4, 0.5, ... [TRUNCATED]

Rd file 'county.Rd':
  \usage lines wider than 90 characters:
     county(fips = NULL, name = NULL, state, level = c("tract", "blk", "blkgrp"), statefips = FALSE, sp.object=NULL, proj=NULL)

These lines will be truncated in the PDF manual.
Malformed Title field: should not end in a period.
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.
GNU make is a SystemRequirements.
Packages suggested but not available for checking: 'vaers', 'vaersND'
Packages suggested but not available for checking: 'vaers', 'vaersND'
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.
Found the following sources/headers not terminated with a newline:
  inst/include/Algorithm.h
  inst/include/AlgorithmCategorical.h
  inst/include/AlgorithmContinuous.h
  inst/include/AlgorithmInteger.h
  inst/include/AlgorithmMixed.h
  inst/include/Data.h
  inst/include/DataCategorical.h
  inst/include/DataContinuous.h
  inst/include/DataInteger.h
  inst/include/DataMixed.h
  inst/include/Param.h
  inst/include/ParamCategorical.h
  inst/include/ParamContinuous.h
  inst/include/ParamInteger.h
  inst/include/ParamMixed.h
  inst/include/XEM.h
  inst/include/XEMCategorical.h
  inst/include/XEMContinuous.h
  inst/include/XEMInteger.h
  inst/include/XEMMixed.h
  inst/include/XEMPen.h
Some compilers warn on such files.
black_scholes: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
burdenPlot: no visible global function definition for ‘density’
burdenPlot: no visible global function definition for ‘axis’
burdenPlot: no visible global function definition for ‘points’
burdenPlot: no visible global function definition for ‘lines’
burdenPlot: no visible global function definition for ‘abline’
burdenPlot: no visible global function definition for ‘text’
burdenPlot: no visible global function definition for ‘sd’
burdenPlot: no visible global function definition for ‘segments’
vbdm: no visible global function definition for ‘var’
vbdm: no visible global function definition for ‘pchisq’
vbdmR : run_discrete_mixture_vanilla: no visible global function
  definition for ‘var’
vbdmR: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  abline axis density lines pchisq points sd segments text var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "points", "segments",
             "text")
  importFrom("stats", "density", "pchisq", "sd", "var")
to your NAMESPACE file.
compute_KL : rtnorm: no visible global function definition for ‘runif’
compute_KL : rtnorm: no visible global function definition for ‘dnorm’
compute_KL: no visible global function definition for ‘qnorm’
compute_KL: no visible global function definition for ‘dnorm’
compute_KL: no visible global function definition for ‘pnorm’
compute_KL: no visible global function definition for ‘var’
compute_KL: no visible global function definition for ‘rbinom’
compute_KL: no visible global function definition for ‘rnorm’
compute_KL: no visible global function definition for ‘sd’
vbsr: no visible global function definition for ‘qchisq’
vbsr: no visible global function definition for ‘var’
vbsr: no visible global function definition for ‘pchisq’
vbsr: no visible global function definition for ‘sd’
vbsr: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  dnorm pchisq pnorm qchisq qnorm rbinom rnorm runif sd var
Consider adding
  importFrom("stats", "dnorm", "pchisq", "pnorm", "qchisq", "qnorm",
             "rbinom", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
Package suggested but not available for checking: ‘ggtern’
Compare2FDS: no visible global function definition for ‘runif’
Compare2FDS: no visible global function definition for ‘lm’
Compare2FDS: no visible global function definition for ‘model.matrix’
Compare2FDS: no visible global function definition for ‘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.
calculateParameters,AffineTransformation: no visible global function
  definition for ‘lm’
calculateParameters,AffineTransformation: no visible global function
  definition for ‘coef’
calculateParameters,SimilarityTransformation: no visible global
  function definition for ‘lm’
calculateParameters,SimilarityTransformation: no visible global
  function definition for ‘coef’
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for ‘points’
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for ‘legend’
Undefined global functions or variables:
  coef legend lm points
Consider adding
  importFrom("graphics", "legend", "points")
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
DrawDensity3D: no visible global function definition for ‘colorRamp’
DrawDensity3D: no visible global function definition for ‘rgb’
ReadFromFile3D: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  colorRamp read.table rgb
Consider adding
  importFrom("grDevices", "colorRamp", "rgb")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'library' or 'require' call to ‘stats’ which was already attached by Depends.
  Please remove these calls from your code.
H: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = H, func.arg = list(func.arg), boot.arg)):
  partial argument match of ‘arg’ to ‘args’
M.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = M.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
Rel.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = Rel.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
bootstrap: warning in do.call(what = func, arg = list(boots[, , i])):
  partial argument match of ‘arg’ to ‘args’
bootstrap: warning in do.call(what = func, arg = c(abundances =
  list(boots[, , i]), func.arg)): partial argument match of ‘arg’ to
  ‘args’
d: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = d, func.arg = list(func.arg), boot.arg)):
  partial argument match of ‘arg’ to ‘args’
sim.groups: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of ‘arg’ to ‘args’
sim.table: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of ‘arg’ to ‘args’
similarity: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = similarity, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
turnover: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = turnover, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
prepare_Rd: H.Rd:41-42: Dropping empty section \note
prepare_Rd: M.homog.Rd:19-21: Dropping empty section \details
prepare_Rd: M.homog.Rd:35-36: Dropping empty section \note
prepare_Rd: Rel.homog.Rd:24-25: Dropping empty section \note
prepare_Rd: bootstrap.Rd:34: Dropping empty section \note
prepare_Rd: d.Rd:35-36: Dropping empty section \note
prepare_Rd: normalize.rows.Rd:26-27: Dropping empty section \note
prepare_Rd: p.q.sum.Rd:23-24: Dropping empty section \note
prepare_Rd: p.q.sum.Rd:26: Dropping empty section \examples
prepare_Rd: sim.groups.Rd:27-28: Dropping empty section \note
prepare_Rd: sim.table.Rd:25-26: Dropping empty section \note
prepare_Rd: similarity.Rd:25-26: Dropping empty section \note
prepare_Rd: turnover.Rd:17-18: Dropping empty section \details
prepare_Rd: turnover.Rd:29-30: Dropping empty section \note
Malformed Description field: should contain one or more complete sentences.
Checking should be performed on sources prepared by ‘R CMD build’.
Non-standard file/directory found at top level:
  ‘src-java’
plot.VennDiagram : <anonymous>: no visible global function definition
  for ‘hcl’
plot.VennDiagram: no visible global function definition for ‘plot.new’
plot.VennDiagram: no visible global function definition for
  ‘plot.window’
plot.VennDiagram: no visible global function definition for ‘col2rgb’
plot.VennDiagram: no visible global function definition for ‘rgb’
plot.VennDiagram: no visible global function definition for ‘polygon’
plot.VennDiagram: no visible global function definition for ‘text’
plot.VennDiagram: no visible global function definition for ‘title’
Undefined global functions or variables:
  col2rgb hcl plot.new plot.window polygon rgb text title
Consider adding
  importFrom("grDevices", "col2rgb", "hcl", "rgb")
  importFrom("graphics", "plot.new", "plot.window", "polygon", "text",
             "title")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
vif: no visible global function definition for ‘sd’
vif: no visible global function definition for ‘lm’
vif: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  lm pnorm sd
Consider adding
  importFrom("stats", "lm", "pnorm", "sd")
to your NAMESPACE file.
Rd file 'vif.Rd':
  \usage lines wider than 90 characters:
             vif(y, x, w0 = 0.05, dw = 0.05, subsize = 200, trace = TRUE, mode = c("dense", "sparse"))
  \examples lines wider than 100 characters:
             vif.sel <- vif(housingexp$y, housingexp$x, w0 = 0.0005, dw = 0.005, subsize = 300, trace = FALSE);

These lines will be truncated in the PDF manual.
hyperpara: no visible binding for global variable ‘var’
hyperpara: no visible global function definition for ‘hist’
Undefined global functions or variables:
  hist var
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "var")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
panel.meansdplot : meansdplot.stats: no visible global function
  definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
prepare_Rd: panel.meansdplot.Rd:42-45: Dropping empty section \value
prepare_Rd: panel.meansdplot.Rd:49-51: Dropping empty section \note
prepare_Rd: panel.violinm.Rd:40-42: Dropping empty section \details
prepare_Rd: panel.violinm.Rd:43-49: Dropping empty section \value
prepare_Rd: panel.violinm.Rd:53-55: Dropping empty section \note
prepare_Rd: panel.violinm.Rd:50-52: Dropping empty section \author
prepare_Rd: violinmplot.Rd:34-36: Dropping empty section \details
prepare_Rd: violinmplot.Rd:48-50: Dropping empty section \note
'library' or 'require' call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
viopoints.default: no visible global function definition for ‘par’
viopoints.default: no visible global function definition for ‘plot.new’
viopoints.default: no visible global function definition for
  ‘plot.window’
viopoints.default: no visible global function definition for ‘axis’
viopoints.default: no visible global function definition for ‘arrows’
viopoints.default: no visible global function definition for
  ‘getFromNamespace’
viopoints.default: no visible global function definition for ‘title’
viopoints.default: no visible global function definition for ‘box’
Undefined global functions or variables:
  arrows axis box getFromNamespace par plot.new plot.window title
Consider adding
  importFrom("graphics", "arrows", "axis", "box", "par", "plot.new",
             "plot.window", "title")
  importFrom("utils", "getFromNamespace")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Missing or unexported object: ‘jsonlite::rbind.pages’
Decile.Plot: no visible global function definition for ‘barplot’
Decile.Plot: no visible global function definition for ‘axis’
Sliding.Window: no visible global function definition for ‘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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘vortexRguide.Rmd’ using rmarkdown
Quitting from lines 284-288 (vortexRguide.Rmd) 
Error: processing vignette 'vortexRguide.Rmd' failed with diagnostics:
replacement has 1 row, data has 0
--- failed re-building ‘vortexRguide.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘raster’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
level: no visible global function definition for ‘quantile’
obj.rec: no visible global function definition for ‘txtProgressBar’
obj.rec: no visible global function definition for ‘setTxtProgressBar’
project: no visible global function definition for ‘aggregate’
raster.proj: no visible global function definition for ‘quantile’
raster.proj: no visible global function definition for ‘rasterFromXYZ’
raster.proj: no visible global function definition for ‘plot.new’
raster.proj: no visible global function definition for ‘plot’
raster.proj: no visible global function definition for ‘legend’
sub.obj: no visible global function definition for ‘aggregate’
sub.obj: no visible global function definition for ‘txtProgressBar’
sub.obj: no visible global function definition for ‘setTxtProgressBar’
surface: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  aggregate legend plot plot.new quantile rasterFromXYZ
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "plot", "plot.new")
  importFrom("stats", "aggregate", "quantile")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
'library' or 'require' call to ‘misc3d’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
Non-standard file/directory found at top level:
  ‘vwr-Ex.R’
Packages in Depends field not imported from:
  ‘lattice’ ‘latticeExtra’ ‘stringdist’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ald: no visible global function definition for ‘detectCores’
ald: no visible global function definition for ‘mclapply’
coltheart.N: no visible global function definition for ‘detectCores’
coltheart.N: no visible global function definition for ‘mclapply’
hamming.distance: no visible global function definition for
  ‘stringdist’
ldknn: no visible global function definition for ‘detectCores’
ldknn: no visible global function definition for ‘mclapply’
ldknn.odds: no visible global function definition for ‘glm’
ldknn.odds: no visible binding for global variable ‘binomial’
ldknn.odds: no visible global function definition for ‘coefficients’
levenshtein.damerau.distance: no visible global function definition for
  ‘stringdist’
levenshtein.distance: no visible global function definition for
  ‘stringdist’
plot.ldknn.run: no visible global function definition for ‘histogram’
plot.ldknn.run: no visible global function definition for
  ‘theEconomist.theme’
plot.ldknn.run: no visible global function definition for ‘xyplot’
plot.ldknn.run: no visible global function definition for ‘as.layer’
Undefined global functions or variables:
  as.layer binomial coefficients detectCores glm histogram mclapply
  stringdist theEconomist.theme xyplot
Consider adding
  importFrom("stats", "binomial", "coefficients", "glm")
to your NAMESPACE file.
Package in Depends field not imported from: ‘Rcpp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'waffect-package.Rd':
  \examples lines wider than 100 characters:
     ## Not run: Typical usage to simulate case/control phenotypes under H1 (in this example: 5 individuals, 2 cases, 3 controls, the probab ... [TRUNCATED]
     ## Not run: Simulation of phenotypes in the multiclass case (in this example: 4 individuals and  3 classes, 1 individual in class 1, 2  ... [TRUNCATED]

Rd file 'waffect.Rd':
  \examples lines wider than 100 characters:
     ## Not run: Typical usage to simulate case/control phenotypes under H1 (in this example: 12 individuals, 7 cases, 5 controls, the proba ... [TRUNCATED]
     waffect(prob =  c(0.2, 0.4, 0.9, 0.6, 0.9, 0.1, 0.4, 0.6, 0.6, 0.3, 0.8, 0.1), count=c(7,5), label=c(1,0))
     waffect(prob =  c(0.2, 0.4, 0.9, 0.6, 0.9, 0.1, 0.4, 0.6, 0.6, 0.3, 0.8, 0.1), count=c(7,5), label=c(1,0))
     waffect(prob =  c(0.2, 0.4, 0.9, 0.6, 0.9, 0.1, 0.4, 0.6, 0.6, 0.3, 0.8, 0.1), count=7, label=c(1,0))
     ## Not run: If prob is not specified then a constant vector of probabilities is assumed by default. This is equivalent to simulate phen ... [TRUNCATED]

These lines will be truncated in the PDF manual.
File ‘waffect/libs/waffect.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘waffect.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
summary.whc: no visible global function definition for ‘printCoefmat’
wahc.fit: no visible global function definition for ‘pt’
wahc.fit: no visible global function definition for ‘cor’
whc: no visible global function definition for ‘model.frame’
whc: no visible global function definition for ‘model.matrix’
whc: no visible global function definition for ‘model.response’
Undefined global functions or variables:
  cor model.frame model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.frame", "model.matrix",
             "model.response", "printCoefmat", "pt")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Rd file 'p.storage.Rd':
  \examples lines wider than 100 characters:
     d.wasim.out <- read.results("", "weisseritz",ts.length=21937,subcatchments=2, ending="ww100.txt")    # Datensatz heisst jetzt d.wasim.o ... [TRUNCATED]
     d.meas.all<-read.table("weisseritz/ww100-rh.txt",header=TRUE, na.strings ="999", skip=4)  # gemessene Daten einlesen

Rd file 'read.results.Rd':
  \examples lines wider than 100 characters:
     d.wasim.out <- read.results("", "weisseritz",ts.length=21937,subcatchments=2, ending="ww100.txt")    # Datensatz heisst jetzt d.wasim.o ... [TRUNCATED]

Rd file 'wasim-package.Rd':
  \examples lines wider than 100 characters:
     d.wasim.out <- read.results("", "weisseritz",ts.length=21937,subcatchments=2, ending="ww100.txt")    # Datensatz heisst jetzt d.wasim.o ... [TRUNCATED]
     d.meas.all<-read.table("weisseritz/ww100-rh.txt",header=TRUE, na.strings ="999", skip=4)  # gemessene Daten einlesen

These lines will be truncated in the PDF manual.
Foreign function call to a different package:
  .C("comwr", ..., PACKAGE = "wavethresh")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘rPeaks’
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.
GNU make is a SystemRequirements.
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.
Dependence on R version ‘3.4.2’ not with patchlevel 0
Malformed Description field: should contain one or more complete sentences.
Bundesliga.Mannschaft: no visible global function definition for ‘data’
Bundesliga.Mannschaft: no visible binding for global variable
  ‘Bundesliga’
Bundesliga.Tabelle: no visible global function definition for ‘data’
Bundesliga.Tabelle: no visible binding for global variable ‘Bundesliga’
Bundesliga.XML: no visible global function definition for ‘data’
Bundesliga.XML: no visible binding for global variable ‘Bundesliga’
sens.spec: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘wikibooks/R/Bundesliga.Mannschaft.R’:
  data(Bundesliga)
File ‘wikibooks/R/Bundesliga.Tabelle.R’:
  data(Bundesliga)
File ‘wikibooks/R/Bundesliga.XML.R’:
  data(Bundesliga)
See section ‘Good practice’ in ‘?data’.
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.
plotTrait: no visible global function definition for ‘plot’
plotTrait: no visible global function definition for ‘points’
plotTrait: no visible global function definition for ‘legend’
test.windex: no visible global function definition for ‘hist’
test.windex: no visible global function definition for ‘abline’
test.windex: no visible global function definition for ‘legend’
windex: no visible global function definition for ‘sd’
windex: no visible global function definition for ‘var’
windex: no visible global function definition for ‘dist’
windex: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline dist hist legend plot points quantile sd var
Consider adding
  importFrom("graphics", "abline", "hist", "legend", "plot", "points")
  importFrom("stats", "dist", "quantile", "sd", "var")
to your NAMESPACE file.
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.
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
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Malformed Title field: should not end in a period.
Package unavailable to check Rd xrefs: ‘cleaver’
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.
Rd file 'simul.wsvm.Rd':
  \usage lines wider than 90 characters:
         simul.wsvm(set.seeds = 123, obs.num = 1000, mu = c(0,0), cov.mat = 0.2*diag(2), X = NULL, Y = NULL)

Rd file 'wsvm.boost.Rd':
  \usage lines wider than 90 characters:
         wsvm.boost(X, Y, new.X, new.Y, c.n, B = 50, kernel.type = list(type = "rbf", par= 0.5), C = 4, eps = 1e-10, plotting = FALSE)

These lines will be truncated in the PDF manual.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
File
  inst/LICENCE
will install at top-level and is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  ‘CONTENTS’
Rd file 'classroom.Rd':
  \examples lines wider than 100 characters:
     {boxplot(classroom.first8$mathgain[classroom.first8$schoolid==i] ~ classroom.first8$classid[classroom.first8$schoolid==i],ylab="Mathgai ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Malformed Description field: should contain one or more complete sentences.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/x13binary.Rcheck/00install.out’ for details.
Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred.
  Output from running autoreconf:
  aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in'
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.
R5.value.default: no visible binding for global variable ‘data.table’
R5.value.default: no visible global function definition for
  ‘as.data.table’
R5.value.parse: no visible binding for global variable ‘data.table’
R5.value.parse: no visible global function definition for
  ‘is.data.table’
R5.value.parse: no visible global function definition for
  ‘as.data.table’
stampme: no visible global function definition for ‘flush.console’
stampmsg: no visible global function definition for ‘flush.console’
write.data.table: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  as.data.table data.table flush.console is.data.table write.table
Consider adding
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
LPGM: no visible global function definition for ‘flush.console’
PGM: no visible global function definition for ‘flush.console’
PGM.path.neighborhood: no visible global function definition for
  ‘runif’
PGMSim: no visible global function definition for ‘rpois’
PGMSim: no visible global function definition for ‘par’
WPGMSim: no visible global function definition for ‘rpois’
XMRF.Sim: no visible global function definition for ‘cov2cor’
XMRF.Sim: no visible global function definition for ‘rbinom’
XMRF.Sim: no visible global function definition for ‘rnorm’
glm.generic: no visible global function definition for ‘flush.console’
mymult: no visible global function definition for ‘rmultinom’
plot.GMS: no visible global function definition for ‘pdf’
plot.GMS: no visible global function definition for ‘dev.off’
plotNet: no visible global function definition for ‘pdf’
plotNet: no visible global function definition for ‘dev.off’
print.GMS: no visible global function definition for ‘str’
processSeq: no visible binding for global variable ‘quantile’
processSeq: no visible binding for global variable ‘var’
processSeq: no visible global function definition for ‘ks.test’
rmpois : <anonymous>: no visible global function definition for ‘rpois’
Undefined global functions or variables:
  cov2cor dev.off flush.console ks.test par pdf quantile rbinom
  rmultinom rnorm rpois runif str var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par")
  importFrom("stats", "cov2cor", "ks.test", "quantile", "rbinom",
             "rmultinom", "rnorm", "rpois", "runif", "var")
  importFrom("utils", "flush.console", "str")
to your NAMESPACE file.
Running ‘testthat.R’ [44s/47s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(xpose)
  Loading required package: ggplot2
  
  Attaching package: 'xpose'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("xpose")
  ── 1. Failure: parial xp_themes are properly added (@test-update_themes.R#39)  ─
  update_themes(xpdb = xpdb_ex_pk, xp_theme = c(point_color = "green"))$xp_theme not equivalent to `theme_xp_custom`.
  Component "labeller": target, current do not match when deparsed
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 521 | SKIPPED: 7 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: parial xp_themes are properly added (@test-update_themes.R#39) 
  
  Error: testthat unit tests failed
  Execution halted
Non-standard file/directory found at top level:
  ‘CONTRIBUTORS’
Malformed Title field: should not end in a period.
big.read.table: no visible global function definition for ‘read.table’
big.read.table: no visible global function definition for ‘object.size’
sparkline: no visible global function definition for ‘is.ts’
sparkline: no visible global function definition for ‘time’
sparkline: no visible global function definition for ‘boxplot’
Undefined global functions or variables:
  boxplot is.ts object.size read.table time
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "is.ts", "time")
  importFrom("utils", "object.size", "read.table")
to your NAMESPACE file.
Package in Depends field not imported from: ‘compiler’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bootstrapswapcurve: no visible global function definition for ‘ts’
fitted: no visible global function definition for ‘ts’
forwardrates: no visible global function definition for ‘ts’
residuals: no visible global function definition for ‘ts’
tZC_NS: no visible global function definition for ‘cmpfun’
tZC_NS_extra: no visible global function definition for ‘cmpfun’
tZC_SV: no visible global function definition for ‘cmpfun’
tZC_SV_extra: no visible global function definition for ‘cmpfun’
ycextra: no visible global function definition for ‘new’
ycinter: no visible global function definition for ‘new’
ycplot: no visible global function definition for ‘par’
ycplot: no visible global function definition for ‘points’
ycplot: no visible global function definition for ‘abline’
ycplot: no visible global function definition for ‘hist’
ycplot: no visible global function definition for ‘lines’
ycplot: no visible global function definition for ‘density’
ycplot: no visible global function definition for ‘qqnorm’
ycplot: no visible global function definition for ‘qqline’
ycsummary: no visible global function definition for ‘shapiro.test’
ycsummary: no visible global function definition for ‘pf’
Undefined global functions or variables:
  abline cmpfun density hist lines new par pf points qqline qqnorm
  shapiro.test ts
Consider adding
  importFrom("graphics", "abline", "hist", "lines", "par", "points")
  importFrom("methods", "new")
  importFrom("stats", "density", "pf", "qqline", "qqnorm",
             "shapiro.test", "ts")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.NS.estimator: no visible global function definition for ‘lm’
.NS.estimator: no visible global function definition for ‘coef’
.NS.estimator: no visible global function definition for ‘na.omit’
.NS.estimator: no visible global function definition for ‘resid’
.NSS.estimator: no visible global function definition for ‘lm’
.NSS.estimator: no visible global function definition for ‘coef’
.NSS.estimator: no visible global function definition for ‘na.omit’
.NSS.estimator: no visible global function definition for ‘resid’
NSrates: no visible global function definition for ‘time’
Nelson.Siegel: no visible global function definition for ‘optimize’
Srates: no visible global function definition for ‘time’
Svensson: no visible global function definition for ‘median’
Svensson: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  coef lm median na.omit optimize resid time
Consider adding
  importFrom("stats", "coef", "lm", "median", "na.omit", "optimize",
             "resid", "time")
to your NAMESPACE file.
Rd file 'ECBYieldCurve.Rd':
  \examples lines wider than 100 characters:
     plot(mat.ECB, ECBYieldCurve[i,], type="o", xlab="Maturities structure in years", ylab="Interest rates values")

Rd file 'FedYieldCurve.Rd':
  \examples lines wider than 100 characters:
     plot(mat, FedYieldCurve[i,], type="o", xlab="Maturities structure in years", ylab="Interest rates values")

These lines will be truncated in the PDF manual.
kmeansN: no visible global function definition for ‘kmeans’
kmeansN: no visible global function definition for ‘aggregate’
kmeansN2: no visible global function definition for ‘aggregate’
kmeansN2: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  aggregate kmeans sd
Consider adding
  importFrom("stats", "aggregate", "kmeans", "sd")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Missing or unexported object: ‘devtools::use_data’
Package suggested but not available for checking: ‘zeligverse’
Package suggested but not available for checking: ‘zeligverse’
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(AER)
  Loading required package: car
  Loading required package: carData
  Loading required package: lmtest
  Loading required package: zoo
  
  Attaching package: 'zoo'
  
  The following objects are masked from 'package:base':
  
      as.Date, as.Date.numeric
  
  Loading required package: sandwich
  Loading required package: survival
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:car':
  
      recode
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > library(geepack)
  > library(survey)
  Loading required package: grid
  Loading required package: Matrix
  
  Attaching package: 'survey'
  
  The following object is masked from 'package:graphics':
  
      dotchart
  
  > library(testthat)
  
  Attaching package: 'testthat'
  
  The following object is masked from 'package:dplyr':
  
      matches
  
  > library(zeligverse)
  Error in library(zeligverse) : there is no package called 'zeligverse'
  Execution halted
Malformed Description field: should contain one or more complete sentences.
S3 methods shown with full name in documentation object 'merge':
  ‘cbind.zoocat’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
Package suggested but not available for checking: ‘SDMTools’
Namespaces in Imports field not imported from:
  ‘DT’ ‘shinydashboard’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘aaSEA_Documentation.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 RColorBrewer::brewer.pal(N, "Set2") :
  n too large, allowed maximum for palette Set2 is 8
Returning the palette you asked for with that many colors

Warning in RColorBrewer::brewer.pal(N, "Set2") :
  n too large, allowed maximum for palette Set2 is 8
Returning the palette you asked for with that many colors

Quitting from lines 90-91 (aaSEA_Documentation.Rmd) 
Error: processing vignette 'aaSEA_Documentation.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘aaSEA_Documentation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
Found the following files/directories:
  ‘CVrej.ps’ ‘linhc.pdf’
multiplot: no visible global function definition for ‘rainbow’
multiplot: no visible global function definition for ‘text’
multiplot: no visible global function definition for ‘lines’
multiplot: no visible global function definition for ‘par’
plot.abf2: no visible global function definition for ‘abline’
plot.abf2: no visible global function definition for ‘text’
Undefined global functions or variables:
  abline lines par rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "par", "text")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘httr’ ‘progress’
  All declared Imports should be used.
Missing or unexported object: ‘devtools::use_package’
Package suggested but not available for checking: ‘INLA’
Found the following files/directories:
  ‘geneset.txt’
Found the following files/directories:
  ‘acceldata2.RData’
Malformed Description field: should contain one or more complete sentences.
fillCSVData: no visible global function definition for ‘read.table’
fillData: no visible global function definition for ‘edit’
plotGraphs: no visible global function definition for ‘par’
plotGraphs: no visible global function definition for ‘lines’
plotGraphs: no visible global function definition for ‘legend’
plotGraphs: no visible global function definition for ‘dev.new’
Undefined global functions or variables:
  dev.new edit legend lines par read.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "lines", "par")
  importFrom("utils", "edit", "read.table")
to your NAMESPACE file.
Package has no Sweave vignette sources and no VignetteBuilder field.
Namespaces in Imports field not imported from:
  ‘rARPACK’ ‘sparseLDA’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
print.funlinWLS: no visible global function definition for ‘pchisq’
print.linML: no visible global function definition for ‘pchisq’
print.loglinML: no visible global function definition for ‘pchisq’
print.satMarML: no visible global function definition for ‘pchisq’
print.satMcarWLS: no visible global function definition for ‘pchisq’
summary.funlinWLS: no visible global function definition for ‘pchisq’
summary.linML: no visible global function definition for ‘pchisq’
summary.loglinML: no visible global function definition for ‘pchisq’
summary.satMarML: no visible global function definition for ‘pchisq’
summary.satMcarWLS: no visible global function definition for ‘pchisq’
summary.waldTest: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
Package in Depends field not imported from: ‘MASS’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
acm: no visible global function definition for ‘read.table’
clusters: no visible global function definition for ‘write.matrix’
clusters: no visible global function definition for ‘dev.new’
clusters: no visible global function definition for ‘par’
clusters: no visible global function definition for ‘hist’
clusters: no visible global function definition for ‘legend’
clusters: no visible global function definition for ‘pdf’
clusters: no visible global function definition for ‘dev.off’
erra: no visible global function definition for ‘read.table’
erra: no visible global function definition for ‘pbeta’
Undefined global functions or variables:
  dev.new dev.off hist legend par pbeta pdf read.table write.matrix
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("graphics", "hist", "legend", "par")
  importFrom("stats", "pbeta")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘BABLBS_ID distribution’ ‘BABLBS_Singletons’ ‘BABLBS_clustered’
  ‘BABLBS_clustered_and_single’ ‘Genetic_Distance_1ID distribution’
  ‘Genetic_Distance_1Singletons’ ‘Genetic_Distance_1clustered’
  ‘Genetic_Distance_1clustered_and_single’ ‘acm.out.1’ ‘acm.par’
  ‘erra.out.1’ ‘erra.out.1.acm’ ‘erra.out.1_d.ite’ ‘erra.out.1_s.ite’
  ‘erra.rcm’ ‘exact_matching_ID distribution’
  ‘exact_matching_Singletons’ ‘exact_matching_clustered’
  ‘exact_matching_clustered_and_single’ ‘experiments.in’
  ‘hist_both.pdf’ ‘hist_clust.pdf’ ‘replicates.in’
Aggregate: no visible global function definition for ‘aggregate’
Aggregate: no visible binding for global variable ‘tail’
Aggregate: no visible binding for global variable ‘var’
cocktailEnsemble: no visible global function definition for ‘glm’
cocktailEnsemble: no visible global function definition for ‘binomial’
cocktailEnsemble: no visible global function definition for ‘step’
cocktailEnsemble: no visible binding for global variable ‘na.omit’
imputeMissings : <anonymous>: no visible global function definition for
  ‘median’
predict.cocktailEnsemble: no visible global function definition for
  ‘predict’
Undefined global functions or variables:
  aggregate binomial glm median na.omit predict step tail var
Consider adding
  importFrom("stats", "aggregate", "binomial", "glm", "median",
             "na.omit", "predict", "step", "var")
  importFrom("utils", "tail")
to your NAMESPACE file.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    R  13.6Mb
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
Found the following files/directories:
  ‘Example.jpeg’
Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinydashboard’
  All declared Imports should be used.
Missing or unexported object: ‘devtools::clean_source’
'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.
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.
Namespace in Imports field not imported from: ‘Benchmarking’
  All declared Imports should be used.
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  8.1Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    data       2.8Mb
    pictures   2.5Mb
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R       1.4Mb
    data    1.3Mb
    files   1.9Mb
Namespace in Imports field not imported from: ‘filehash’
  All declared Imports should be used.
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    data  20.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    4.8Mb
    help   1.0Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   2.8Mb
Found the following files/directories:
  ‘Bestmatches.csv’ ‘ID.csv’ ‘listsp.csv’ ‘mylabels.csv’
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  inst/include/ADMMnet.h
  inst/include/ADMMnet_RcppExports.h
Some Unix compilers require LF line endings.
Namespaces in Imports field not imported from:
  ‘fields’ ‘knitr’
  All declared Imports should be used.
Found the following files/directories:
  ‘table_AeRobiology’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       2.9Mb
    extdata   1.9Mb
Namespaces in Imports field not imported from:
  ‘DBI’ ‘assertthat’ ‘tibble’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Found the following files/directories:
  ‘myplot.pdf’ ‘myplot.png’
Namespaces in Imports field not imported from:
  ‘devtools’ ‘mixexp’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘ahn.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 66-67 (ahn.Rmd) 
Error: processing vignette 'ahn.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘ahn.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package unavailable to check Rd xrefs: ‘Starr’
Namespaces in Imports field not imported from:
  ‘knitr’ ‘randomNames’ ‘tidyr’
  All declared Imports should be used.
Package required but not available: ‘rscala’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following files/directories:
  ‘ans_19-2.jpg’ ‘display2d_19-2.jpg’ ‘dist(3)_19-2.jpg’
  ‘dist(4)_19-2.jpg’ ‘dist(mirror)_19-2.jpg’ ‘dist(mirror2)_19-2.jpg’
Namespace with empty importFrom: ‘survival’
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘survival’
A package should be listed in only one of these fields.
backfit.cox.interaction: no visible global function definition for
  ‘coxph’
backfit.lm.interaction: no visible global function definition for ‘lm’
backfit.logistic.interaction: no visible global function definition for
  ‘glm’
backfit.logistic.main: no visible global function definition for ‘glm’
cox.interaction: no visible global function definition for ‘coxph’
cv.cox.interaction: no visible global function definition for ‘coxph’
cv.cox.main: no visible global function definition for ‘coxph’
cv.lm.interaction: no visible global function definition for ‘lm’
cv.lm.main: no visible global function definition for ‘lm’
cv.logistic.interaction: no visible global function definition for
  ‘glm’
cv.logistic.main: no visible global function definition for ‘glm’
lm.interaction: no visible global function definition for ‘lm’
logistic.interaction: no visible global function definition for ‘glm’
logistic.main: no visible global function definition for ‘glm’
Undefined global functions or variables:
  coxph glm lm
Consider adding
  importFrom("stats", "glm", "lm")
to your NAMESPACE file.
Note: found 53 marked UTF-8 strings
Note: found 710 marked UTF-8 strings
Found the following files/directories:
  ‘stuve.pdf’
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.
Namespace in Imports field not imported from: ‘taxize’
  All declared Imports should be used.
Found the following files/directories:
  ‘candidate_alignments.csv’ ‘open.with.excel.csv’
Malformed Description field: should contain one or more complete sentences.
allanVarSelect: no visible global function definition for ‘read.csv’
fitvbiglm: no visible global function definition for ‘read.csv’
fitvbiglm: no visible global function definition for ‘update’
getbestchunksize: no visible global function definition for ‘read.csv’
getbestchunksize: no visible global function definition for
  ‘object.size’
predictvbiglm: no visible global function definition for ‘read.csv’
predictvbiglm: no visible global function definition for ‘predict’
predictvbiglm: no visible global function definition for
  ‘weighted.mean’
readinbigdata : <anonymous>: no visible global function definition for
  ‘read.csv’
Undefined global functions or variables:
  object.size predict read.csv update weighted.mean
Consider adding
  importFrom("stats", "predict", "update", "weighted.mean")
  importFrom("utils", "object.size", "read.csv")
to your NAMESPACE file.
prepare_Rd: allan-package.Rd:49-51: Dropping empty section \seealso
prepare_Rd: allanVarSelect.Rd:59-60: Dropping empty section \details
prepare_Rd: allanVarSelect.Rd:66-67: Dropping empty section \references
prepare_Rd: allanVarSelect.Rd:78-79: Dropping empty section \seealso
prepare_Rd: fitvbiglm.Rd:38-39: Dropping empty section \details
prepare_Rd: fitvbiglm.Rd:49-50: Dropping empty section \note
prepare_Rd: fitvbiglm.Rd:43-44: Dropping empty section \references
prepare_Rd: fitvbiglm.Rd:53-54: Dropping empty section \seealso
prepare_Rd: getbestchunksize.Rd:35-36: Dropping empty section \details
prepare_Rd: getbestchunksize.Rd:46-47: Dropping empty section \note
prepare_Rd: getbestchunksize.Rd:40-41: Dropping empty section \references
prepare_Rd: getbestchunksize.Rd:50-51: Dropping empty section \seealso
prepare_Rd: predictvbiglm.Rd:44-45: Dropping empty section \details
prepare_Rd: predictvbiglm.Rd:56-57: Dropping empty section \note
prepare_Rd: predictvbiglm.Rd:50-51: Dropping empty section \references
prepare_Rd: predictvbiglm.Rd:60-61: Dropping empty section \seealso
prepare_Rd: readinbigdata.Rd:42-43: Dropping empty section \note
prepare_Rd: readinbigdata.Rd:45-46: Dropping empty section \seealso
Namespaces in Imports field not imported from:
  ‘MASS’ ‘tibble’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
batch.possSpells.fnc: no visible binding for global variable ‘words’
possSpells.fnc: no visible binding for global variable ‘len.phons’
possSpells.fnc: no visible binding for global variable ‘phon1’
possSpells.fnc: no visible binding for global variable ‘len.total’
possSpells.fnc: no visible binding for global variable ‘poss.spells’
Undefined global functions or variables:
  len.phons len.total phon1 poss.spells words
Found the following files/directories:
  ‘more.words.rda’ ‘more.words.txt’ ‘more.words_log.txt’
  ‘other.words.rda’ ‘other.words.txt’ ‘other.words_log.txt’
  ‘some.words.rda’ ‘some.words.txt’ ‘some.words_log.txt’
  ‘yet.more.words.rda’ ‘yet.more.words.txt’ ‘yet.more.words_log.txt’
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Package suggested but not available for checking: ‘rsvg’
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 12.8Mb
  sub-directories of 1Mb or more:
    extdata  12.1Mb
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
Running examples in ‘amber-Ex.R’ failed
The error most likely occurred in:

> ### Name: plotNc
> ### Title: Plots the time-mean of a variable stored in NetCDF model output
> ###   on a regular grid
> ### Aliases: plotNc
> 
> ### ** Examples
> 
> 
> library(amber)
> library(ncdf4)
> library(raster)
Loading required package: sp
> 
> long.name <- 'Gross primary productivity'
> nc.mod <- system.file('extdata/modelRegular', 'gpp_monthly.nc', package = 'amber')
> mod.id <- 'CLASSIC' # define a model experiment ID
> unit.conv.mod <- 86400*1000 # optional unit conversion for model data
> variable.unit <- 'gC m$^{-2}$ day$^{-1}$' # unit after conversion (LaTeX notation)
> timePeriod <- c('1980-01', '2017-12')
> outlier.factor <- 1
> 
> plotNc(long.name, nc.mod, mod.id, unit.conv.mod, variable.unit, timePeriod, outlier.factor)
Warning in .local(x, ...) :
  this does not look like an appropriate object for this function
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: plotNc -> plot -> plot.default -> xy.coords
Execution halted
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    data  15.6Mb
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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.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.
Quitting from lines 49-64 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
EXPR must be a length 1 vector
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘devtools’ ‘gridExtra’
  All declared Imports should be used.
AMOEBA : Classi: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Note: found 2380 marked UTF-8 strings
Found the following files/directories:
  ‘Pindoba_domicilios.dbf’ ‘Pindoba_geo.dbf’
Namespace in Imports field not imported from: ‘kernlab’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shinyjs’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   3.4Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘magrittr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘ssh’
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
Analyz.loadSteps,Analyz: no visible global function definition for
  ‘read.csv’
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Found the following files/directories:
  ‘BH-0.05-ListOfGenes.txt’ ‘BH-0.05-VM-ListOfGenes.txt’
  ‘CompleteListOfGenes.txt’ ‘GenesOutOfAnalysis.txt’
  ‘GenesOutOfAnalysis_NotEnoughObs.txt’
  ‘GenesOutOfAnalysis_NullVar.txt’ ‘VM-CompleteListOfGenes.txt’
  ‘bonferroni-0.05-ListOfGenes.txt’
  ‘bonferroni-0.05-VM-ListOfGenes.txt’
Packages in Depends field not imported from:
  ‘discretization’ ‘foreign’ ‘functional’ ‘stringr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
aode: no visible global function definition for ‘Compose’
mdl: no visible global function definition for ‘cutPoints’
setVar: no visible global function definition for ‘Compose’
Undefined global functions or variables:
  Compose cutPoints
Malformed Description field: should contain one or more complete sentences.
andrews: no visible global function definition for ‘plot.new’
andrews: no visible global function definition for ‘plot.window’
andrews: no visible global function definition for ‘title’
andrews: no visible global function definition for ‘axis’
andrews: no visible global function definition for ‘box’
andrews: no visible global function definition for ‘lines’
andrews: no visible global function definition for ‘rainbow’
andrews: no visible global function definition for ‘hsv’
selectand: no visible global function definition for ‘lines’
Undefined global functions or variables:
  axis box hsv lines plot.new plot.window rainbow title
Consider adding
  importFrom("grDevices", "hsv", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "title")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Found the following files/directories:
  ‘BM-motion-chart.html’ ‘css’ ‘images’ ‘index.html’ ‘js’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   2.9Mb
Namespaces in Imports field not imported from:
  ‘lazyeval’ ‘tibble’
  All declared Imports should be used.
Running examples in ‘animint2-Ex.R’ failed
The error most likely occurred in:

> ### Name: aes
> ### Title: Define aesthetic mappings.
> ### Aliases: aes
> 
> ### ** Examples
> 
> aes(x = mpg, y = wt)
* x -> mpg
* y -> wt
> aes(mpg, wt)
* x -> mpg
* y -> wt
> 
> # You can also map aesthetics to functions of variables
> aes(x = mpg ^ 2, y = wt / cyl)
* x -> mpg^2
* y -> wt/cyl
> 
> # Aesthetic names are automatically standardised
> aes(col = x)
* colour -> x
> aes(fg = x)
* colour -> x
> aes(color = x)
* colour -> x
> aes(colour = x)
* colour -> x
> 
> # aes is almost always used with ggplot() or a layer
> ggplot(mpg, aes(displ, hwy)) + geom_point()
Error in unit(unclass(x), attr(x, "unit"), attr(x, "data")) : 
  Invalid unit
Calls: <Anonymous> ... [ -> [.unit -> upgradeUnit -> upgradeUnit.unit -> unit
Execution halted
Malformed Title field: should not end in a period.
'library' or 'require' call to ‘tcltk’ which was already attached by Depends.
  Please remove these calls from your code.
annot : annotlist: no visible global function definition for
  ‘read.table’
annot : annotlist: no visible global function definition for
  ‘write.table’
annot: no visible global function definition for ‘flush.console’
annot: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  flush.console read.table write.table
Consider adding
  importFrom("utils", "flush.console", "read.table", "write.table")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from ‘anoint’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
Namespaces in Imports field not imported from:
  ‘car’ ‘datasets’ ‘dplyr’ ‘ggplot2’ ‘plotly’ ‘shiny’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DescTools’ ‘HH’ ‘datasets’ ‘dplyr’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    testdata   5.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘antares.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 ‘antares.Rmd’

--- re-building ‘antaresH5.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 38-72 (antaresH5.Rmd) 
Error: processing vignette 'antaresH5.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘antaresH5.Rmd’

SUMMARY: processing the following file failed:
  ‘antaresH5.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘MASS’ ‘evd’
  All declared Imports should be used.
aw_map: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘curl’ ‘httr’
  All declared Imports should be used.
'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.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(aoos)
  > 
  > test_check("aoos")
  ── 1. Failure: Type inheritance (@test-S4-types.R#75)  ─────────────────────────
  inherits(Child(), "Test2") isn't true.
  
  ── 2. Failure: Type with VIRTUAL (@test-S4-types.R#111)  ───────────────────────
  names(Test(x = 2)) == "x" isn't true.
  
  ── 3. Failure: Type with VIRTUAL (@test-S4-types.R#112)  ───────────────────────
  inherits(Test(), "Type") isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 187 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: Type inheritance (@test-S4-types.R#75) 
  2. Failure: Type with VIRTUAL (@test-S4-types.R#111) 
  3. Failure: Type with VIRTUAL (@test-S4-types.R#112) 
  
  Error: testthat unit tests failed
  Execution halted
Malformed Description field: should contain one or more complete sentences.
Found the following files/directories:
  ‘ex.CorTable1.doc’ ‘ex1_anova_table.doc’ ‘ex1_d_table.doc’
  ‘ex1_desc_table.doc’ ‘ex1_ez_independent.doc’ ‘ex2_anova_table.doc’
  ‘ex2_desc_table.doc’ ‘ex2_repeated_table.doc’ ‘ex3_anova_table.doc’
  ‘ex3_desc_table.doc’ ‘ex3_mixed_table.doc’ ‘exInteraction1.doc’
  ‘exInteraction2.doc’ ‘exInteraction3.doc’ ‘exRegBlocksTable.doc’
  ‘exRegTable.doc’
Package suggested but not available for checking: ‘kebabs’
Error(s) in re-building vignettes:
  ...
--- re-building ‘apcluster.Rnw’ using knitr

Attaching package: 'apcluster'

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

    heatmap

Quitting from lines 387-408 (apcluster.Rnw) 
Error: processing vignette 'apcluster.Rnw' failed with diagnostics:
object 'apres2c' not found
--- failed re-building ‘apcluster.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘pls’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
Note: found 230 marked UTF-8 strings
Running ‘testthat.R’ [20s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(apex)
  Loading required package: ape
  Loading required package: phangorn
  > 
  > test_check("apex")
  ── 1. Error: (unknown) (@test_export.R#8)  ─────────────────────────────────────
  subscript out of bounds
  Backtrace:
   1. apex::multidna2genind(x, mlst = TRUE, gapIsNA = TRUE)
   2. adegenet::df2genind(xdfnum, ploidy = 1, ind.names = x@labels)
   3. base::vapply(...)
   4. adegenet:::FUN(X[[i]], ...)
   5. base::rowSums(out[, i, drop = FALSE], na.rm = TRUE)
   6. base::is.data.frame(x)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 1 ]
  1. Error: (unknown) (@test_export.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘apex.Rmd’ using rmarkdown
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 294-299 (apex.Rmd) 
Error: processing vignette 'apex.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘apex.Rmd’

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

Error: Vignette re-building failed.
Execution halted
TSPM: no visible global function definition for ‘glm’
TSPM: no visible binding for global variable ‘poisson’
TSPM: no visible global function definition for ‘hatvalues’
TSPM: no visible global function definition for ‘residuals’
TSPM: no visible global function definition for ‘deviance’
TSPM: no visible global function definition for ‘qchisq’
TSPM: no visible global function definition for ‘qf’
TSPM: no visible global function definition for ‘pf’
TSPM: no visible global function definition for ‘pchisq’
TSPM: no visible global function definition for ‘p.adjust’
norm.inttable: no visible global function definition for ‘median’
norm.inttable : <anonymous>: no visible global function definition for
  ‘quantile’
saint_permF: no visible global function definition for ‘read.table’
saint_permF: no visible global function definition for ‘write.table’
saint_permF: no visible global function definition for ‘write.csv2’
tspm_apms: no visible global function definition for ‘read.table’
varFilter : <anonymous>: no visible global function definition for
  ‘median’
varFilter: no visible global function definition for ‘median’
varFilter: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  deviance glm hatvalues median p.adjust pchisq pf poisson qchisq qf
  quantile read.table residuals write.csv2 write.table
Consider adding
  importFrom("stats", "deviance", "glm", "hatvalues", "median",
             "p.adjust", "pchisq", "pf", "poisson", "qchisq", "qf",
             "quantile", "residuals")
  importFrom("utils", "read.table", "write.csv2", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘1.png’ ‘2.png’ ‘output.png’
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘MASS’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
apple: no visible global function definition for ‘ginv’
apple: no visible global function definition for ‘runif’
deri: no visible global function definition for ‘ginv’
logit: no visible global function definition for ‘qlogis’
plot.apple: no visible global function definition for ‘matplot’
plot.apple: no visible global function definition for ‘lines’
y.app: no visible global function definition for ‘ginv’
Undefined global functions or variables:
  ginv lines matplot qlogis runif
Consider adding
  importFrom("graphics", "lines", "matplot")
  importFrom("stats", "qlogis", "runif")
to your NAMESPACE file.
prepare_Rd: plot.apple.Rd:51-53: Dropping empty section \examples
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
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.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following files/directories:
  ‘APBinary_PPV.csv’ ‘APBinary_TPF.csv’
  ‘APBinary_ap_summary(method=perturbation,B=1500).csv’
  ‘APBinary_auc_summary(method=perturbation,B=1500).csv’
  ‘APSurv_PPV.csv’ ‘APSurv_TPF.csv’
  ‘APSurv_ap_summary(method=bootstrap,B=500).csv’
  ‘APSurv_auc_summary(method=bootstrap,B=500).csv’
  ‘CompareAP_Binary_dap_summary(method=none).csv’
  ‘CompareAP_Survival_dap_summary(method=bootstrap,B=500).csv’
Note: found 1 marked Latin-1 string
Malformed Description field: should contain one or more complete sentences.
aqDayOfWeekStat: no visible global function definition for ‘index’
aqDropHour: no visible global function definition for ‘index’
aqFilterOHLCSD: no visible binding for global variable ‘sd’
aqHourIndex: no visible global function definition for ‘index’
aqHourlyStat: no visible global function definition for ‘index’
aqLoadOHLC: no visible global function definition for ‘read.csv’
aqLoadSeriesField: no visible global function definition for ‘read.csv’
aqLoadXtsFromCsv: no visible global function definition for ‘read.csv2’
aqLoadYahooEOD: no visible global function definition for ‘read.csv’
aqSaveXtsToCsv: no visible global function definition for ‘write.csv2’
aqStoreSeriesField: no visible global function definition for ‘index’
aqStoreSeriesField: no visible global function definition for
  ‘capture.output’
aqStoreSeriesField: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  capture.output index read.csv read.csv2 sd write.csv2 write.table
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "capture.output", "read.csv", "read.csv2",
             "write.csv2", "write.table")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
AR1seg_func: no visible global function definition for ‘median’
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
Found the following files/directories:
  ‘CharacteristicsOfPhase.svg’ ‘Characteristics_Event.2.svg’
  ‘MinMaxPhases.csv’ ‘MultiPhasePlot.png’ ‘MultiSuccessionPlot.svg’
  ‘Succession.png’ ‘data.csv’ ‘fishpond_MCMC.csv’
Note: found 76 marked Latin-1 strings
Package suggested but not available for checking: ‘qCBA’
'library' or 'require' call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
ardec: no visible global function definition for ‘filter’
ardec.lm: no visible global function definition for ‘ar’
ardec.lm: no visible global function definition for ‘lm’
Undefined global functions or variables:
  ar filter lm
Consider adding
  importFrom("stats", "ar", "filter", "lm")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘purrr’ ‘shinyBS’ ‘shinydashboard’ ‘shinyjs’
  All declared Imports should be used.
arfimaOLS: no visible global function definition for ‘lm’
arfimaPrep: no visible global function definition for ‘aggregate’
arfimaPrep: no visible global function definition for ‘arima’
arfimaPrep: no visible global function definition for ‘lm’
arfimaPrep: no visible global function definition for ‘residuals’
Undefined global functions or variables:
  aggregate arima lm residuals
Consider adding
  importFrom("stats", "aggregate", "arima", "lm", "residuals")
to your NAMESPACE file.
Package suggested but not available for checking: ‘MonetDBLite’
Error(s) in re-building vignettes:
  ...
--- re-building ‘arkhe.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]="webshot1b231a4a5b98.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot1b231a4a5b98.png': No such file or directory
Quitting from lines 46-70 (arkhe.Rmd) 
Error: processing vignette 'arkhe.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘arkhe.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Packages suggested but not available for checking: 'oligo', 'pdInfoBuilder'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    help   1.1Mb
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘gmm’ ‘graphics’ ‘sandwich’ ‘stats4’ ‘utils’
  All declared Imports should be used.
binarize.array: no visible binding for global variable ‘sd’
mskmeans: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  kmeans sd
Consider adding
  importFrom("stats", "kmeans", "sd")
to your NAMESPACE file.
Running ‘testthat.R’ [19s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ARTool)
  > 
  > test_check("ARTool")
  ── 1. Failure: anova.art of Higgins1990Table5 matches results of the original AR
  `a` not equal to `ref`.
  Component "Term": 'current' is not a factor
  Component "Error": 'current' is not a factor
  
  ── 2. Failure: anova.art of Higgins1990Table5 matches results of the original AR
  `a` not equal to ref[-2].
  Component "Term": 'current' is not a factor
  
  ── 3. Failure: anova.art of Higgins1990Table1 matches results of the original AR
  `a` not equal to `ref`.
  Component "Term": 'current' is not a factor
  
  ── 4. Failure: anova.art of HigginsABC matches results of the original ARTool (@
  `a` not equal to `ref`.
  Component "Term": 'current' is not a factor
  Component "Error": 'current' is not a factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 108 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: anova.art of Higgins1990Table5 matches results of the original ARTool (@test.anova.art.R#45) 
  2. Failure: anova.art of Higgins1990Table5 matches results of the original ARTool (@test.anova.art.R#50) 
  3. Failure: anova.art of Higgins1990Table1 matches results of the original ARTool (@test.anova.art.R#69) 
  4. Failure: anova.art of HigginsABC matches results of the original ARTool (@test.anova.art.R#89) 
  
  Error: testthat unit tests failed
  Execution halted
Package which this enhances but not available for checking: ‘ARTP’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata   3.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    testdata   4.2Mb
Package suggested but not available for checking: ‘REBayes’
Error(s) in re-building vignettes:
  ...
--- re-building ‘asmapvignette.Rnw’ using knitr
Warning in summary.cross(cross) :
  Some markers at the same position on chr 1B1,1D,2B,2D1,3A,3B,3D,4A,5A,5B,5D,6D,7A,7B,7D; use jittermap().
Warning in summary.cross(cross) :
  Some chromosomes > 1000 cM in length; there may be a problem with the genetic map.
  (Perhaps it is in basepairs?)
Warning in summary.cross(cross) :
  Some markers at the same position on chr L.1,L.2,L.3,L.4,L.5,L.6,L.7,L.8,L.9; use jittermap().
Warning in heatMap(mapBC6, chr = c("L.3", "L.5", "L.8", "L.9"), lmax = 70) :
  Running est.rf.
Warning in summary.cross(cross) :
  Some markers at the same position on chr L.1,L.2,L.3,L.4,L.5,L.6,L.7; use jittermap().
Found the following files/directories:
  ‘MSToutput.txt’
'library' or 'require' calls to packages already attached by Depends:
  ‘Hmisc’ ‘splancs’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Hmisc’ ‘shapefiles’ ‘splancs’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following files/directories:
  ‘BOX_Output.txt’ ‘CF2PTS_Output.txt’ ‘CF_Output.txt’ ‘CMD_Output.txt’
  ‘SDD_Output.txt’ ‘SDE_Output.txt’ ‘mean_centre_Output.txt’
  ‘median_centre_Output.txt’
ASP.Score: no visible global function definition for ‘pnorm’
Graphs.Bayesian: no visible global function definition for ‘dev.new’
colorhex: no visible global function definition for ‘gray’
colorhex: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  dev.new gray pnorm rgb
Consider adding
  importFrom("grDevices", "dev.new", "gray", "rgb")
  importFrom("stats", "pnorm")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘asreml’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc        2.4Mb
    full_doc   2.6Mb
Namespaces in Imports field not imported from:
  ‘arules’ ‘arulesViz’ ‘dplyr’ ‘methods’ ‘plotly’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
Found the following files/directories:
  ‘eigenstrat.result.list’ ‘eigenstrat.result.txt’ ‘eigenstratG.eg.txt’
  ‘pcoc.result.txt’ ‘pcocG.eg.txt’
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CALPHA: no visible global function definition for ‘dbinom’
CALPHA: no visible global function definition for ‘pchisq’
CAST: no visible global function definition for ‘fisher.test’
CAST: no visible global function definition for ‘chisq.test’
CMC: no visible global function definition for ‘pf’
MULTI: no visible global function definition for ‘complete.cases’
RVT1: no visible global function definition for ‘pchisq’
RVT2: no visible global function definition for ‘pchisq’
RWAS: no visible global function definition for ‘pnorm’
SKAT: no visible global function definition for ‘dbeta’
SKAT: no visible global function definition for ‘pchisq’
TTEST: no visible global function definition for ‘complete.cases’
TTEST: no visible global function definition for ‘pf’
WST: no visible global function definition for ‘mvfft’
WST: no visible global function definition for ‘pnorm’
my_cmc_method: no visible global function definition for
  ‘complete.cases’
my_getUV: no visible global function definition for ‘complete.cases’
my_orwss_method: no visible global function definition for ‘sd’
my_rarecov_method: no visible global function definition for
  ‘chisq.test’
my_rbt_method: no visible global function definition for ‘ppois’
my_score_method: no visible global function definition for ‘pchisq’
my_ssu_method: no visible global function definition for ‘pchisq’
my_ssuw_method: no visible global function definition for ‘pchisq’
my_sum_method: no visible global function definition for ‘pchisq’
my_uminp_method: no visible global function definition for ‘pchisq’
my_uminp_method: no visible global function definition for ‘pmvnorm’
Undefined global functions or variables:
  chisq.test complete.cases dbeta dbinom fisher.test mvfft pchisq pf
  pmvnorm pnorm ppois sd
Consider adding
  importFrom("stats", "chisq.test", "complete.cases", "dbeta", "dbinom",
             "fisher.test", "mvfft", "pchisq", "pf", "pnorm", "ppois",
             "sd")
to your NAMESPACE file.
beamDiskOverlap: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
fm_unred: no visible global function definition for ‘spline’
galage: no visible global function definition for ‘integrate’
lumdist: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate spline
Consider adding
  importFrom("stats", "integrate", "spline")
to your NAMESPACE file.
VPC.graph : findQuantile: no visible global function definition for
  ‘quantile’
VPC.graph : findQuantileCI : <anonymous>: no visible global function
  definition for ‘quantile’
asVPC.binW: no visible global function definition for ‘median’
asVPC.binW : <anonymous>: no visible global function definition for
  ‘quantile’
asVPC.binW: no visible global function definition for ‘quantile’
asVPC.distanceW: no visible global function definition for ‘median’
asVPC.distanceW : <anonymous>: no visible global function definition
  for ‘quantile’
asVPC.distanceW: no visible global function definition for ‘quantile’
makeCOVbin: no visible global function definition for ‘quantile’
makeCOVbin: no visible global function definition for ‘median’
read_Simdata: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  median quantile read.table
Consider adding
  importFrom("stats", "median", "quantile")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  ‘cairoDevice’ ‘gWidgetsRGtk2’ ‘partitions’ ‘proto’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
get.est.ATT: no visible global function definition for ‘tail’
get.est.MT: no visible global function definition for ‘tail’
get.est.simple: no visible global function definition for ‘tail’
newton.r: no visible global function definition for ‘tail’
plot.ATE: no visible global function definition for ‘par’
plot.ATE: no visible global function definition for ‘axis’
plot.ATE: no visible global function definition for ‘abline’
plot.ATE: no visible global function definition for ‘lines’
plot.ATE: no visible global function definition for ‘legend’
plot.ATE: no visible global function definition for ‘points’
print.summary.ATE: no visible global function definition for
  ‘printCoefmat’
summary.ATE: no visible global function definition for ‘qnorm’
summary.ATE: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline axis legend lines par pnorm points printCoefmat qnorm tail
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "points")
  importFrom("stats", "pnorm", "printCoefmat", "qnorm")
  importFrom("utils", "tail")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
atmcmc : rmvtnorm: no visible global function definition for ‘rnorm’
atmcmc: no visible global function definition for ‘rnorm’
atmcmc: no visible global function definition for ‘runif’
atmcmc: no visible global function definition for ‘par’
atmcmc: no visible global function definition for ‘lm’
atmcmc: no visible global function definition for ‘lines’
atmcmc: no visible global function definition for ‘var’
atmcmc: no visible global function definition for ‘cov’
atmcmc: no visible global function definition for ‘quantile’
atmcmc: no visible global function definition for ‘sd’
plotmcmc: no visible global function definition for ‘pdf’
plotmcmc: no visible global function definition for ‘par’
plotmcmc: no visible global function definition for ‘dev.new’
plotmcmc: no visible global function definition for ‘png’
plotmcmc: no visible global function definition for ‘hist’
plotmcmc: no visible global function definition for ‘dev.off’
plotmcmc: no visible global function definition for ‘lines’
Undefined global functions or variables:
  cov dev.new dev.off hist lines lm par pdf png quantile rnorm runif sd
  var
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf", "png")
  importFrom("graphics", "hist", "lines", "par")
  importFrom("stats", "cov", "lm", "quantile", "rnorm", "runif", "sd",
             "var")
to your NAMESPACE file.
LHSdesign: no visible global function definition for ‘qnorm’
LHSdesign: no visible global function definition for ‘qunif’
LHSdesign: no visible global function definition for ‘qt’
MCdesign: no visible global function definition for ‘rnorm’
MCdesign: no visible global function definition for ‘runif’
MCdesign: no visible global function definition for ‘rt’
Undefined global functions or variables:
  qnorm qt qunif rnorm rt runif
Consider adding
  importFrom("stats", "qnorm", "qt", "qunif", "rnorm", "rt", "runif")
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.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   9.6Mb
Malformed Title field: should not end in a period.
plot.AUC: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines
Consider adding
  importFrom("graphics", "lines")
to your NAMESPACE file.
AUCRFcv: no visible global function definition for ‘predict’
plot.AUCRF: no visible global function definition for ‘par’
plot.AUCRF: no visible global function definition for ‘dotchart’
plot.AUCRF: no visible global function definition for ‘title’
plot.AUCRF: no visible global function definition for ‘text’
Undefined global functions or variables:
  dotchart par predict text title
Consider adding
  importFrom("graphics", "dotchart", "par", "text", "title")
  importFrom("stats", "predict")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
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.
License components which are templates and need '+ file LICENSE':
  MIT
simulateD: no visible global function definition for ‘rgamma’
simulateT: no visible global function definition for ‘runif’
simulateT: no visible global function definition for ‘rbeta’
simulateT: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  rbeta rbinom rgamma runif
Consider adding
  importFrom("stats", "rbeta", "rbinom", "rgamma", "runif")
to your NAMESPACE file.
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/augmentedRCBD.Rcheck/00install.out’ for details.
Note: found 552 marked UTF-8 strings
Found the following files/directories:
  ‘model.txt’
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘broom’ ‘diptest’ ‘ggplot2’ ‘hexbin’ ‘moments’
  All declared Imports should be used.
Running examples in ‘autocogs-Ex.R’ failed
The error most likely occurred in:

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

$remove
character(0)

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

$remove
[1] "scagnostics"

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

$remove
character(0)

attr(,"class")
[1] "cog_spec"
[1] FALSE
> 
> # set up data
> p <- ggplot2::qplot(Sepal.Length, Sepal.Width, data = iris, geom = c("point", "smooth"))
> dt <- tibble::data_frame(panel = list(p))
Warning: `data_frame()` is deprecated, use `tibble()`.
This warning is displayed once per session.
> 
> # compute cognostics like normal
> add_panel_cogs(dt)
Error in switch(as.character(layer$stat_params$method), loess = "geom_smooth_loess",  : 
  EXPR must be a length 1 vector
Calls: add_panel_cogs ... get_layer_info -> layer_info -> layer_info.ggplot -> lapply -> FUN
Execution halted
Running ‘testthat.R’ [21s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(autocogs)
  > 
  > test_check("autocogs")
  ── 1. Error: ggplot2::geom_smooth (@test-plot_cogs.R#246)  ─────────────────────
  EXPR must be a length 1 vector
  Backtrace:
    1. ggplot2::qplot(cty, hwy, data = mpg, geom = "smooth")
    9. autocogs:::expect_auto_cogs(...)
   11. autocogs:::plot_cogs(.)
   19. autocogs:::get_layer_info(p, keep = keep_layers, ...)
   21. autocogs:::layer_info.ggplot(p, keep = keep, ...)
   22. base::lapply(...)
   23. autocogs:::FUN(X[[i]], ...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 242 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: ggplot2::geom_smooth (@test-plot_cogs.R#246) 
  
  Error: testthat unit tests failed
  Execution halted
'library' or 'require' calls in package code:
  ‘ggplot2’ ‘gpclib’ ‘maptools’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.
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 suggested but not available for checking: ‘BiocInstaller’
Namespace in Imports field not imported from: ‘R.utils’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    java   7.8Mb
installed size is 73.8Mb
  sub-directories of 1Mb or more:
    java  73.8Mb
Namespace in Imports field not imported from: ‘openssl’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘jose’ ‘openssl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
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.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   3.4Mb
Namespace in Imports field not imported from: ‘glpkAPI’
  All declared Imports should be used.
Running examples in ‘BacArena-Ex.R’ failed
The error most likely occurred in:

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

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

Error: Vignette re-building failed.
Execution halted
BACprior.CV: no visible global function definition for ‘na.fail’
BACprior.CV: no visible global function definition for ‘abline’
BACprior.boot: no visible global function definition for ‘na.fail’
BACprior.boot: no visible global function definition for ‘abline’
BACprior.lm: no visible global function definition for ‘na.fail’
BACprior.lm: no visible global function definition for ‘coef’
BACprior.lm: no visible global function definition for ‘vcov’
Undefined global functions or variables:
  abline coef na.fail vcov
Consider adding
  importFrom("graphics", "abline")
  importFrom("stats", "coef", "na.fail", "vcov")
to your NAMESPACE file.
'library' or 'require' call to ‘mvtnorm’ which was already attached by Depends.
  Please remove these calls from your code.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
GNU make is a SystemRequirements.
bagging: no visible global function definition for ‘predict’
samme: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
Running ‘test-all.R’
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(bagRboostR)
  > 
  > test_package("bagRboostR")
  ── 1. Error: bagging returns a character vector of predicted classes (@test_bagg
  no applicable method for 'droplevels' applied to an object of class "character"
  Backtrace:
   1. bagRboostR::bagging(...) tests/test_bagging.R:6:4
   2. base::droplevels(t[, outcome.label])
  
  ── 2. Error: samme returns a character vector of predicted classes (@test_samme.
  no applicable method for 'droplevels' applied to an object of class "character"
  Backtrace:
   1. bagRboostR::samme(activity ~ ., train, test, 3, ntree = 5, trace = F) tests/test_samme.R:6:2
   2. base::droplevels(t[, outcome.label])
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 37 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: bagging returns a character vector of predicted classes (@test_bagging.R#6) 
  2. Error: samme returns a character vector of predicted classes (@test_samme.R#6) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  Placing tests in `inst/tests` is deprecated. Please use `tests/testthat` instead 
  Execution halted
Package suggested but not available for checking: ‘mzR’
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Found the following files/directories:
  ‘exemplary_input1.txt’ ‘exemplary_input2.txt’
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘docopt’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘ranger’
  All declared Imports should be used.
Note: found 148 marked UTF-8 strings
Package suggested but not available for checking: ‘ArrayExpress’
extractAffybatch: no visible global function definition for ‘new’
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' calls to packages already attached by Depends:
  ‘grid’ ‘lattice’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘grid’ ‘lattice’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
barcode: no visible global function definition for ‘unit’
barcode: no visible global function definition for ‘grid.newpage’
barcode: no visible global function definition for ‘grid.text’
barcode: no visible global function definition for ‘gpar’
barcode: no visible global function definition for ‘pushViewport’
barcode: no visible global function definition for ‘viewport’
barcode: no visible global function definition for ‘convertHeight’
barcode: no visible global function definition for ‘convertWidth’
barcode: no visible global function definition for ‘grid.rect’
barcode: no visible global function definition for ‘popViewport’
barcode.panel: no visible global function definition for ‘unit’
barcode.panel: no visible global function definition for ‘hist’
barcode.panel: no visible global function definition for ‘pushViewport’
barcode.panel: no visible global function definition for ‘viewport’
barcode.panel: no visible global function definition for ‘grid.xaxis’
barcode.panel: no visible global function definition for ‘gpar’
barcode.panel: no visible global function definition for ‘grid.text’
barcode.panel: no visible global function definition for ‘popViewport’
barcode.panel: no visible global function definition for
  ‘grid.segments’
barcode.panel: no visible global function definition for ‘grid.points’
Undefined global functions or variables:
  convertHeight convertWidth gpar grid.newpage grid.points grid.rect
  grid.segments grid.text grid.xaxis hist popViewport pushViewport unit
  viewport
Consider adding
  importFrom("graphics", "hist")
to your NAMESPACE file.
Found the following files/directories:
  ‘bbsi_tmp.RData’
Namespace in Imports field not imported from: ‘mvnfast’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.1Mb
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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘article2-vignette.Rnw’ using knitr
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-8'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
'library' or 'require' call to ‘hwriter’ which was already attached by Depends.
  Please remove these calls from your code.
prepare_Rd: mkhtml.Rd:31-33: Dropping empty section \details
prepare_Rd: mkhtml.Rd:43-45: Dropping empty section \note
prepare_Rd: mkhtml.Rd:40-42: Dropping empty section \author
prepare_Rd: mkhtml.Rd:37-39: Dropping empty section \references
prepare_Rd: mkhtml.Rd:49-51: Dropping empty section \seealso
Found the following files/directories:
  ‘sample.html’ ‘sample.png’
Running ‘testthat.R’ [72s/109s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # setting R_TESTS to empty string because of
  > # https://github.com/hadley/testthat/issues/144
  > # revert this when that issue in R is fixed.
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(batchtools)
  > 
  > test_check("batchtools")
  ### [bt]: Setting seed to 2767 ...
  ── 1. Failure: addExperiments / user provided designs (@test_addExperiments.R#64
  `addExperiments(reg = reg, prob.designs = pd)` did not produce any warnings.
  
  ── 2. Failure: addExperiments / user provided designs (@test_addExperiments.R#67
  `addExperiments(reg = reg, prob.designs = pd)` did not produce any warnings.
  
  ### [bt]: Setting seed to 3080 ...
  ### [bt]: Setting seed to 3082 ...
  ### [bt]: Setting seed to 3081 ...
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1444 | SKIPPED: 11 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: addExperiments / user provided designs (@test_addExperiments.R#64) 
  2. Failure: addExperiments / user provided designs (@test_addExperiments.R#67) 
  
  Error: testthat unit tests failed
  Execution halted
Note: found 19 marked UTF-8 strings
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   4.8Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘msm’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MatrixModels’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   5.5Mb
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.
Namespaces in Imports field not imported from:
  ‘shinytest’ ‘testthat’
  All declared Imports should be used.
Found the following sources/headers not terminated with a newline:
  inst/include/bayeslm.h
Some compilers warn on such files.
GNU make is a SystemRequirements.
Namespace in Imports field not imported from: ‘FastGP’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.0Mb
    libs   1.8Mb
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  7.0Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   4.2Mb
Namespaces in Imports field not imported from:
  ‘HDInterval’ ‘carData’ ‘runjags’
  All declared Imports should be used.
Running ‘testthat.R’ [21s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BayesPostEst)
  > 
  > test_check("BayesPostEst")
  ── 1. Failure: pars subsetting works (@test_mcmcTab.R#61)  ─────────────────────
  object$Variable not equal to factor(c(sprintf("b[%s]", 1:3))).
  Types not compatible: character is not integer
  
  ── 2. Failure: pars subsetting works (@test_mcmcTab.R#83)  ─────────────────────
  object$Variable not equal to factor(c(sprintf("b[%s]", 1:2))).
  Types not compatible: character is not integer
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 52 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: pars subsetting works (@test_mcmcTab.R#61) 
  2. Failure: pars subsetting works (@test_mcmcTab.R#83) 
  
  Error: testthat unit tests failed
  Execution halted
MHratioPopPref: no visible global function definition for ‘runif’
MratioPopMult: no visible global function definition for ‘dunif’
MratioPopMult: no visible global function definition for ‘runif’
bayesPref: no visible global function definition for ‘runif’
calcP: no visible global function definition for ‘dunif’
calcP: no visible global function definition for ‘dmultinom’
calcdic: no visible global function definition for ‘median’
calcdic: no visible binding for global variable ‘median’
calcdic: no visible global function definition for ‘dmultinom’
calcdicExtern: no visible global function definition for ‘median’
calcdicExtern: no visible global function definition for ‘dmultinom’
calcdicExtern: no visible binding for global variable ‘median’
credibleIntervals: no visible global function definition for ‘quantile’
prefPlot: no visible global function definition for ‘postscript’
prefPlot: no visible global function definition for ‘lines’
prefPlot: no visible global function definition for ‘density’
prefPlot: no visible global function definition for ‘median’
prefPlot: no visible global function definition for ‘legend’
prefPlot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  density dev.off dmultinom dunif legend lines median postscript
  quantile runif
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "density", "dmultinom", "dunif", "median",
             "quantile", "runif")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘MASS’ ‘combinat’ ‘gplots’ ‘mnormt’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bayes.regress: no visible binding for global variable ‘var’
bayesregressB1S1: no visible global function definition for ‘rgamma’
bayesregressB1S2: no visible global function definition for ‘rgamma’
bayesregressB2S1: no visible global function definition for ‘rgamma’
bayesregressB2S2: no visible global function definition for ‘rgamma’
bayesregressB3S1: no visible global function definition for ‘rWishart’
bayesregressB3S1: no visible global function definition for ‘rgamma’
bayesregressB3S2: no visible global function definition for ‘rWishart’
bayesregressB3S2: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  rWishart rgamma var
Consider adding
  importFrom("stats", "rWishart", "rgamma", "var")
to your NAMESPACE file.
validate: no visible binding for global variable ‘qnorm’
validate: no visible global function definition for ‘pchisq’
validate: no visible global function definition for ‘qnorm’
validate: no visible global function definition for ‘axis’
validate: no visible global function definition for ‘points’
validate: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline axis pchisq points qnorm
Consider adding
  importFrom("graphics", "abline", "axis", "points")
  importFrom("stats", "pchisq", "qnorm")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    libs  20.3Mb
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.
Found the following files/directories:
  ‘diagnostics.pdf’ ‘post.rda’
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘mvnmle’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
BilogData: no visible global function definition for ‘write.table’
CohensD.rawData: no visible global function definition for ‘var’
EtaSq: no visible global function definition for ‘summary.aov’
HedgesG.rawData: no visible global function definition for ‘var’
LittleMCAR: no visible global function definition for ‘mlest’
LittleMCAR: no visible global function definition for ‘pchisq’
PseudoR2: no visible global function definition for ‘predict’
Undefined global functions or variables:
  mlest pchisq predict summary.aov var write.table
Consider adding
  importFrom("stats", "pchisq", "predict", "summary.aov", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘Test5.dat’ ‘mydata.dat’
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.
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘matrixStats’ ‘reshape2’ ‘scales’
  All declared Imports should be used.
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.
Found the following files/directories:
  ‘_saveDF’ ‘dataCensored.test.rda’ ‘dataCensored_TEST.csv’
Package in Depends field not imported from: ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Malformed Description field: should contain one or more complete sentences.
LaplaceMetropolis_admkr: no visible binding for global variable
  ‘median’
LaplaceMetropolis_admkr: no visible global function definition for
  ‘mad’
LaplaceMetropolis_gaussian: no visible binding for global variable
  ‘median’
LaplaceMetropolis_gaussian: no visible global function definition for
  ‘mad’
cost_admkr: no visible global function definition for ‘sd’
cov_chol: no visible global function definition for ‘qchisq’
cov_chol_admkr: no visible global function definition for ‘qchisq’
gibbs_admkr_erro: no visible global function definition for ‘rnorm’
gibbs_admkr_erro: no visible global function definition for ‘runif’
gibbs_admkr_nw: no visible global function definition for ‘qnorm’
gibbs_admkr_nw: no visible global function definition for ‘rnorm’
gibbs_admkr_nw: no visible global function definition for ‘runif’
loglikelihood_admkr: no visible global function definition for ‘sd’
margin_like_admkr: no visible global function definition for ‘sd’
np_gibbs: no visible global function definition for ‘qnorm’
np_gibbs: no visible global function definition for ‘rnorm’
np_gibbs: no visible global function definition for ‘runif’
np_gibbs: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  mad median qchisq qnorm rgamma rnorm runif sd
Consider adding
  importFrom("stats", "mad", "median", "qchisq", "qnorm", "rgamma",
             "rnorm", "runif", "sd")
to your NAMESPACE file.
bbmm.contour: no visible global function definition for ‘na.omit’
bbmm.contour: no visible global function definition for ‘optimize’
bbmm.contour: no visible global function definition for ‘contour’
bbmm.contour: no visible global function definition for ‘points’
bbmm.contour: no visible global function definition for ‘lines’
brownian.bridge: no visible global function definition for ‘sd’
brownian.motion.variance: no visible global function definition for
  ‘optimize’
Undefined global functions or variables:
  contour lines na.omit optimize points sd
Consider adding
  importFrom("graphics", "contour", "lines", "points")
  importFrom("stats", "na.omit", "optimize", "sd")
to your NAMESPACE file.
bbo: no visible global function definition for ‘runif’
bbo: no visible global function definition for ‘tail’
Undefined global functions or variables:
  runif tail
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "tail")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘locfit’ ‘secr’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘rgl’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following files/directories:
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_31_p_4026_nfsel_50_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_20_biascor_1.RData’
  ‘.fitbcbcsf_alpha1_mu_3_n_53_p_4026_nfsel_50_biascor_1.RData’
Found the following files/directories:
  ‘fabiabreast.txt’
Package suggested but not available for checking: ‘INLA’
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.
Running ‘testthat.R’ [24s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bcgam)
  Loading required package: nimble
  nimble version 0.9.0 is loaded.
  For more information on NIMBLE and a User Manual,
  please visit http://R-nimble.org.
  
  Attaching package: 'nimble'
  
  The following object is masked from 'package:stats':
  
      simulate
  
  > 
  > test_check("bcgam")
  thin = 1: tau, betalpha, sigma, eta
  ── 1. Error: (unknown) (@testthat.R#3)  ────────────────────────────────────────
  Failed to create the shared library.
  Backtrace:
   1. bcgam::bcgam(...)
   2. bcgam:::bcgam.fit(...)
   3. nimble::compileNimble(gaus)
   4. project$compileModel(units[[i]], control = control, showCompilerOutput = showCompilerOutput)
   5. cppProj$compileFile(compileList, showCompilerOutput)
   6. nimble:::compileDynamicRegistrations(showCompilerOutput = showCompilerOutput)
   7. nimble:::compileStaticCode(dllName, cppName, showCompilerOutput)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: (unknown) (@testthat.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘coda’ ‘knitr’ ‘plyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Bclim.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Package suggested but not available for checking: ‘bcmapsdata’
bcpmeta.model: no visible global function definition for ‘rbinom’
bcpmeta.model: no visible global function definition for ‘runif’
bcpmeta.parameters: no visible global function definition for ‘runif’
cp.plot: no visible global function definition for ‘postscript’
cp.plot: no visible global function definition for ‘lines’
cp.plot: no visible global function definition for ‘axis’
cp.plot: no visible global function definition for ‘box’
cp.plot: no visible global function definition for ‘points’
cp.plot: no visible global function definition for ‘dev.off’
lMarLik.EB.normAR: no visible global function definition for ‘optimize’
lMarLik.normAR: no visible global function definition for ‘integrate’
marginal.plot: no visible global function definition for ‘postscript’
marginal.plot: no visible global function definition for ‘axis’
marginal.plot: no visible global function definition for ‘box’
marginal.plot: no visible global function definition for ‘points’
marginal.plot: no visible global function definition for ‘dev.off’
simgen: no visible global function definition for ‘rnorm’
up.eta.MH.normAR: no visible global function definition for ‘runif’
up.eta.RS.normAR: no visible global function definition for ‘runif’
up.parameters.EB.normAR: no visible global function definition for
  ‘rnorm’
up.parameters.normAR: no visible global function definition for ‘rnorm’
up.parameters.normAR: no visible global function definition for ‘runif’
up.parameters.normAR: no visible global function definition for
  ‘rgamma’
Undefined global functions or variables:
  axis box dev.off integrate lines optimize points postscript rbinom
  rgamma rnorm runif
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "axis", "box", "lines", "points")
  importFrom("stats", "integrate", "optimize", "rbinom", "rgamma",
             "rnorm", "runif")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.7Mb
Found the following files/directories:
  ‘Example_Lorenz-curve.pdf’
Package suggested but not available for checking: ‘BRugs’
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rlang’
  All declared Imports should be used.
plot.cvsvd: no visible binding for global variable ‘sd’
plot.cvsvd: no visible global function definition for ‘lines’
plot.cvsvd: no visible global function definition for ‘segments’
plot.cvsvd: no visible global function definition for ‘points’
print.cvsvd: no visible binding for global variable ‘sd’
summary.cvsvd: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  lines points sd segments
Consider adding
  importFrom("graphics", "lines", "points", "segments")
  importFrom("stats", "sd")
to your NAMESPACE file.
Note: found 72 marked UTF-8 strings
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
mise: no visible global function definition for ‘integrate’
density,BrVitale : density.vitale : <anonymous>: no visible global
  function definition for ‘dbeta’
density,Chen99Kernel : <anonymous>: no visible global function
  definition for ‘dbeta’
density,HirukawaJLNKernel : <anonymous>: no visible global function
  definition for ‘dbeta’
density,MicroBetaChen99Kernel : <anonymous>: no visible global function
  definition for ‘dbeta’
density,Vitale : <anonymous>: no visible global function definition for
  ‘dbeta’
distribution,BernsteinPolynomials : <anonymous>: no visible global
  function definition for ‘integrate’
distribution,KernelDensity : <anonymous>: no visible global function
  definition for ‘integrate’
print,BoundedDensity: no visible global function definition for ‘str’
print,KernelDensity: no visible global function definition for ‘str’
rsample,BoundedDensity: no visible global function definition for
  ‘runif’
setNormalizationConst,MacroBetaChen99Kernel: no visible global function
  definition for ‘integrate’
setNormalizationConst,MacroBetaHirukawaTSKernel: no visible global
  function definition for ‘integrate’
setNormalizationConstant,MacroBetaHirukawaJLNKernel: no visible global
  function definition for ‘integrate’
setNormalizationConstants,MicroBetaChen99Kernel :
  density.kernelFunction: no visible global function definition for
  ‘dbeta’
setNormalizationConstants,MicroBetaChen99Kernel : <anonymous>: no
  visible global function definition for ‘integrate’
show,BoundedDensity: no visible global function definition for ‘str’
show,KernelDensity: no visible global function definition for ‘str’
Undefined global functions or variables:
  dbeta integrate runif str
Consider adding
  importFrom("stats", "dbeta", "integrate", "runif")
  importFrom("utils", "str")
to your NAMESPACE file.
Found the following files/directories:
  ‘dump.txt’
Package suggested but not available for checking: ‘rinat’
Found the following files/directories:
  ‘bferrbars.eps’ ‘dataplot.eps’ ‘ppdat.eps’ ‘ppmod.eps’
Package suggested but not available for checking: ‘lumi’
Packages in Depends field not imported from:
  ‘RColorBrewer’ ‘beadarray’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
beadtypeFilter: no visible global function definition for ‘na.omit’
beadtypeFilter: no visible global function definition for ‘exprs’
beadtypeFilter: no visible global function definition for ‘se.exprs’
beadtypeFilter: no visible global function definition for ‘beadNum’
beadtypeFilter: no visible global function definition for ‘fData’
emCDF: no visible global function definition for ‘brewer.pal’
emCDF: no visible global function definition for ‘ecdf’
emCDF: no visible global function definition for ‘legend’
emCDF: no visible global function definition for ‘lines’
emCDF: no visible global function definition for ‘text’
emCDF: no visible global function definition for ‘reshape’
iccFun : <anonymous>: no visible global function definition for
  ‘quantile’
varianceplot: no visible global function definition for ‘reshape’
varianceplot: no visible global function definition for ‘points’
varianceplot: no visible global function definition for ‘legend’
Undefined global functions or variables:
  beadNum brewer.pal ecdf exprs fData legend lines na.omit points
  quantile reshape se.exprs text
Consider adding
  importFrom("graphics", "legend", "lines", "points", "text")
  importFrom("stats", "ecdf", "na.omit", "quantile", "reshape")
to your NAMESPACE file.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘chron’ ‘colorspace’ ‘gtable’ ‘htmltools’ ‘htmlwidgets’
  ‘httpuv’ ‘magrittr’ ‘munsell’ ‘plyr’ ‘scales’ ‘stringi’ ‘xtable’
  ‘yaml’
  All declared Imports should be used.
Found the following files/directories:
  ‘beast_plot_toy.pdf’
Package suggested but not available for checking: ‘gifski’
Found the following files/directories:
  ‘example_Initial.parameters.Robj’ ‘example_MCMC_output1.Robj’
Found the following files/directories:
  ‘alist.txt’ ‘rpkg’
Package suggested but not available for checking: ‘rsvg’
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘png’
  All declared Imports should be used.
Found the following files/directories:
  ‘temp.csv’
Namespace in Imports field not imported from: ‘compiler’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘dplyr’ ‘ggplot2’ ‘readxl’ ‘rlist’ ‘shinyBS’ ‘shinyWidgets’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
Note: found 20 marked UTF-8 strings
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’.
Found the following files/directories:
  ‘vert.txt’ ‘vert_1.txt’ ‘vert_2.txt’
Malformed Title field: should not end in a period.
Found the following files/directories:
  ‘BGData_chr1’
block.gibbs: no visible global function definition for ‘rmultinom’
rdirichlet: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  rgamma rmultinom
Consider adding
  importFrom("stats", "rgamma", "rmultinom")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
global: no visible global function definition for ‘par’
global: no visible global function definition for ‘runif’
global: no visible global function definition for ‘cov’
mymcmc: no visible global function definition for ‘par’
mymcmc: no visible global function definition for ‘rnorm’
mymcmc: no visible global function definition for ‘runif’
mymcmc: no visible global function definition for ‘cov’
mymcmc: no visible global function definition for ‘lines’
plkhci: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  cov lines par qchisq rnorm runif
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "cov", "qchisq", "rnorm", "runif")
to your NAMESPACE file.
installed size is 124.9Mb
  sub-directories of 1Mb or more:
    include  124.9Mb
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.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    1.9Mb
Namespace in Imports field not imported from: ‘nycflights13’
  All declared Imports should be used.
Found the following files/directories:
  ‘BiDimRegrOutput.txt’
Running examples in ‘bigchess-Ex.R’ failed
The error most likely occurred in:

> ### Name: browse_opening
> ### Title: Browse opening
> ### Aliases: browse_opening
> 
> ### ** Examples
> 
> f <- system.file("extdata", "Kasparov.gz", package = "bigchess")
> con <- gzfile(f,encoding = "latin1")
> df <- read.pgn(con,quiet = TRUE,ignore.other.games = TRUE,stat.moves = FALSE)
> # Analyze best Kasparov openings:
> bo <- browse_opening(subset(df,grepl("Kasparov",White)))
Error in UseMethod("droplevels") : 
  no applicable method for 'droplevels' applied to an object of class "character"
Calls: browse_opening -> tree_move -> droplevels
Execution halted
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  ‘DBI’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Call with DUP:
   .Fortran("regcf", as.integer(p), as.integer(p * p/2), bigQR$D, 
       bigQR$rbar, bigQR$thetab, bigQR$tol, beta = numeric(p), nreq = as.integer(nvar), 
       ier = integer(1), DUP = FALSE)
DUP is no longer supported and will be ignored.
bigglm.RODBC: no visible global function definition for ‘odbcQuery’
bigglm.RODBC : chunk: no visible global function definition for
  ‘odbcQuery’
bigglm.RODBC : chunk: no visible global function definition for
  ‘sqlGetResults’
bigglm,ANY-DBIConnection: no visible global function definition for
  ‘dbSendQuery’
bigglm,ANY-DBIConnection: no visible global function definition for
  ‘dbClearResult’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘dbClearResult’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘dbSendQuery’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘fetch’
Undefined global functions or variables:
  dbClearResult dbSendQuery fetch odbcQuery sqlGetResults
Error(s) in re-building vignettes:
  ...
--- re-building ‘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.
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Removed 199 rows containing non-finite values (stat_contour).
Warning in normalizePath(f2) :
  path[1]="webshot36192de4494c.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot36192de4494c.png': No such file or directory
Quitting from lines 245-248 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘analysis.Rmd’

--- re-building ‘methodology.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 ‘methodology.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       3.1Mb
    extdata   2.5Mb
GNU make is a SystemRequirements.
Checking should be performed on sources prepared by ‘R CMD build’.
Found the following files/directories:
  ‘outputs’
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Running examples in ‘bigsnpr-Ex.R’ failed
The error most likely occurred in:

> ### Name: bed_tcrossprodSelf
> ### Title: Tcrossprod
> ### Aliases: bed_tcrossprodSelf
> 
> ### ** Examples
> 
> bedfile <- system.file("extdata", "example.bed", package = "bigsnpr")
> obj.bed <- bed(bedfile)
> 
> K <- bed_tcrossprodSelf(obj.bed)

 *** caught segfault ***
address f7c83000, cause 'invalid permissions'

Traceback:
 1: incr_FBM_mat(X, add)
 2: big_increment(K, tcrossprod(tmp))
 3: bed_tcrossprodSelf(obj.bed)
An irrecoverable exception occurred. R is aborting now ...
Namespaces in Imports field not imported from:
  ‘MASS’ ‘lattice’ ‘zoo’
  All declared Imports should be used.
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.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
plot,bild-missing: no visible global function definition for
  ‘dev.interactive’
plot,bild-missing: no visible global function definition for
  ‘devAskNewPage’
plot,bild-missing: no visible global function definition for
  ‘extendrange’
Undefined global functions or variables:
  dev.interactive devAskNewPage extendrange
Consider adding
  importFrom("grDevices", "dev.interactive", "devAskNewPage",
             "extendrange")
to your NAMESPACE file.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Note: found 660 marked UTF-8 strings
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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘bimets.Rnw’ using Sweave
Loading required package: xts
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

 
bimets is active - version 1.4.2
For help type '?bimets'


Error: processing vignette 'bimets.Rnw' failed with diagnostics:
 chunk 19 
Error in value[[3L]](cond) : 
  LOAD_MODEL(): error while building incidence vector for behavioral cn. .getIncidenceVendogs(): inputs need to be strings

--- failed re-building ‘bimets.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘ccf_ccf_ID31_ID32_res.jpg’ ‘ccf_ccf_ID31_ID32_res.pdf’
  ‘output_ENSO_NHSST.tmp’ ‘plot_plot_ts_RAW_BIN_enso_sst.pdf’
  ‘plot_plot_ts_RAW_BIN_enso_sst01.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst02.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst03.png’
  ‘plot_plot_ts_RAW_BIN_enso_sst04.png’ ‘plot_ts_ACER_ABRUPT.pdf’
  ‘plot_ts_ACER_ABRUPT01.png’ ‘plot_ts_ACER_ABRUPT02.png’
  ‘plot_ts_ACER_ABRUPT03.png’ ‘plot_ts_ACER_ABRUPT04.png’
  ‘salida_ACER_ABRUPT.tmp’ ‘scaterplot_scatterplot_ENSO_SST.jpg’
  ‘scaterplot_scatterplot_ENSO_SST.pdf’
commonprob2sigma: no visible global function definition for ‘approxfun’
rmvbin: no visible global function definition for ‘qnorm’
simul.commonprob: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  approxfun qnorm
Consider adding
  importFrom("stats", "approxfun", "qnorm")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
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.
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("binomialMix")
  Loading required package: binomialMix
  ── 1. Error: beta is correctly initialized (@test-init-beta.R#20)  ─────────────
  missing value where TRUE/FALSE needed
  Backtrace:
   1. testthat::expect_is(init_subset(input, 3, "group_num"), "list")
   4. binomialMix::init_subset(input, 3, "group_num")
  
  ── 2. Error: design matrices are correctly initialized (@test-init_design_matric
  missing value where TRUE/FALSE needed
  Backtrace:
   1. testthat::expect_is(...)
   4. binomialMix::init_design_matrices(mod_form, input, "group_num")
  
  ── 3. Error: tau is correctly initialized (@test-init_tau.R#16)  ───────────────
  missing value where TRUE/FALSE needed
  Backtrace:
   1. testthat::expect_is(init_tau(input, 3, "group_num"), "matrix")
   4. binomialMix::init_tau(input, 3, "group_num")
  
  ── 4. Error: Test the good input/output of the log density  ────────────────────
  subscript out of bounds
  Backtrace:
   1. stats::model.frame(...)
   2. stats::model.frame.default(...)
   3. base::is.data.frame(data)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 16 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 4 ]
  1. Error: beta is correctly initialized (@test-init-beta.R#20) 
  2. Error: design matrices are correctly initialized (@test-init_design_matrices.R#21) 
  3. Error: tau is correctly initialized (@test-init_tau.R#16) 
  4. Error: Test the good input/output of the log density 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘methods’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-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: correlbinom
Loading required package: Rmpfr
Loading required package: gmp

Attaching package: 'gmp'

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

    %*%, apply, crossprod, matrix, tcrossprod

C code of R package 'Rmpfr': GMP using 32 bits per limb


Attaching package: 'Rmpfr'

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

    outer

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

    dbinom, dgamma, dnorm, dpois, pnorm

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

    cbind, pmax, pmin, rbind

Quitting from lines 107-113 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
The melt generic in data.table has been passed a data.frame, but data.table::melt currently only has a method for data.tables. Please confirm your input is a data.table, with setDT(rc.main.effects) or as.data.table(rc.main.effects). If you intend to use a method from reshape2, try installing that package first, but do note that reshape2 is deprecated and you should be migrating your code away from using it.
--- failed re-building ‘my-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
bins.quantiles: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Package suggested but not available for checking: ‘msa’
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘BioCircos.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 64-67 (BioCircos.Rmd) 
Error: processing vignette 'BioCircos.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘BioCircos.Rmd’

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

Error: Vignette re-building failed.
Execution halted
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
   use the Contact field instead
Found the following files/directories:
  ‘Plots.pdf’
Found the following files/directories:
  ‘pointshape.dbf’ ‘pointshape.shp’ ‘pointshape.shx’
Running examples in ‘biogram-Ex.R’ failed
The error most likely occurred in:

> ### Name: calc_si
> ### Title: Compute similarity index
> ### Aliases: calc_si
> 
> ### ** Examples
> 
> # example from Stephenson & Freeland, 2013 (Fig. 6)
> enc1 <- list(`1` = "A",
+              `2` = c("F", "E"),
+              `3` = c("C", "D", "G"))
> 
> enc2 <- list(`1` = c("A", "G"),
+              `2` = c("C", "D", "E", "F"))
> 
> enc3 <- list(`1` = c("D", "G"),
+              `2` = c("E", "F"),
+              `3` = c("A", "C"))
>              
> calc_si(enc1, enc2)
Error in order(levels(res[["element"]])) : argument 1 is not a vector
Calls: calc_si ... encoding2matrix -> encoding2df -> [ -> [.data.frame -> order
Execution halted
Found the following files/directories:
  ‘sum.otu.txt’
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    extdata   7.8Mb
Found the following files/directories:
  ‘GRCh37_MT_ensGene.txt’
Namespace in Imports field not imported from: ‘fs’
  All declared Imports should be used.
Package suggested but not available for checking: ‘ecospat’
Unknown package ‘ecospat’ in Rd xrefs
Found the following files/directories:
  ‘GuloGulo’
'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  6.0Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    doc       1.4Mb
    extdata   1.7Mb
Running examples in ‘bioRad-Ex.R’ failed
The error most likely occurred in:

> ### Name: beam_profile_overlap
> ### Title: Calculate overlap between a vertical profile ('vp') of
> ###   biological scatterers and the vertical radiation profile emitted by
> ###   the radar
> ### Aliases: beam_profile_overlap
> 
> ### ** Examples
> 
> # locate example volume file:
> pvolfile <- system.file("extdata", "volume.h5", package = "bioRad")
> 
> # load the example polar volume file:
> pvol <- read_pvolfile(pvolfile)
Error in H5Fopen(file, "H5F_ACC_RDONLY", native = native) : 
  HDF5. File accessibilty. Unable to open file.
Calls: read_pvolfile ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bioRad.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building ‘bioRad.Rmd’

--- re-building ‘rad_aero_19.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Welcome to bioRad version 0.5.0
Warning: Docker daemon not found
Warning: bioRad functionality requiring Docker has been disabled

To enable Docker functionality, first install Docker
--- finished re-building ‘rad_aero_19.Rmd’

--- re-building ‘range_correction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 63-70 (range_correction.Rmd) 
Error: processing vignette 'range_correction.Rmd' failed with diagnostics:
HDF5. File accessibilty. Unable to open file.
--- failed re-building ‘range_correction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘bios2mds-Ex.R’ failed
The error most likely occurred in:

> ### Name: bios2mds-package
> ### Title: From BIOlogical Sequences to MultiDimensional Scaling
> ### Aliases: bios2mds-package bios2mds
> ### Keywords: package
> 
> ### ** Examples
> 
> # The MSA files provided with the package correspond to the sequence 
> # alignment of non-olfactory class A G-protein-coupled receptors from
> # H. sapiens and D. melanogaster prepared by Deville et al. (2009).  
> 
> # loading GPCR data
> data(gpcr)
> 
> # building distance matrices between the aligned GPCR sequences from
> # H. sapiens and D. melanogaster
> human <- import.fasta(system.file("msa/human_gpcr.fa", package = "bios2mds"))
> drome <- import.fasta(system.file("msa/drome_gpcr.fa", package = "bios2mds"))
> 
> #active <- mat.dif(human, human)
> # or
> active <- gpcr$dif$sapiens.sapiens
> 
> #sup <- mat.dif(drome, human)
> # or
> sup <- gpcr$dif$melanogaster.sapiens
> 
> # performing MDS analysis of the GPCR sequences from H. sapiens 
> mmds_active <- mmds(active, group.file=system.file(
+ "csv/human_gpcr_group.csv",package = "bios2mds"))
Error in rbind(col, matrix(c(names[i], levels(element[, 2])[element[j,  : 
  number of columns of matrices must match (see arg 2)
Calls: mmds -> col.group -> rbind
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Found the following files/directories:
  ‘JSBP.css’ ‘JSBP.js’ ‘vizjs.js’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    help   2.2Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BisqueRNA)
  > 
  > test_check("BisqueRNA")
  ── 1. Error: Catches data where zero variance in training data (@test_ref_based.
  incorrect number of dimensions
  Backtrace:
   1. testthat::expect_equal(...)
   4. BisqueRNA::ReferenceBasedDecomposition(bulk.eset, sc.eset, use.overlap = F)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 49 | SKIPPED: 0 | WARNINGS: 9 | FAILED: 1 ]
  1. Error: Catches data where zero variance in training data (@test_ref_based.R#125) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘IHW’
Namespaces in Imports field not imported from:
  ‘corrgram’ ‘rpivotTable’ ‘shinyAce’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
bivarcalcn: no visible global function definition for ‘qnorm’
bivarcalcn: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
prepare_Rd: bivarcalcn.Rd:49-50: Dropping empty section \details
prepare_Rd: bivarcalcn.Rd:59-61: Dropping empty section \note
prepare_Rd: bivarcalcn.Rd:65-67: Dropping empty section \seealso
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
biwt.cor: no visible global function definition for ‘covMcd’
biwt.cor: no visible binding for global variable ‘mad’
biwt.est: no visible global function definition for ‘covMcd’
biwt.est: no visible global function definition for ‘mahalanobis’
chi.int: no visible global function definition for ‘pchisq’
chi.int.p: no visible global function definition for ‘dchisq’
chi.int2: no visible global function definition for ‘pchisq’
chi.int2.p: no visible global function definition for ‘dchisq’
rejpt.bw: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  covMcd dchisq mad mahalanobis pchisq
Consider adding
  importFrom("stats", "dchisq", "mad", "mahalanobis", "pchisq")
to your NAMESPACE file.
Package suggested but not available for checking: ‘RQuantLib’
Namespaces in Imports field not imported from:
  ‘R6’ ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RGtk2’ ‘cairoDevice’ ‘ergm’ ‘foreign’ ‘gWidgets’ ‘gWidgetsRGtk2’
  ‘haven’ ‘plot3D’ ‘plot3Drgl’ ‘rgl’ ‘sna’ ‘statnet.common’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Package suggested but not available for checking: ‘bigrf’
Invalid maximum heap size: -Xmx4G
The specified size exceeds the maximum representable size.
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘gtools’ ‘knitr’ ‘nnet’ ‘parallel’ ‘rJava’ ‘reshape’
  ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
Missing or unexported object: ‘xgboost::predict’
bglmer: no visible global function definition for ‘packageVersion’
getBglmerDevianceFunctionBody: no visible global function definition
  for ‘packageVersion’
getParInfo : <anonymous>: no visible global function definition for
  ‘sd’
makeRefitDevFun: no visible global function definition for
  ‘packageVersion’
mkBglmerDevfun: no visible global function definition for
  ‘packageVersion’
namedList: no visible global function definition for ‘setNames’
refit.bmerMod: no visible global function definition for
  ‘packageVersion’
refit.bmerMod: no visible global function definition for ‘model.frame’
refit.bmerMod: no visible global function definition for ‘family’
refit.bmerMod: no visible global function definition for ‘getCall’
Undefined global functions or variables:
  family getCall model.frame packageVersion sd setNames
Consider adding
  importFrom("stats", "family", "getCall", "model.frame", "sd",
             "setNames")
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
Found the following files/directories:
  ‘core’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.0Mb
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.
Running examples in ‘blockmodeling-Ex.R’ failed
The error most likely occurred in:

> ### Name: REGE
> ### Title: REGE - Algorithms for compiting (dis)similarities in terms of
> ###   regular equivalnece
> ### Aliases: REGE REGE.for REGE.nm.for REGE.ow REGE.ow.for REGE.ownm.for
> ###   REGD.for REGD.ow.for REGE.FC REGE.FC.ow REGD.ne.for REGD.ow.ne.for
> ###   REGE.ne.for REGE.nm.diag.for REGE.nm.ne.for REGE.ow.ne.for
> ###   REGE.ownm.diag.for REGE.ownm.ne.for
> ### Keywords: cluster graphs
> 
> ### ** Examples
> 
> n <- 20
> net <- matrix(NA, ncol = n, nrow = n)
> clu <- rep(1:2, times = c(5, 15))
> tclu <- table(clu)
> net[clu == 1, clu == 1] <- 0
> net[clu == 1, clu == 2] <- rnorm(n = tclu[1] * tclu[2], mean = 4, sd = 1) * sample(c(0, 1),
+    size = tclu[1] * tclu[2], replace = TRUE, prob = c(3/5, 2/5))
> net[clu == 2, clu == 1] <- 0
> net[clu == 2, clu == 2] <- 0
> 
> D <- REGE.for(M = net)$E # Any other REGE function can be used
> plot.mat(net, clu = cutree(hclust(d = as.dist(1 - D), method = "ward.D"),
+    k = 2))
> # REGE returns similarities, which have to be converted to
> # disimilarities
> 
> res <- optRandomParC(M = net, k = 2, rep = 10, approaches = "hom", homFun = "ss", blocks = "reg")


Starting optimization of the partiton 1 of 10 partitions.
Starting partition: 1 2 1 1 1 1 1 1 1 2 2 1 2 2 2 2 2 1 1 1 

 *** caught segfault ***
address 6f5ec1ac, cause 'memory not mapped'

Traceback:
 1: optParC(M = M, clu = temppar, approaches = approaches, blocks = blocks,     useMulti = useMulti, save.initial.param = save.initial.param.opt,     ...)
 2: optRandomParC(M = net, k = 2, rep = 10, approaches = "hom", homFun = "ss",     blocks = "reg")
An irrecoverable exception occurred. R is aborting now ...
blockmodelskmeans: no visible global function definition for ‘dist’
matrixplot: no visible global function definition for ‘image’
matrixplot: no visible global function definition for ‘hsv’
matrixplot: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis dist hsv image
Consider adding
  importFrom("grDevices", "hsv")
  importFrom("graphics", "axis", "image")
  importFrom("stats", "dist")
to your NAMESPACE file.
plotblockrand: no visible global function definition for ‘pdf’
plotblockrand: no visible global function definition for ‘dev.off’
plotblockrand: no visible global function definition for ‘par’
plotblockrand: no visible global function definition for ‘plot.new’
plotblockrand: no visible global function definition for ‘strheight’
plotblockrand: no visible global function definition for ‘strwidth’
plotblockrand: no visible global function definition for ‘text’
plotblockrand: no visible global function definition for ‘lines’
Undefined global functions or variables:
  dev.off lines par pdf plot.new strheight strwidth text
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot.new", "strheight",
             "strwidth", "text")
to your NAMESPACE file.
Found the following files/directories:
  ‘Groupa.csv’ ‘Groupa.tex’ ‘Groupb.csv’ ‘Groupb.tex’ ‘Groupc.csv’
  ‘Groupc.tex’ ‘file1.csv’ ‘file1.tex’ ‘file2.csv’ ‘file2.tex’
  ‘file3.csv’ ‘file3.tex’
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘ggplot2’ ‘rhandsontable’ ‘shiny’
  All declared Imports should be used.
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.
Packages in Depends field not imported from:
  ‘Amelia’ ‘MASS’ ‘lavaan’ ‘sem’ ‘snowfall’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following files/directories:
  ‘model.txt’
Namespaces in Imports field not imported from:
  ‘formula.tools’ ‘plm’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls to packages already attached by Depends:
  ‘coda’ ‘functional’ ‘plyr’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘coda’ ‘functional’ ‘plyr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HDistNoSize: no visible global function definition for ‘density’
HDistSize: no visible global function definition for ‘density’
bmkconverge: no visible global function definition for ‘Compose’
bmksensitive: no visible global function definition for ‘Compose’
bmksummary: no visible global function definition for ‘Compose’
bmksummary: no visible global function definition for ‘Curry’
bmksummary: no visible binding for global variable ‘quantile’
bmksummary : std.error: no visible global function definition for ‘var’
bmksummary: no visible global function definition for ‘mcmc’
bmksummary: no visible global function definition for ‘mcmc.list’
bmksummary: no visible global function definition for ‘median’
bmksummary: no visible global function definition for ‘effectiveSize’
bmksummary: no visible global function definition for ‘gelman.diag’
Undefined global functions or variables:
  Compose Curry density effectiveSize gelman.diag mcmc mcmc.list median
  quantile var
Consider adding
  importFrom("stats", "density", "median", "quantile", "var")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
bmmix : LL.y: no visible global function definition for ‘dmultinom’
bmmix : LL.x : <anonymous>: no visible global function definition for
  ‘dmultinom’
bmmix : LPrior.alpha: no visible global function definition for ‘dexp’
bmmix : alpha.move: no visible global function definition for ‘rnorm’
bmmix : alpha.move: no visible global function definition for ‘runif’
bmmix : phi.move: no visible global function definition for ‘rnorm’
bmmix : phi.move: no visible global function definition for ‘runif’
bmmix: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  dexp dmultinom read.table rnorm runif
Consider adding
  importFrom("stats", "dexp", "dmultinom", "rnorm", "runif")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘mcmc.txt’
Running ‘testthat.R’ [63s/69s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BMTME)
  > 
  > test_check("BMTME")
  ── 1. Failure: RandomPartition (@test.R#52)  ───────────────────────────────────
  RP_Test$Environments inherits from `character` not `factor`.
  
  ── 2. Failure: RandomPartition (@test.R#72)  ───────────────────────────────────
  RP_Test2$Traits inherits from `character` not `factor`.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 164 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: RandomPartition (@test.R#52) 
  2. Failure: RandomPartition (@test.R#72) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Namespaces in Imports field not imported from:
  ‘Rgraphviz’ ‘fastDummies’
  All declared Imports should be used.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
BOGest: no visible global function definition for ‘read.table’
BOGstat: no visible global function definition for ‘phyper’
BOGstat: no visible global function definition for ‘wilcox.test’
BOGstat: no visible global function definition for ‘p.adjust’
gseaplot: no visible global function definition for ‘par’
gseaplot: no visible global function definition for ‘points’
gseaplot: no visible global function definition for ‘axis’
gseaplot: no visible global function definition for ‘segments’
hgplot: no visible global function definition for ‘par’
hgplot: no visible global function definition for ‘barplot’
Undefined global functions or variables:
  axis barplot p.adjust par phyper points read.table segments
  wilcox.test
Consider adding
  importFrom("graphics", "axis", "barplot", "par", "points", "segments")
  importFrom("stats", "p.adjust", "phyper", "wilcox.test")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Error(s) in re-building vignettes:
  ...
--- re-building ‘BoolNet_package_vignette.Snw.Rnw’ using Sweave

Error: processing vignette 'BoolNet_package_vignette.Snw.Rnw' failed with diagnostics:
 chunk 13 
Error in net$interactions[[idx]][[functionIndices[idx]]] : 
  subscript out of bounds

--- failed re-building ‘BoolNet_package_vignette.Snw.Rnw’

SUMMARY: processing the following file failed:
  ‘BoolNet_package_vignette.Snw.Rnw’

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘attractors.tex’ ‘cellcycle.sbml’ ‘cellcycle.txt’ ‘pajek_export.net’
  ‘sequence.txt’ ‘testNet.bn’
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.
Namespace in Imports field not imported from: ‘psychTools’
  All declared Imports should be used.
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.
bootSVD: no visible global function definition for ‘object.size’
bootSVD : <anonymous> : <anonymous>: no visible global function
  definition for ‘quantile’
bootSVD_LD: no visible global function definition for ‘txtProgressBar’
bootSVD_LD: no visible global function definition for
  ‘setTxtProgressBar’
genQ: no visible global function definition for ‘rnorm’
getHDpercentiles : <anonymous>: no visible global function definition
  for ‘quantile’
getMomentsAndMomentCI: no visible binding for global variable ‘var’
os: no visible global function definition for ‘object.size’
simEEG: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  object.size quantile rnorm setTxtProgressBar txtProgressBar var
Consider adding
  importFrom("stats", "quantile", "rnorm", "var")
  importFrom("utils", "object.size", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
boottol: no visible global function definition for ‘setNames’
boottol : shift: no visible global function definition for ‘tail’
boottol : shift: no visible global function definition for ‘head’
boottol: no visible global function definition for ‘na.omit’
vastol: no visible global function definition for ‘setNames’
vastol: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  head na.omit setNames tail
Consider adding
  importFrom("stats", "na.omit", "setNames")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Found the following files/directories:
  ‘for_krona.txt’ ‘test.jplace’
bPeaksAnalysis: no visible global function definition for ‘write.table’
dataReading: no visible global function definition for ‘read.table’
dataSmoothing: no visible global function definition for ‘filter’
peakDetection: no visible global function definition for ‘quantile’
peakDetection: no visible global function definition for ‘pdf’
peakDetection: no visible global function definition for ‘par’
peakDetection: no visible global function definition for ‘text’
peakDetection: no visible global function definition for ‘abline’
peakDetection: no visible global function definition for ‘points’
peakDetection: no visible global function definition for ‘dev.off’
peakDetection: no visible global function definition for ‘write.table’
peakDrawing: no visible global function definition for ‘par’
peakDrawing: no visible global function definition for ‘abline’
peakLocation: no visible global function definition for ‘read.table’
peakLocation: no visible global function definition for ‘pdf’
peakLocation: no visible global function definition for ‘barplot’
peakLocation: no visible global function definition for ‘dev.off’
peakLocation: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  abline barplot dev.off filter par pdf points quantile read.table text
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "barplot", "par", "points", "text")
  importFrom("stats", "filter", "quantile")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘bPeaks_example-chrIV.bed’ ‘bPeaks_example-chrIV_bPeaksDrawing.pdf’
  ‘bPeaks_example-chrIV_dataSummary.pdf’
  ‘bPeaks_example_bPeaks_allGenome.bed’
  ‘bPeaks_example_bPeaks_parameterSummary.txt’
  ‘bPeaks_example_chrIV.bed’ ‘bPeaks_example_chrIV_bPeaksDrawing.pdf’
  ‘bPeaks_example_chrIV_dataSummary.pdf’
  ‘bPeaks_example_peakLocation.pdf’
  ‘bPeaks_example_peakLocation_inCDS.txt’
  ‘bPeaks_example_peakLocation_inPromoters.txt’ ‘peakStats.Robject’
Package suggested but not available for checking: ‘installr’
Namespaces in Imports field not imported from:
  ‘CCA’ ‘brainR’ ‘elasticnet’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Package in Depends field not imported from: ‘waveslim’
  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

const.cor.list: no visible global function definition for
  ‘wave.correlation’
const.var.list: no visible global function definition for
  ‘wave.variance’
fitting: no visible global function definition for ‘hist’
fitting: no visible global function definition for ‘nlm’
fitting: no visible global function definition for ‘write.table’
p.value.compute: no visible global function definition for ‘pnorm’
p.value.compute: no visible global function definition for ‘pt’
random.attack: no visible global function definition for ‘runif’
read.convert_1_2: no visible global function definition for
  ‘read.table’
read.cor.txt: no visible global function definition for ‘read.table’
read.var.txt: no visible global function definition for ‘read.table’
save.cor.txt: no visible global function definition for ‘write.table’
save.var.txt: no visible global function definition for ‘write.table’
sim.equadist: no visible global function definition for ‘write.table’
small.world: no visible global function definition for ‘dist’
small.world: no visible global function definition for ‘write.table’
wave.trans: no visible global function definition for ‘dwt’
wave.trans: no visible global function definition for ‘modwt’
wave.trans: no visible global function definition for ‘brick.wall’
Undefined global functions or variables:
  brick.wall dist dwt hist modwt nlm pnorm pt read.table runif
  wave.correlation wave.variance write.table
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "dist", "nlm", "pnorm", "pt", "runif")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
File ‘brainwaver/libs/brainwaver.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘connexity_small_world.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘example-1.ps’ ‘fitting.txt’ ‘wave_cor_lower_mat_level_1.txt’
  ‘wave_cor_lower_mat_level_2.txt’ ‘wave_cor_lower_mat_level_3.txt’
  ‘wave_cor_lower_mat_level_4.txt’ ‘wave_cor_mat_level_1.txt’
  ‘wave_cor_mat_level_2.txt’ ‘wave_cor_mat_level_3.txt’
  ‘wave_cor_mat_level_4.txt’ ‘wave_cor_upper_mat_level_1.txt’
  ‘wave_cor_upper_mat_level_2.txt’ ‘wave_cor_upper_mat_level_3.txt’
  ‘wave_cor_upper_mat_level_4.txt’ ‘wave_var_lower_mat_level_1.txt’
  ‘wave_var_lower_mat_level_2.txt’ ‘wave_var_lower_mat_level_3.txt’
  ‘wave_var_lower_mat_level_4.txt’ ‘wave_var_mat_level_1.txt’
  ‘wave_var_mat_level_2.txt’ ‘wave_var_mat_level_3.txt’
  ‘wave_var_mat_level_4.txt’ ‘wave_var_upper_mat_level_1.txt’
  ‘wave_var_upper_mat_level_2.txt’ ‘wave_var_upper_mat_level_3.txt’
  ‘wave_var_upper_mat_level_4.txt’
Found the following files/directories:
  ‘core’
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
apply.breaks: no visible binding for global variable ‘median’
break.clust: no visible global function definition for ‘median’
breakage.plot: no visible binding for global variable ‘median’
breakage.plot: no visible global function definition for ‘abline’
breakage.plot: no visible global function definition for ‘lm’
find.bottom: no visible global function definition for ‘filter’
fit.breakage: no visible global function definition for ‘optim’
fit.breakage: no visible global function definition for ‘points’
fit.sensitivity.plot: no visible global function definition for
  ‘contour’
fit.sensitivity.plot: no visible global function definition for
  ‘points’
fit.sensitivity.plot: no visible global function definition for ‘text’
Undefined global functions or variables:
  abline contour filter lm median optim points text
Consider adding
  importFrom("graphics", "abline", "contour", "points", "text")
  importFrom("stats", "filter", "lm", "median", "optim")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘break_caret.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: lattice
Loading required package: ggplot2
--- finished re-building ‘break_caret.Rmd’

--- re-building ‘break_glm.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 ‘break_glm.Rmd’

--- re-building ‘break_lm.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 ‘break_lm.Rmd’

--- re-building ‘break_randomForest.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 ‘break_randomForest.Rmd’

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

--- re-building ‘break_xgboost.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 ‘break_xgboost.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following sources/headers with CR or CRLF line endings:
  inst/include/meta_header.hpp
Some Unix compilers require LF line endings.
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘brew-test-1-1.eps’ ‘brew-test-1-2.eps’ ‘brew-test-1.tex’
  ‘brew-test-2.html’
Namespace in Imports field not imported from: ‘hexbin’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘profileModel’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R     3.8Mb
    doc   2.8Mb
Package suggested but not available for checking: ‘glmmADMB’
Packages suggested but not available for checking: 'btergm', 'xergm'
Unknown package ‘btergm’ in Rd xrefs
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    bin    3.1Mb
    doc    1.3Mb
    libs   3.1Mb
Namespaces in Imports field not imported from:
  ‘rworldxtra’ ‘sp’
  All declared Imports should be used.
BSGS.Sample: no visible global function definition for ‘rgamma’
BSGS.Simple: no visible global function definition for ‘rgamma’
CompWiseGibbs: no visible global function definition for ‘runif’
CompWiseGibbs: no visible global function definition for ‘rnorm’
CompWiseGibbsSMP: no visible global function definition for ‘rbinom’
CompWiseGibbsSMP: no visible global function definition for ‘runif’
CompWiseGibbsSMP: no visible global function definition for ‘rnorm’
CompWiseGibbsSimple: no visible global function definition for ‘runif’
CompWiseGibbsSimple: no visible global function definition for ‘rnorm’
CompWiseGibbsSimple: no visible global function definition for ‘rgamma’
GroupMH: no visible global function definition for ‘runif’
GroupZ.MH: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rbinom rgamma rnorm runif
Consider adding
  importFrom("stats", "rbinom", "rgamma", "rnorm", "runif")
to your NAMESPACE file.
plot.bspec: no visible global function definition for ‘par’
plot.bspec: no visible global function definition for ‘matlines’
plot.bspec: no visible global function definition for ‘points’
plot.bspec: no visible global function definition for ‘axis’
plot.bspec: no visible global function definition for ‘mtext’
plot.bspec: no visible global function definition for ‘axTicks’
plot.bspec: no visible global function definition for ‘box’
plot.bspecACF: no visible global function definition for ‘abline’
plot.bspecACF: no visible global function definition for ‘matlines’
Undefined global functions or variables:
  abline axTicks axis box matlines mtext par points
Consider adding
  importFrom("graphics", "abline", "axTicks", "axis", "box", "matlines",
             "mtext", "par", "points")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   2.8Mb
Namespaces in Imports field not imported from:
  ‘mvtnorm’ ‘ssmn’
  All declared Imports should be used.
Found the following files/directories:
  ‘irregularGrid.dbf’ ‘irregularGrid.prj’ ‘irregularGrid.shp’
  ‘irregularGrid.shx’ ‘regularGrid.dbf’ ‘regularGrid.prj’
  ‘regularGrid.shp’ ‘regularGrid.shx’
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
alpha.proxy: no visible global function definition for ‘filled.contour’
alpha.proxy: no visible global function definition for ‘axis’
alpha.proxy: no visible global function definition for ‘contour’
factor.model.stat: no visible global function definition for ‘quantile’
factor.model.stat: no visible global function definition for ‘lsfit’
partial.rainbow: no visible binding for global variable ‘rainbow’
var.shrink.eqcor: no visible global function definition for ‘var’
var.shrink.eqcor: no visible global function definition for ‘quantile’
var.shrink.eqcor: no visible global function definition for ‘cov2cor’
Undefined global functions or variables:
  axis contour cov2cor filled.contour lsfit quantile rainbow var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "contour", "filled.contour")
  importFrom("stats", "cov2cor", "lsfit", "quantile", "var")
to your NAMESPACE file.
plot.bursts: no visible global function definition for ‘axis’
plot.bursts: no visible global function definition for ‘arrows’
Undefined global functions or variables:
  arrows axis
Consider adding
  importFrom("graphics", "arrows", "axis")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘modeldata’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘haplo.stats’ ‘msm’
  Please remove these calls from your code.
fitBVS: no visible global function definition for ‘qnorm’
fitBVS: no visible global function definition for ‘model.matrix’
fitBVS: no visible global function definition for ‘as.formula’
fitBVS: no visible global function definition for ‘glm’
fitBVS: no visible global function definition for ‘deviance’
fitBVS: no visible global function definition for ‘pnorm’
plotBVS: no visible global function definition for ‘par’
plotBVS: no visible global function definition for ‘image’
plotBVS: no visible global function definition for ‘axis’
sampleBVS: no visible global function definition for ‘qnorm’
sampleBVS: no visible global function definition for ‘pnorm’
sampleBVS: no visible global function definition for ‘runif’
summaryBVS: no visible global function definition for ‘qnorm’
summaryBVS : inc.prob: no visible global function definition for
  ‘pnorm’
summaryBVS: no visible global function definition for ‘pnorm’
summaryBVS: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  as.formula axis deviance glm image model.matrix par pnorm qnorm runif
Consider adding
  importFrom("graphics", "axis", "image", "par")
  importFrom("stats", "as.formula", "deviance", "glm", "model.matrix",
             "pnorm", "qnorm", "runif")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘simple_plotting.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: Removed 4550 row(s) containing missing values (geom_path).
Quitting from lines 173-174 (simple_plotting.Rmd) 
Error: processing vignette 'simple_plotting.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘simple_plotting.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(jsonlite)
  > library(c3)
  
  Attaching package: 'c3'
  
  The following object is masked from 'package:testthat':
  
      %>%
  
  The following objects are masked from 'package:graphics':
  
      grid, legend
  
  > 
  > test_check("c3")
  ── 1. Failure: regions can be added (@test_c3.R#135)  ──────────────────────────
  reg$x$regions$axis not equal to factor("x").
  Types not compatible: character is not integer
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 132 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: regions can be added (@test_c3.R#135) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘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.

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: 'c3'

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

    %>%

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

    grid, legend

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]="webshot4be120cb73fc.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot4be120cb73fc.png': No such file or directory
Quitting from lines 56-65 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘R6’ ‘here’ ‘withr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
File ‘cairoDevice/R/zzz.R’:
  .onLoad calls:
    message("R session is headless; GTK+ not initialized.")

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.
File ‘cairoDevice/libs/cairoDevice.so’:
  Found non-API call to R: ‘R_CStackLimit’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package which this enhances but not available for checking: ‘FastRWeb’
File ‘Cairo/libs/Cairo.so’:
  Found non-API calls to R: ‘R_InputHandlers’, ‘addInputHandler’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following files/directories:
  ‘tmp.txt’
Found the following files/directories:
  ‘MDA231_tree.pdf’
Note: found 59 marked UTF-8 strings
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
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.
Running examples in ‘carat-Ex.R’ failed
The error most likely occurred in:

> ### Name: AdjBCD
> ### Title: Covariate-adjusted Biased Coin Design
> ### Aliases: AdjBCD AdjBCD.carandom
> ### Keywords: carandom Covariate-ajusted biased coin design
> 
> ### ** Examples
> 
> # a simple use
> ## Real Data
> ## create a dataframe
> df <- data.frame("gender" = sample(c("female", "male"), 1000, TRUE, c(1 / 3, 2 / 3)), 
+                  "age" = sample(c("0-30", "30-50", ">50"), 1000, TRUE), 
+                  "jobs" = sample(c("stu.", "teac.", "others"), 1000, TRUE))
> Res <- AdjBCD(df, a = 2)
Warning in lapply(X = X, FUN = FUN, ...) : NAs introduced by coercion
Warning in lapply(X = X, FUN = FUN, ...) : NAs introduced by coercion
Warning in lapply(X = X, FUN = FUN, ...) : NAs introduced by coercion

error: Mat::operator(): index out of bounds
Error in C_RAdjustBCD(data_proc, cov_num, level_num, adoub) : 
  Mat::operator(): index out of bounds
Calls: AdjBCD -> C_RAdjustBCD
Execution halted
Namespace in Imports field not imported from: ‘details’
  All declared Imports should be used.
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  7.1Mb
  sub-directories of 1Mb or more:
    R        1.3Mb
    data     1.8Mb
    models   2.5Mb
Running examples in ‘caret-Ex.R’ failed
The error most likely occurred in:

> ### Name: dummyVars
> ### Title: Create A Full Set of Dummy Variables
> ### Aliases: dummyVars dummyVars.default predict.dummyVars contr.dummy
> ###   contr.ltfr class2ind print.dummyVars
> ### Keywords: models
> 
> ### ** Examples
> 
> when <- data.frame(time = c("afternoon", "night", "afternoon",
+                             "morning", "morning", "morning",
+                             "morning", "afternoon", "afternoon"),
+                    day = c("Mon", "Mon", "Mon",
+                            "Wed", "Wed", "Fri",
+                            "Sat", "Sat", "Fri"))
> 
> levels(when$time) <- list(morning="morning",
+                           afternoon="afternoon",
+                           night="night")
> levels(when$day) <- list(Mon="Mon", Tue="Tue", Wed="Wed", Thu="Thu",
+                          Fri="Fri", Sat="Sat", Sun="Sun")
> 
> ## Default behavior:
> model.matrix(~day, when)
  (Intercept) dayMon daySat dayWed
1           1      1      0      0
2           1      1      0      0
3           1      1      0      0
4           1      0      0      1
5           1      0      0      1
6           1      0      0      0
7           1      0      1      0
8           1      0      1      0
9           1      0      0      0
attr(,"assign")
[1] 0 1 1 1
attr(,"contrasts")
attr(,"contrasts")$day
[1] "contr.treatment"

> 
> mainEffects <- dummyVars(~ day + time, data = when)
> mainEffects
Dummy Variable Object

Formula: ~day + time
2 variables, 0 factors
Variables and levels will be separated by '.'
A less than full rank encoding is used
> predict(mainEffects, when[1:3,])
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: predict ... model.matrix -> model.matrix.default -> contrasts<-
Execution halted
Running ‘testthat.R’ [470s/470s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(caret)
  Loading required package: lattice
  Loading required package: ggplot2
  > 
  > test_check("caret")
  ── 1. Failure: Good names for dummies with reocurring patterns (@test_Dummies.R#
  all(exp_names_lvls %in% res_names_lvls) isn't true.
  
  ── 2. Error: Multiclass logloss returns expected values (@test_mnLogLoss.R#12)  
  'data$obs' should have levels consistent with 'lev'
  Backtrace:
   1. caret::mnLogLoss(test_dat1, classes)
  
  ── 3. Error: Twoclass logloss returns expected values (@test_mnLogLoss.R#38)  ──
  'data$obs' should have levels consistent with 'lev'
  Backtrace:
   1. caret::mnLogLoss(test_dat1.b, classes.b)
  
  ── 4. Failure: handles situation when there's a single column per transformation
  `preprocessed` not equal to data.frame(x = c("a", "a"), y = c(-0.5, 0.5)).
  Component "x": 'current' is not a factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 135 | SKIPPED: 33 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: Good names for dummies with reocurring patterns (@test_Dummies.R#126) 
  2. Error: Multiclass logloss returns expected values (@test_mnLogLoss.R#12) 
  3. Error: Twoclass logloss returns expected values (@test_mnLogLoss.R#38) 
  4. Failure: handles situation when there's a single column per transformation (@test_preProcess_internals.R#11) 
  
  Error: testthat unit tests failed
  Execution halted
abundance: no visible global function definition for ‘D’
Undefined global functions or variables:
  D
Consider adding
  importFrom("stats", "D")
to your NAMESPACE file.
barplotEQR: no visible global function definition for ‘barplot’
barplotEQR: no visible global function definition for ‘abline’
barplotEQR: no visible global function definition for ‘par’
barplotEQR: no visible global function definition for ‘text’
Undefined global functions or variables:
  abline barplot par text
Consider adding
  importFrom("graphics", "abline", "barplot", "par", "text")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘MASS’ ‘RSQLite’ ‘grid’ ‘sm’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following files/directories:
  ‘foo.tab’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Namespace in Imports field not imported from: ‘g.data’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘cartograflow.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

Warning: Use of `x$flowcum` is discouraged. Use `flowcum` instead.
Warning: Use of `x$linkcum` is discouraged. Use `linkcum` instead.
Warning: Use of `x$flowcum` is discouraged. Use `flowcum` instead.
Warning: Use of `x$flowcum` is discouraged. Use `flowcum` instead.
Quitting from lines 451-480 (cartograflow.Rmd) 
Error: processing vignette 'cartograflow.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘cartograflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘animation’ ‘devtools’ ‘gapminder’ ‘knitr’ ‘rlist’ ‘rmarkdown’
  ‘roxygen2’ ‘sde’ ‘shiny’ ‘tidyverse’ ‘usethis’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘crayon’ ‘dplyr’ ‘tidyr’
  All declared Imports should be used.
Found the following sources/headers with CR or CRLF line endings:
  inst/include/FilterIntervals.h
  inst/include/chi2.h
  inst/include/gamma.h
Some Unix compilers require LF line endings.
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘broom’ ‘epitools’
  All declared Imports should be used.
Package suggested but not available for checking: ‘spacodiR’
Found the following files/directories:
  ‘catmapdata.fixed.effects.plot.pdf’ ‘catmapdata.funnel.plot.pdf’
  ‘catmapdata.output.txt’ ‘catmapdata.random.effects.plot.pdf’
Malformed Description field: should contain one or more complete sentences.
mi.inference: no visible binding for global variable ‘var’
mi.inference: no visible global function definition for ‘qt’
mi.inference: no visible global function definition for ‘pt’
Undefined global functions or variables:
  pt qt var
Consider adding
  importFrom("stats", "pt", "qt", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
ctab: no visible global function definition for ‘xtabs’
mob.eqmain: no visible global function definition for ‘model.matrix’
mob.qi: no visible global function definition for ‘C’
mob.qi: no visible binding for global variable ‘contr.treatment’
mob.rc1: no visible global function definition for ‘C’
mob.rc1: no visible binding for global variable ‘contr.treatment’
mob.rc1: no visible global function definition for ‘model.matrix’
mob.symint: no visible global function definition for ‘model.matrix’
print.ctab: no visible global function definition for ‘ftable’
Undefined global functions or variables:
  C contr.treatment ftable model.matrix xtabs
Consider adding
  importFrom("stats", "C", "contr.treatment", "ftable", "model.matrix",
             "xtabs")
to your NAMESPACE file.
GNU make is a SystemRequirements.
binParamPosteriorSampling: no visible global function definition for
  ‘rbeta’
bindagMonteCarloCausalEffect: no visible global function definition for
  ‘runif’
getBinDAGModelData: no visible global function definition for ‘runif’
logitDist: no visible global function definition for ‘runif’
logitDist: no visible global function definition for ‘rnorm’
simulateWitnessModel: no visible global function definition for ‘runif’
summary.covsearch: no visible global function definition for ‘quantile’
summary.iv: no visible global function definition for ‘quantile’
summary.wpp: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile rbeta rnorm runif
Consider adding
  importFrom("stats", "quantile", "rbeta", "rnorm", "runif")
to your NAMESPACE file.
Found the following files/directories:
  ‘tetradLite.jar’
Malformed Title field: should not end in a period.
BinaryCut: no visible global function definition for ‘quantile’
CleanNaFromContinuousFunction: no visible global function definition
  for ‘median’
CleanNaFromContinuousFunction: no visible global function definition
  for ‘na.omit’
GetMetadata.Connect: no visible global function definition for
  ‘dbGetQuery’
GetRawData.Connect: no visible global function definition for
  ‘dbGetQuery’
Linearity: no visible global function definition for ‘median’
PredictivePowerCv: no visible global function definition for ‘sd’
ReadCausataCsv: no visible global function definition for ‘read.csv’
ToPmml.GlmnetModelDefinition: no visible global function definition for
  ‘coef’
ToPmml.GlmnetModelDefinition: no visible global function definition for
  ‘terms.formula’
ValidateModel: no visible global function definition for ‘predict’
predict.GlmnetModelDefinition: no visible global function definition
  for ‘model.matrix’
predict.GlmnetModelDefinition: no visible binding for global variable
  ‘contrasts’
predict.GlmnetModelDefinition: no visible global function definition
  for ‘predict’
Undefined global functions or variables:
  coef contrasts dbGetQuery median model.matrix na.omit predict
  quantile read.csv sd terms.formula
Consider adding
  importFrom("stats", "coef", "contrasts", "median", "model.matrix",
             "na.omit", "predict", "quantile", "sd", "terms.formula")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘grDevices’ ‘rgdal’ ‘spatialEco’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘prettydoc’
  All declared Imports should be used.
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
GNU make is a SystemRequirements.
estim.regul: warning in matrix(res, nc = length(grid2)): partial
  argument match of 'nc' to 'ncol'
comput: no visible global function definition for ‘cor’
img.estim.regul: no visible global function definition for ‘par’
img.estim.regul: no visible global function definition for ‘image’
img.estim.regul: no visible global function definition for
  ‘heat.colors’
img.estim.regul: no visible global function definition for ‘axis’
img.estim.regul: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘par’
img.matcor: no visible global function definition for ‘image’
img.matcor: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘abline’
img.matcor: no visible global function definition for ‘layout’
loo: no visible global function definition for ‘cor’
matcor: no visible global function definition for ‘cor’
plt.cc: no visible global function definition for ‘par’
plt.cc: no visible global function definition for ‘layout’
plt.indiv: no visible global function definition for ‘text’
plt.indiv: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘points’
plt.var: no visible global function definition for ‘text’
plt.var: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘lines’
rcc: no visible global function definition for ‘var’
rcc: no visible global function definition for ‘cov’
Undefined global functions or variables:
  abline axis box cor cov heat.colors image layout lines par points
  text var
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "layout",
             "lines", "par", "points", "text")
  importFrom("stats", "cor", "cov", "var")
to your NAMESPACE file.
prepare_Rd: estim.regul.Rd:24-26: Dropping empty section \details
prepare_Rd: img.estim.regul.Rd:15-17: Dropping empty section \details
prepare_Rd: img.estim.regul.Rd:24-25: Dropping empty section \examples
ccd.sequential: no visible global function definition for ‘qchisq’
dominate.random.sample: no visible global function definition for
  ‘runif’
draw.circle: no visible global function definition for ‘polygon’
juggle2: no visible global function definition for ‘rbinom’
plot.cccd: no visible global function definition for ‘gray’
plot.cccd: no visible global function definition for ‘points’
plot.cccdClassifier: no visible global function definition for ‘points’
Undefined global functions or variables:
  gray points polygon qchisq rbinom runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "points", "polygon")
  importFrom("stats", "qchisq", "rbinom", "runif")
to your NAMESPACE file.
VD: no visible binding for global variable ‘var’
stratcc : <anonymous>: no visible global function definition for
  ‘hclust’
stratcc : <anonymous>: no visible global function definition for
  ‘cutree’
Undefined global functions or variables:
  cutree hclust var
Consider adding
  importFrom("stats", "cutree", "hclust", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
p.Roy: no visible global function definition for ‘pf’
p.asym: no visible global function definition for ‘pf’
p.perm: no visible global function definition for ‘cancor’
plt.asym: no visible global function definition for ‘qf’
plt.asym: no visible global function definition for ‘df’
plt.asym: no visible global function definition for ‘abline’
plt.perm: no visible global function definition for ‘hist’
plt.perm: no visible global function definition for ‘mtext’
plt.perm: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline cancor df hist mtext pf qf
Consider adding
  importFrom("graphics", "abline", "hist", "mtext")
  importFrom("stats", "cancor", "df", "pf", "qf")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Found the following files/directories:
  ‘hotcold.csv’
'library' or 'require' call to ‘bitops’ which was already attached by Depends.
  Please remove these calls from your code.
Found the following files/directories:
  ‘Base.txt’
CDFt: no visible global function definition for ‘ecdf’
CDFt: no visible global function definition for ‘quantile’
CDFt: no visible global function definition for ‘approx’
KolmogorovSmirnov: no visible global function definition for ‘ecdf’
KolmogorovSmirnov: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx ecdf quantile
Consider adding
  importFrom("stats", "approx", "ecdf", "quantile")
to your NAMESPACE file.
prepare_Rd: CramerVonMisesTwoSamples.Rd:23: Dropping empty section \examples
prepare_Rd: KolmogorovSmirnov.Rd:26: Dropping empty section \examples
Malformed Description field: should contain one or more complete sentences.
Found the following files/directories:
  ‘out.png’ ‘out1.txt’ ‘out2.txt’
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extdata   9.8Mb
Found the following files/directories:
  ‘figure01ceg.pdf’ ‘figure02ceg.pdf’ ‘staged.tree.graph.pdf’
  ‘stratified-event-tree-plot.pdf’
Packages in Depends field not imported from:
  ‘gplots’ ‘minpack.lm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
erf: no visible global function definition for ‘pnorm’
fitVolDist: no visible global function definition for ‘nls.lm’
fitVolDist: no visible global function definition for ‘nls.lm.control’
fitVolDist: no visible global function definition for ‘optim’
fitVolDist: no visible global function definition for ‘relist’
print.fitVolDist: no visible global function definition for ‘coef’
print.fitVolDist: no visible global function definition for ‘deviance’
print.fitVolDist: no visible global function definition for ‘pt’
print.fitVolDist: no visible global function definition for
  ‘printCoefmat’
resFunChiSq: no visible global function definition for ‘relist’
volEq7: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  coef deviance integrate nls.lm nls.lm.control optim pnorm
  printCoefmat pt relist
Consider adding
  importFrom("stats", "coef", "deviance", "integrate", "optim", "pnorm",
             "printCoefmat", "pt")
  importFrom("utils", "relist")
to your NAMESPACE file.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.9Mb
cenNID: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Unexported objects imported by ':::' calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
Malformed Description field: should contain one or more complete sentences.
MomNIT: no visible global function definition for ‘dnorm’
MomNIT: no visible global function definition for ‘pnorm’
cdfNI: no visible global function definition for ‘pnorm’
cdfNI: no visible global function definition for ‘pt’
em.cens: no visible global function definition for ‘lm’
em.cens: no visible global function definition for ‘coefficients’
em.cens : ft: no visible global function definition for ‘dt’
em.cens : ft: no visible global function definition for ‘pt’
em.cens: no visible global function definition for ‘optimize’
em.cens: no visible global function definition for ‘dnorm’
em.cens: no visible global function definition for ‘pnorm’
em.cens: no visible global function definition for ‘sd’
Undefined global functions or variables:
  coefficients dnorm dt lm optimize pnorm pt sd
Consider adding
  importFrom("stats", "coefficients", "dnorm", "dt", "lm", "optimize",
             "pnorm", "pt", "sd")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
CM: no visible global function definition for ‘sd’
Erf: no visible global function definition for ‘pnorm’
Erfc: no visible global function definition for ‘pnorm’
boot.Cenarma: no visible global function definition for ‘coef’
boot.Cenarma: no visible global function definition for ‘arima.sim’
cenarma: no visible global function definition for ‘arima’
cenarma: no visible global function definition for ‘coef’
cenarma: no visible global function definition for ‘ARMAacf’
cenarma: no visible global function definition for ‘var’
plot.cents: no visible global function definition for ‘segments’
plot.cents: no visible global function definition for ‘rgb’
plot.cents: no visible global function definition for ‘points’
rcarma: no visible global function definition for ‘arima.sim’
rcarma: no visible global function definition for ‘quantile’
scenNID: no visible global function definition for ‘sd’
se.Cenarma: no visible global function definition for ‘coef’
se.Cenarma: no visible global function definition for ‘sd’
Undefined global functions or variables:
  ARMAacf arima arima.sim coef pnorm points quantile rgb sd segments
  var
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "points", "segments")
  importFrom("stats", "ARMAacf", "arima", "arima.sim", "coef", "pnorm",
             "quantile", "sd", "var")
to your NAMESPACE file.
Found the following Makefile(s) without a final LF:
  src/Makevars
Some ‘make’ programs ignore lines not ending in LF.
Note: found 287 marked UTF-8 strings
select_lambda: 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:
  ‘base’ ‘stats’ ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
cf_estimate_quantiles: no visible global function definition for
  ‘qnorm’
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
sw.plot : <anonymous>: no visible global function definition for
  ‘median’
sw.plot : <anonymous>: no visible global function definition for ‘mad’
sw.plot : my.line: no visible global function definition for ‘lines’
sw.plot : island.line: no visible global function definition for
  ‘lines’
sw.plot: no visible global function definition for ‘rug’
sw.plot: no visible global function definition for ‘axis’
sw.plot: no visible global function definition for ‘mtext’
sw.plot: no visible global function definition for ‘abline’
sw.plot: no visible global function definition for ‘points’
sw.rob : <anonymous>: no visible global function definition for
  ‘median’
sw.rob : <anonymous>: no visible global function definition for ‘mad’
sw.threshold : <anonymous>: no visible global function definition for
  ‘median’
sw.threshold : <anonymous>: no visible global function definition for
  ‘mad’
Undefined global functions or variables:
  abline axis lines mad median mtext points rug
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "mtext", "points",
             "rug")
  importFrom("stats", "mad", "median")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Found the following files/directories:
  ‘blue.Rdata’ ‘foo.Rdata’
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
Checking should be performed on sources prepared by ‘R CMD build’.
Hartree2Joule: no visible binding for global variable
  ‘universalConstants’
Hertz2Joule: no visible binding for global variable
  ‘universalConstants’
Joule2Hartree: no visible binding for global variable
  ‘universalConstants’
Joule2Hertz: no visible binding for global variable
  ‘universalConstants’
Joule2Kelvin: no visible binding for global variable
  ‘universalConstants’
Joule2centimeterMinusOne: no visible binding for global variable
  ‘universalConstants’
Joule2electronVolt: no visible binding for global variable
  ‘universalConstants’
Joule2kiloCaloriePerMole: no visible binding for global variable
  ‘universalConstants’
Joule2kiloJoulePerMole: no visible binding for global variable
  ‘universalConstants’
KMC: no visible global function definition for ‘runif’
Kelvin2Joule: no visible binding for global variable
  ‘universalConstants’
LandauZener: no visible binding for global variable
  ‘universalConstants’
LandauZenerProbability: no visible binding for global variable
  ‘universalConstants’
Marcus: no visible binding for global variable ‘universalConstants’
MarcusLevichJortner: no visible binding for global variable
  ‘universalConstants’
centimeterMinusOne2Joule: no visible binding for global variable
  ‘universalConstants’
electronVolt2Joule: no visible binding for global variable
  ‘universalConstants’
kiloCaloriePerMole2Joule: no visible binding for global variable
  ‘universalConstants’
kiloJoulePerMole2Joule: no visible binding for global variable
  ‘universalConstants’
Undefined global functions or variables:
  runif universalConstants
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: ‘iptools’
'library' or 'require' call to ‘RCurl’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RCurl’ ‘bitops’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
createDataset: no visible global function definition for ‘read.csv’
createInventory: no visible global function definition for ‘read.csv’
downloadMaster: no visible global function definition for
  ‘getURLContent’
downloadMaster: no visible global function definition for ‘read.csv’
downloadMaster: no visible global function definition for ‘write.csv’
getMissingScrape: no visible global function definition for ‘read.csv’
readLocalMaster: no visible global function definition for ‘read.csv’
readMonthlyCsv: no visible global function definition for ‘read.csv’
scrapeToCsv: no visible global function definition for ‘download.file’
writeData: no visible global function definition for ‘write.csv’
writeGhcn: no visible global function definition for ‘write.table’
writeInventory: no visible global function definition for ‘write.table’
writeMonthlyStations: no visible global function definition for
  ‘read.csv’
writeMonthlyStations: no visible global function definition for
  ‘write.csv’
Undefined global functions or variables:
  download.file getURLContent read.csv write.csv write.table
Consider adding
  importFrom("utils", "download.file", "read.csv", "write.csv",
             "write.table")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Malformed Description field: should contain one or more complete sentences.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘foreach’
  All declared Imports should be used.
Found the following files/directories:
  ‘stepres00.txt’
Package suggested but not available for checking: ‘rda’
Package suggested but not available for checking: ‘rgl’
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘countreg’
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gamlss.dist’
  All declared Imports should be used.
Note: found 27 marked UTF-8 strings
Running ‘testthat.R’ [85s/101s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(CHNOSZ)
  CHNOSZ version 1.3.5 (2020-02-16)
  reset: creating "thermo" object
  obigt: loading default database with 1849 aqueous, 3374 total species
  > 
  > # as fix for https://github.com/hadley/testthat/issues/129, https://github.com/hadley/testthat/issues/144
  > # (since we use makeCluster() etc via palply)
  > Sys.setenv("R_TESTS" = "") 
  > 
  > test_check("CHNOSZ")
  ── 1. Failure: add.protein works as expected (@test-add.protein.R#13)  ─────────
  `ip <- add.protein(aa)` did not throw an error.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 568 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 1 ]
  1. Failure: add.protein works as expected (@test-add.protein.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
File
  LICENSE
is not mentioned in the DESCRIPTION file.
choicemodelr : drawDelta: no visible global function definition for
  ‘rnorm’
choicemodelr : mnlRwMetropOnce: no visible global function definition
  for ‘rnorm’
choicemodelr : mnlRwMetropOnce: no visible global function definition
  for ‘runif’
choicemodelr : rmultireg: no visible global function definition for
  ‘rnorm’
choicemodelr : rwishart: no visible global function definition for
  ‘rchisq’
choicemodelr : rwishart: no visible global function definition for
  ‘rnorm’
choicemodelr : fsh: no visible global function definition for
  ‘flush.console’
choicemodelr: no visible global function definition for ‘matplot’
choicemodelr: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  flush.console matplot rchisq rnorm runif write.table
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "rchisq", "rnorm", "runif")
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
Found the following files/directories:
  ‘RBetas.csv’ ‘RLog.txt’ ‘restart.txt’
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    doc    1.7Mb
    help   2.3Mb
Malformed Description field: should contain one or more complete sentences.
Qh.times.dhyper: no visible global function definition for ‘var’
Qh.times.dhyper: no visible global function definition for ‘pnorm’
Qh.times.dhyper: no visible global function definition for ‘dhyper’
TDiM: no visible global function definition for ‘sd’
choplump.default: no visible global function definition for
  ‘flush.console’
choplump.formula: no visible global function definition for ‘terms’
cm.compact: no visible global function definition for ‘dhyper’
Undefined global functions or variables:
  dhyper flush.console pnorm sd terms var
Consider adding
  importFrom("stats", "dhyper", "pnorm", "sd", "terms", "var")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
Namespace in Imports field not imported from: ‘forcats’
  All declared Imports should be used.
Note: found 4004 marked UTF-8 strings
Malformed Description field: should contain one or more complete sentences.
parse_counts: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
combineToSingleMatrix: no visible global function definition for
  ‘read.table’
combineToSingleMatrix: no visible global function definition for
  ‘write.table’
compareCIM: no visible global function definition for ‘sd’
correctData: no visible global function definition for ‘wd’
correctData: no visible global function definition for ‘threshold’
correctData: no visible binding for global variable ‘madmad’
correctData: no visible global function definition for ‘wr’
Undefined global functions or variables:
  madmad read.table sd threshold wd wr write.table
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘stringr’
  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: ‘circlize’
  All declared Imports should be used.
cin: no visible global function definition for ‘pnorm’
gammaHRF: no visible global function definition for ‘dgamma’
intertest: no visible global function definition for ‘pnorm’
truncSum: no visible global function definition for ‘spline’
Undefined global functions or variables:
  dgamma pnorm spline
Consider adding
  importFrom("stats", "dgamma", "pnorm", "spline")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘RInside’ ‘circular’
  All declared Imports should be used.
cit.assignBcmst: no visible binding for global variable ‘citbcmst’
cit.assignBcmst : <anonymous>: no visible global function definition
  for ‘median’
cit.assignBcmst: no visible global function definition for ‘prcomp’
cit.assignBcmst: no visible global function definition for ‘par’
cit.assignBcmst: no visible global function definition for ‘lines’
cit.assignBcmst: no visible global function definition for ‘legend’
cit.centroids : <anonymous>: no visible global function definition for
  ‘median’
cit.centroids : <anonymous>: no visible global function definition for
  ‘var’
cit.dist: no visible global function definition for ‘dist’
cit.dist: no visible global function definition for ‘as.dist’
cit.dist: no visible global function definition for ‘cor’
cit.distToCentroids: no visible global function definition for
  ‘quantile’
cit.distToCentroids : <anonymous>: no visible global function
  definition for ‘median’
cit.distToCentroids : <anonymous>: no visible global function
  definition for ‘mad’
Undefined global functions or variables:
  as.dist citbcmst cor dist legend lines mad median par prcomp quantile
  var
Consider adding
  importFrom("graphics", "legend", "lines", "par")
  importFrom("stats", "as.dist", "cor", "dist", "mad", "median",
             "prcomp", "quantile", "var")
to your NAMESPACE file.
cit.assignCcmst: no visible binding for global variable ‘citccmst’
cit.assignCcmst : <anonymous>: no visible global function definition
  for ‘median’
cit.assignCcmst : median.na: no visible global function definition for
  ‘median’
cit.assignCcmst: no visible global function definition for ‘prcomp’
cit.assignCcmst: no visible global function definition for ‘par’
cit.assignCcmst: no visible global function definition for ‘lines’
cit.assignCcmst: no visible global function definition for ‘legend’
cit.centroids : <anonymous>: no visible global function definition for
  ‘median’
cit.centroids : <anonymous>: no visible global function definition for
  ‘var’
cit.dist: no visible global function definition for ‘dist’
cit.dist: no visible global function definition for ‘as.dist’
cit.dist: no visible global function definition for ‘cor’
cit.distToCentroids: no visible global function definition for
  ‘quantile’
cit.distToCentroids : <anonymous>: no visible global function
  definition for ‘median’
cit.distToCentroids : <anonymous>: no visible global function
  definition for ‘mad’
Undefined global functions or variables:
  as.dist citccmst cor dist legend lines mad median par prcomp quantile
  var
Consider adding
  importFrom("graphics", "legend", "lines", "par")
  importFrom("stats", "as.dist", "cor", "dist", "mad", "median",
             "prcomp", "quantile", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
CityPlot: no visible global function definition for ‘read.table’
CityPlot: no visible global function definition for ‘tail’
CityPlot: no visible global function definition for ‘pdf’
CityPlot: no visible global function definition for ‘split.screen’
CityPlot: no visible global function definition for ‘screen’
CityPlot: no visible global function definition for ‘par’
CityPlot: no visible global function definition for ‘rect’
CityPlot: no visible global function definition for ‘text’
CityPlot: no visible global function definition for ‘lines’
CityPlot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off lines par pdf read.table rect screen split.screen tail text
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "rect", "screen",
             "split.screen", "text")
  importFrom("utils", "read.table", "tail")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘shinyBS’
  All declared Imports should be used.
Note: found 29 marked UTF-8 strings
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rggobi’
'library' or 'require' call to ‘rggobi’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
generate_data : <anonymous>: no visible global function definition for
  ‘runif’
knnf: no visible global function definition for ‘terms’
rescaler.default: no visible global function definition for ‘sd’
rescaler.default: no visible global function definition for ‘median’
rescaler.default: no visible global function definition for ‘mad’
simvar.numeric: no visible global function definition for ‘runif’
Undefined global functions or variables:
  mad median runif sd terms
Consider adding
  importFrom("stats", "mad", "median", "runif", "sd", "terms")
to your NAMESPACE file.
Running examples in ‘cleanNLP-Ex.R’ failed
The error most likely occurred in:

> ### Name: cnlp_annotate
> ### Title: Run the annotation pipeline on a set of documents
> ### Aliases: cnlp_annotate
> 
> ### ** Examples
> 
> cnlp_init_stringi()
> cnlp_annotate(un)
Error in stri_detect_regex(str, regex, ...) : 
  Start of codes indicating failure. (U_ILLEGAL_ARGUMENT_ERROR)
Calls: cnlp_annotate ... annotate_with_stringi -> <Anonymous> -> stri_detect_regex
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(cleanNLP)
  > 
  > test_check("cleanNLP")
  ── 1. Error: testing stringi (@test-annotation.R#9)  ───────────────────────────
  Start of codes indicating failure. (U_ILLEGAL_ARGUMENT_ERROR)
  Backtrace:
   1. cleanNLP::cnlp_annotate(un, verbose = FALSE)
   2. cleanNLP:::annotate_with_stringi(input, verbose)
   3. stringi::stri_detect(...)
   4. stringi::stri_detect_regex(str, regex, ...)
  
  ── 2. Error: testing utils_tfidf (@test-tools.R#9)  ────────────────────────────
  Start of codes indicating failure. (U_ILLEGAL_ARGUMENT_ERROR)
  Backtrace:
   1. cleanNLP::cnlp_annotate(un, verbose = FALSE)
   2. cleanNLP:::annotate_with_stringi(input, verbose)
   3. stringi::stri_detect(...)
   4. stringi::stri_detect_regex(str, regex, ...)
  
  ── 3. Error: testing tidy_pca (@test-tools.R#20)  ──────────────────────────────
  Start of codes indicating failure. (U_ILLEGAL_ARGUMENT_ERROR)
  Backtrace:
   1. cleanNLP::cnlp_annotate(un, verbose = FALSE)
   2. cleanNLP:::annotate_with_stringi(input, verbose)
   3. stringi::stri_detect(...)
   4. stringi::stri_detect_regex(str, regex, ...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 3 ]
  1. Error: testing stringi (@test-annotation.R#9) 
  2. Error: testing utils_tfidf (@test-tools.R#9) 
  3. Error: testing tidy_pca (@test-tools.R#20) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘scales’ ‘sp’
  All declared Imports should be used.
clime: no visible global function definition for ‘cov’
cv.clime: no visible global function definition for ‘cov’
cv.clime: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  cov sd
Consider adding
  importFrom("stats", "cov", "sd")
to your NAMESPACE file.
Running examples in ‘climwin-Ex.R’ failed
The error most likely occurred in:

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

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  ||||||||||||||||||||||||                                               |  33%
  |                                                                            
  |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 100%Error in min(modlist$ModelAICc) : invalid 'type' (list) of argument
Calls: slidingwin -> basewin -> %in%
Execution halted
Note: found 1 marked UTF-8 string
Namespaces in Imports field not imported from:
  ‘car’ ‘emmeans’
  All declared Imports should be used.
Running examples in ‘ClinReport-Ex.R’ failed
The error most likely occurred in:

> ### Name: report.quali.hlev
> ### Title: 'Hierarchical Qualitative' statistics reporting (experimental)
> ### Aliases: report.quali.hlev
> 
> ### ** Examples
> 
> 
> data(adverse_event)
> 
> test=report.quali.hlev(data=adverse_event,subjid="SUBJID",var_upper="PTNAME",
+ var_lower="SOCNAME",lower.levels="System Organ Class",upper.levels="Prefered Terms",x1="randtrt")
Error in match.names(clabs, names(xi)) : 
  names do not match previous names
Calls: report.quali.hlev -> report.quali.hlev -> rbind -> rbind -> match.names
Execution halted
gxe.cc: no visible global function definition for ‘qnorm’
gxe.coh: no visible global function definition for ‘qnorm’
utility.cc: no visible global function definition for ‘qnorm’
utility.coh: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
socp: no visible global function definition for ‘as’
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package which this enhances but not available for checking: ‘RWeka’
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Note: found 2 marked Latin-1 strings
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
Found the following files/directories:
  ‘clusterhap_reports’
Running examples in ‘clusterlab-Ex.R’ failed
The error most likely occurred in:

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

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘R6’ ‘purrr’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Error(s) in re-building vignettes:
  ...
--- re-building ‘the_clusterR_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.
Quitting from lines 403-416 (the_clusterR_package.Rmd) 
Error: processing vignette 'the_clusterR_package.Rmd' failed with diagnostics:
std::bad_alloc
--- failed re-building ‘the_clusterR_package.Rmd’

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

Error: Vignette re-building failed.
Execution halted
hopkins: no visible global function definition for ‘runif’
hopkins: no visible global function definition for ‘dist’
Undefined global functions or variables:
  dist runif
Consider adding
  importFrom("stats", "dist", "runif")
to your NAMESPACE file.
License components which are templates and need '+ file LICENSE':
  MIT
clustomit: no visible binding for global variable ‘weighted.mean’
sim_unif : multivariate_unif: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  runif weighted.mean
Consider adding
  importFrom("stats", "runif", "weighted.mean")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Note: found 5626 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cluster’ ‘datasets’ ‘dplyr’ ‘klaR’ ‘psycho’ ‘shiny’
  All declared Imports should be used.
braycurtis: no visible global function definition for ‘as.dist’
czekanowski: no visible global function definition for ‘as.dist’
findComplementaryIndices: no visible global function definition for
  ‘na.omit’
genSimilarityProfile: no visible global function definition for ‘dist’
simprof: no visible global function definition for ‘dist’
simprof: no visible global function definition for ‘hclust’
simprof.plot : <local> : colorizer: no visible global function
  definition for ‘is.leaf’
simprof.plot: no visible global function definition for ‘rainbow’
simprof.plot: no visible global function definition for ‘dendrapply’
simprof.plot: no visible global function definition for ‘as.dendrogram’
Undefined global functions or variables:
  as.dendrogram as.dist dendrapply dist hclust is.leaf na.omit rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("stats", "as.dendrogram", "as.dist", "dendrapply", "dist",
             "hclust", "is.leaf", "na.omit")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘Biobase’ ‘GO.db’ ‘annotate’ ‘kohonen’ ‘mclust’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
cma_es: no visible global function definition for ‘rnorm’
f_rand: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
alpha.cronbach: no visible global function definition for ‘cov’
alpha.curve: no visible global function definition for ‘text’
Undefined global functions or variables:
  cov text
Consider adding
  importFrom("graphics", "text")
  importFrom("stats", "cov")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘caret’ ‘e1071’ ‘epitools’ ‘shiny’ ‘shinyMatrix’
  All declared Imports should be used.
copynumberBootstrap: no visible global function definition for
  ‘txtProgressBar’
copynumberBootstrap: no visible global function definition for
  ‘quantile’
copynumberBootstrap: no visible global function definition for
  ‘setTxtProgressBar’
gethits: no visible global function definition for ‘read.table’
normalizeGC: no visible global function definition for ‘median’
plotCNOGpro: no visible global function definition for ‘par’
plotCNOGpro: no visible global function definition for ‘rainbow’
plotCNOGpro: no visible global function definition for ‘density’
plotCNOGpro: no visible global function definition for ‘polygon’
plotCNOGpro: no visible global function definition for ‘lines’
plotCNOGpro: no visible global function definition for ‘legend’
plotCNOGpro: no visible global function definition for ‘boxplot’
sampleChromosome: no visible global function definition for ‘median’
sampleChromosome: no visible binding for global variable ‘var’
setupEmissionMatrix: no visible global function definition for ‘dgeom’
store: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  boxplot density dgeom legend lines median par polygon quantile
  rainbow read.table setTxtProgressBar txtProgressBar var write.table
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "boxplot", "legend", "lines", "par", "polygon")
  importFrom("stats", "density", "dgeom", "median", "quantile", "var")
  importFrom("utils", "read.table", "setTxtProgressBar",
             "txtProgressBar", "write.table")
to your NAMESPACE file.
CNclusterNcenter: no visible global function definition for ‘median’
CNclusterNcenter: no visible binding for global variable ‘var’
breakIntoGaps: no visible global function definition for ‘runif’
centerprob: no visible global function definition for ‘pnorm’
getz: no visible global function definition for ‘predict’
smad: no visible global function definition for ‘mad’
smedian: no visible global function definition for ‘median’
smedian.sample: no visible global function definition for ‘median’
smedmad: no visible global function definition for ‘median’
smedmad: no visible global function definition for ‘mad’
Undefined global functions or variables:
  mad median pnorm predict runif var
Consider adding
  importFrom("stats", "mad", "median", "pnorm", "predict", "runif",
             "var")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.1Mb
    extdata   1.8Mb
coalescentMCMC: no visible global function definition for
  ‘packageVersion’
coalescentMCMC : getparams: no visible global function definition for
  ‘nlminb’
sim.coalescent: no visible global function definition for ‘segments’
sim.coalescent: no visible global function definition for ‘points’
Undefined global functions or variables:
  nlminb packageVersion points segments
Consider adding
  importFrom("graphics", "points", "segments")
  importFrom("stats", "nlminb")
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘lars’ ‘randomForest’ ‘ridge’ ‘snowfall’ ‘tree’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
COBRA : COBRA.lars: no visible global function definition for ‘lars’
COBRA : COBRA.lars: no visible global function definition for
  ‘predict.lars’
COBRA : COBRA.tree: no visible global function definition for ‘tree’
COBRA : COBRA.tree: no visible global function definition for
  ‘as.formula’
COBRA : COBRA.tree: no visible global function definition for ‘predict’
COBRA : COBRA.ridge: no visible global function definition for
  ‘linearRidge’
COBRA : COBRA.ridge: no visible global function definition for
  ‘as.formula’
COBRA : COBRA.ridge: no visible global function definition for
  ‘predict’
COBRA : COBRA.randomForest: no visible global function definition for
  ‘randomForest’
COBRA : COBRA.randomForest: no visible global function definition for
  ‘predict’
COBRA: no visible global function definition for ‘sfInit’
COBRA: no visible global function definition for ‘sfLibrary’
COBRA: no visible global function definition for ‘sfExportAll’
COBRA: no visible global function definition for ‘sfSapply’
COBRA: no visible global function definition for ‘sfStop’
COBRA: no visible global function definition for ‘write.table’
COBRA: no visible global function definition for ‘pdf’
COBRA: no visible global function definition for ‘points’
COBRA: no visible global function definition for ‘legend’
COBRA: no visible global function definition for ‘abline’
COBRA: no visible global function definition for ‘lines’
COBRA: no visible global function definition for ‘dev.off’
COBRA: no visible global function definition for ‘dev.new’
Undefined global functions or variables:
  abline as.formula dev.new dev.off lars legend linearRidge lines pdf
  points predict predict.lars randomForest sfExportAll sfInit sfLibrary
  sfSapply sfStop tree write.table
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("graphics", "abline", "legend", "lines", "points")
  importFrom("stats", "as.formula", "predict")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Package required but not available: ‘ggtern’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘rkward’
Package which this enhances but not available for checking: ‘rkward’
Note: found 19 marked UTF-8 strings
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.
Namespaces in Imports field not imported from:
  ‘graphics’ ‘jsonlite’ ‘pander’
  All declared Imports should be used.
Note: found 65 marked UTF-8 strings
Found the following files/directories:
  ‘foo.R’ ‘foo.html’
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘codemeta-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 85-86 (codemeta-intro.Rmd) 
Error: processing vignette 'codemeta-intro.Rmd' failed with diagnostics:
Timeout was reached: [sysreqs.r-hub.io] Operation timed out after 10003 milliseconds with 0 out of 0 bytes received
--- failed re-building ‘codemeta-intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘bvpSolve’
Found the following files/directories:
  ‘fda7wnr6u.c’
Namespaces in Imports field not imported from:
  ‘methods’ ‘readr’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Running-CoDiNA.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 100-105 (Running-CoDiNA.Rmd) 
Error: processing vignette 'Running-CoDiNA.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
--- failed re-building ‘Running-CoDiNA.Rmd’

SUMMARY: processing the following file failed:
  ‘Running-CoDiNA.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [93s/111s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat) 
  > library(codyn)
  > test_check("codyn")
  ── 1. Failure: rank_shift loads and returns correct result (@test_rank_shift.R#1
  result[, 1] inherits from `character` not `factor`.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 359 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: rank_shift loads and returns correct result (@test_rank_shift.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
alpha: no visible global function definition for ‘na.omit’
bootstrap: no visible global function definition for ‘sd’
bootstrap: no visible global function definition for ‘qnorm’
bootstrap: no visible global function definition for ‘pnorm’
bootstrap: no visible global function definition for ‘quantile’
bootstrap: no visible global function definition for ‘density’
omega: no visible global function definition for ‘na.omit’
plot.alpha: no visible global function definition for ‘par’
plot.alpha: no visible global function definition for ‘text’
plot.alpha: no visible global function definition for ‘box’
plot.alpha: no visible global function definition for ‘axis’
plot.alpha: no visible global function definition for ‘lines’
plot.alpha: no visible global function definition for ‘legend’
plot.alpha: no visible global function definition for ‘points’
plot.omega: no visible global function definition for ‘par’
plot.omega: no visible global function definition for ‘text’
plot.omega: no visible global function definition for ‘box’
plot.omega: no visible global function definition for ‘axis’
plot.omega: no visible global function definition for ‘lines’
plot.omega: no visible global function definition for ‘legend’
plot.omega: no visible global function definition for ‘points’
summary.alpha: no visible global function definition for ‘pnorm’
summary.alpha: no visible global function definition for ‘qnorm’
summary.omega: no visible global function definition for ‘pnorm’
summary.omega: no visible global function definition for ‘qnorm’
tau.test: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  axis box density legend lines na.omit par pnorm points qnorm quantile
  sd text
Consider adding
  importFrom("graphics", "axis", "box", "legend", "lines", "par",
             "points", "text")
  importFrom("stats", "density", "na.omit", "pnorm", "qnorm", "quantile",
             "sd")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
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 44-47 (Getting_Started.Rmd) 
Error: processing vignette 'Getting_Started.Rmd' failed with diagnostics:

--- failed re-building ‘Getting_Started.Rmd’

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

Error: Vignette re-building failed.
Execution halted
BMDE: no visible global function definition for ‘quantile’
BMDU: no visible global function definition for ‘runif’
BMDU: no visible global function definition for ‘quantile’
FS: no visible global function definition for ‘qnorm’
GM: no visible global function definition for ‘qchisq’
QH: no visible global function definition for ‘qchisq’
SG : sgp: no visible global function definition for ‘ppois’
SG : sgp: no visible global function definition for ‘dpois’
WALD: no visible global function definition for ‘qchisq’
WALDCC: no visible global function definition for ‘qchisq’
WS: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  dpois ppois qchisq qnorm quantile runif
Consider adding
  importFrom("stats", "dpois", "ppois", "qchisq", "qnorm", "quantile",
             "runif")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘coin’ ‘ggplot2’ ‘plyr’
  All declared Imports should be used.
Note: found 237 marked UTF-8 strings
Running examples in ‘colocalization-Ex.R’ failed
The error most likely occurred in:

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

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

The r.model = 'r.med'!
r.min = 0.722833786275035 is used!
r.max = 0.722833786275035 is used!
Because of r.min = r.max, r.count = 1 and r.adjust = 0 are used!
Bi-direction colocalization is considered!
index.d for r = 0.722833786275035 is -0.224788967716664 ;
The average coolocalization index of type d over all choosen r's is = -0.224788967716664!
> 
> plot(twolines.results)
Error in levels(P.all$type) <- c(expression(paste(italic(P), sep = "")),  : 
  unimplemented type 'expression' in 'HashTableSetup'
Calls: plot -> plot.colocal -> <Anonymous>
Execution halted
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Found the following files/directories:
  ‘HeliconiusColorTree.newick’
cICA: no visible global function definition for ‘mvfft’
cICA: no visible global function definition for ‘ar.yw’
cICA: no visible global function definition for ‘rnorm’
scICA: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  ar.yw mvfft rnorm
Consider adding
  importFrom("stats", "ar.yw", "mvfft", "rnorm")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Package in Depends field not imported from: ‘grid’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plotVenn2d : twoWayOverlap: no visible global function definition for
  ‘grid.polygon’
plotVenn2d : twoWayOverlap: no visible global function definition for
  ‘gpar’
plotVenn2d: no visible global function definition for ‘grid.text’
plotVenn2d: no visible global function definition for ‘gpar’
plotVenn2d: no visible global function definition for ‘grid.polygon’
plotVenn3d : twoWayOverlap: no visible global function definition for
  ‘grid.polygon’
plotVenn3d : twoWayOverlap: no visible global function definition for
  ‘gpar’
plotVenn3d: no visible global function definition for ‘grid.text’
plotVenn3d: no visible global function definition for ‘gpar’
plotVenn3d: no visible global function definition for ‘grid.polygon’
plotVenn4d : getCommonEllipse: no visible global function definition
  for ‘aggregate’
plotVenn4d : region.polygon: no visible global function definition for
  ‘head’
plotVenn4d : region.polygon: no visible global function definition for
  ‘grid.polygon’
plotVenn4d : region.polygon: no visible global function definition for
  ‘gpar’
plotVenn4d: no visible global function definition for ‘grid.text’
plotVenn4d: no visible global function definition for ‘gpar’
plotVenn4d: no visible global function definition for ‘pushViewport’
plotVenn4d: no visible global function definition for ‘viewport’
plotVenn4d: no visible global function definition for ‘grid.polygon’
plotVenn4d: no visible global function definition for ‘upViewport’
resizeCircles: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  aggregate gpar grid.polygon grid.text head pushViewport uniroot
  upViewport viewport
Consider adding
  importFrom("stats", "aggregate", "uniroot")
  importFrom("utils", "head")
to your NAMESPACE file.
generateMonochromaticColors: no visible global function definition for
  ‘col2rgb’
generateMonochromaticColors: no visible global function definition for
  ‘rgb’
generateMonochromaticColors: no visible global function definition for
  ‘tail’
hsv2rgb: no visible global function definition for ‘rgb’
rotational_dispersion: no visible global function definition for
  ‘col2rgb’
rotational_dispersion: no visible global function definition for
  ‘rgb2hsv’
tetradicColors: no visible global function definition for ‘head’
triadicColors: no visible global function definition for ‘head’
Undefined global functions or variables:
  col2rgb head rgb rgb2hsv tail
Consider adding
  importFrom("grDevices", "col2rgb", "rgb", "rgb2hsv")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘grid’ ‘gridExtra’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
primary.colors: no visible global function definition for ‘rgb’
rgb.tables: no visible global function definition for ‘rgb’
ygobb: no visible global function definition for ‘approx’
ygobb: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  approx rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "approx")
to your NAMESPACE file.
Found the following files/directories:
  ‘random.txt’
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   2.3Mb
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
competitive.test: no visible global function definition for ‘runif’
selfcontained.test : fun2: no visible global function definition for
  ‘qchisq’
selfcontained.test: no visible global function definition for ‘cov’
selfcontained.test: no visible global function definition for ‘qchisq’
selfcontained.test: no visible global function definition for ‘cor’
selfcontained.test: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  cor cov pchisq qchisq runif
Consider adding
  importFrom("stats", "cor", "cov", "pchisq", "qchisq", "runif")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘lattice’ ‘rgl’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following files/directories:
  ‘cometExactTest_plot.pdf’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
Package suggested but not available for checking: ‘rscala’
Malformed Title field: should not end in a period.
p.Johansen: no visible global function definition for ‘pgamma’
plotComT: no visible global function definition for ‘axis’
plotComT: no visible global function definition for ‘title’
plotComT: no visible global function definition for ‘lines’
plotComT: no visible global function definition for ‘box’
q.Johansen: no visible global function definition for ‘qgamma’
Undefined global functions or variables:
  axis box lines pgamma qgamma title
Consider adding
  importFrom("graphics", "axis", "box", "lines", "title")
  importFrom("stats", "pgamma", "qgamma")
to your NAMESPACE file.
CommT.anova: no visible global function definition for ‘aov’
CommT.legendpos: no visible global function definition for ‘quantile’
CommT.plotcolors: no visible global function definition for ‘hcl’
Undefined global functions or variables:
  aov hcl quantile
Consider adding
  importFrom("grDevices", "hcl")
  importFrom("stats", "aov", "quantile")
to your NAMESPACE file.
addxaxis: no visible global function definition for ‘par’
addxaxis: no visible global function definition for ‘axis’
addxaxis: no visible global function definition for ‘mtext’
eplot: no visible global function definition for ‘par’
eplot: no visible global function definition for ‘axis’
eplot: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  axis mtext par
Consider adding
  importFrom("graphics", "axis", "mtext", "par")
to your NAMESPACE file.
Package suggested but not available for checking: ‘CAM’
compareC: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘stringr’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   2.3Mb
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘XML’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘XML’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
compareODM: no visible global function definition for ‘xmlRoot’
compareODM: no visible global function definition for ‘xmlTreeParse’
compareODM: no visible global function definition for ‘xmlChildren’
compareODM: no visible global function definition for ‘xmlAttrs’
compareODM: no visible global function definition for ‘xmlValue’
Undefined global functions or variables:
  xmlAttrs xmlChildren xmlRoot xmlTreeParse xmlValue
Malformed Description field: should contain one or more complete sentences.
two.level.comparison.items: no visible global function definition for
  ‘complete.cases’
two.level.components: no visible global function definition for
  ‘complete.cases’
plot,ece: no visible global function definition for ‘par’
plot,ece: no visible global function definition for ‘points’
plot,ece: no visible global function definition for ‘mtext’
plot,ece: no visible global function definition for ‘legend’
plot,ece: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline complete.cases legend mtext par points
Consider adding
  importFrom("graphics", "abline", "legend", "mtext", "par", "points")
  importFrom("stats", "complete.cases")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘R6’ ‘checkmate’ ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘PearsonDS’ ‘VGAM’ ‘actuar’ ‘fExtremes’ ‘rmutil’
  All declared Imports should be used.
Package suggested but not available for checking: ‘inSilicoDb’
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Package in Depends field not imported from: ‘numDeriv’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dcomplnorm: no visible global function definition for ‘grad’
dcomplnorm : f1: no visible global function definition for ‘dlnorm’
dcomplnorm : F1: no visible global function definition for ‘plnorm’
dcomplnorm : f1L: no visible global function definition for ‘dlnorm’
dcomplnorm : F1L: no visible global function definition for ‘plnorm’
pcomplnorm: no visible global function definition for ‘grad’
pcomplnorm : f1: no visible global function definition for ‘dlnorm’
pcomplnorm : F1: no visible global function definition for ‘plnorm’
pcomplnorm : F1L: no visible global function definition for ‘plnorm’
qcomplnorm: no visible global function definition for ‘grad’
qcomplnorm : f1: no visible global function definition for ‘dlnorm’
qcomplnorm : F1q: no visible global function definition for ‘qlnorm’
qcomplnorm : F1: no visible global function definition for ‘plnorm’
rcomplnorm: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dlnorm grad plnorm qlnorm runif
Consider adding
  importFrom("stats", "dlnorm", "plnorm", "qlnorm", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘hypergeo’ which was already attached by Depends.
  Please remove these calls from your code.
momentCompound: no visible global function definition for ‘integrate’
pgfIhypergeometric: no visible global function definition for ‘uniroot’
pgfIhyperpoisson: no visible global function definition for ‘uniroot’
pgfIkattitypeh1: no visible global function definition for ‘uniroot’
pgfIkattitypeh2: no visible global function definition for ‘uniroot’
pgfIneymantypeb: no visible global function definition for ‘uniroot’
pgfIneymantypec: no visible global function definition for ‘uniroot’
pgfIpoissonlindley: no visible global function definition for ‘uniroot’
pgfIthomas: no visible global function definition for ‘uniroot’
pgfIwaring: no visible global function definition for ‘uniroot’
pgfIyule: no visible global function definition for ‘uniroot’
rCompound: no visible global function definition for ‘runif’
Undefined global functions or variables:
  integrate runif uniroot
Consider adding
  importFrom("stats", "integrate", "runif", "uniroot")
to your NAMESPACE file.
kef: no visible global function definition for ‘dgamma’
kef: no visible global function definition for ‘dlnorm’
simp_int: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx dgamma dlnorm
Consider adding
  importFrom("stats", "approx", "dgamma", "dlnorm")
to your NAMESPACE file.
Found the following sources/headers with CR or CRLF line endings:
  inst/include/ConConPiWiFun.h
  inst/include/convex_function_manip.hpp
  inst/include/convex_functions_tools.hpp
  inst/include/cplfunction.hpp
  inst/include/cplfunctionvec.hpp
  inst/include/cpqfunction.hpp
  inst/include/cpqfunctionvec.hpp
Some Unix compilers require LF line endings.
prepare_Rd: concor.Rd:4: Dropping empty section \keyword
prepare_Rd: concor.Rd:5: Dropping empty section \keyword
prepare_Rd: concorcano.Rd:4: Dropping empty section \keyword
prepare_Rd: concorcano.Rd:5: Dropping empty section \keyword
prepare_Rd: concoreg.Rd:4: Dropping empty section \keyword
prepare_Rd: concoreg.Rd:5: Dropping empty section \keyword
prepare_Rd: concorgm.Rd:4: Dropping empty section \keyword
prepare_Rd: concorgm.Rd:5: Dropping empty section \keyword
prepare_Rd: concorgmcano.Rd:4: Dropping empty section \keyword
prepare_Rd: concorgmcano.Rd:5: Dropping empty section \keyword
prepare_Rd: concorgmreg.Rd:4: Dropping empty section \keyword
prepare_Rd: concorgmreg.Rd:5: Dropping empty section \keyword
prepare_Rd: concors.Rd:4: Dropping empty section \keyword
prepare_Rd: concors.Rd:5: Dropping empty section \keyword
prepare_Rd: concorscano.Rd:4: Dropping empty section \keyword
prepare_Rd: concorscano.Rd:5: Dropping empty section \keyword
prepare_Rd: concorsreg.Rd:4: Dropping empty section \keyword
prepare_Rd: concorsreg.Rd:5: Dropping empty section \keyword
prepare_Rd: svdbip.Rd:4: Dropping empty section \keyword
prepare_Rd: svdbip.Rd:5: Dropping empty section \keyword
prepare_Rd: svdbip2.Rd:4: Dropping empty section \keyword
prepare_Rd: svdbip2.Rd:5: Dropping empty section \keyword
prepare_Rd: svdbips.Rd:4: Dropping empty section \keyword
prepare_Rd: svdbips.Rd:5: Dropping empty section \keyword
prepare_Rd: svdcp.Rd:4: Dropping empty section \keyword
prepare_Rd: svdcp.Rd:5: Dropping empty section \keyword
Namespaces in Imports field not imported from:
  ‘MASS’ ‘compiler’ ‘rlang’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Missing or unexported object: ‘xlsx::CellBlock.default’
K1.norm: no visible global function definition for ‘dnorm’
K1.norm: no visible global function definition for ‘pnorm’
K1.t3: no visible global function definition for ‘pt’
K2.norm: no visible global function definition for ‘dnorm’
K2.norm: no visible global function definition for ‘pnorm’
K2.t3: no visible global function definition for ‘pt’
Undefined global functions or variables:
  dnorm pnorm pt
Consider adding
  importFrom("stats", "dnorm", "pnorm", "pt")
to your NAMESPACE file.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data      6.5Mb
    extdata   2.8Mb
Malformed Description field: should contain one or more complete sentences.
ml_solver: no visible global function definition for ‘approx’
select_kmax: no visible global function definition for ‘median’
Undefined global functions or variables:
  approx median
Consider adding
  importFrom("stats", "approx", "median")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘cli’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
conicPlot: no visible global function definition for ‘palette’
conicPlotAsymptotes: no visible global function definition for
  ‘palette’
conicPlotAsymptotes: no visible global function definition for ‘abline’
conicPlotAxes: no visible global function definition for ‘palette’
conicPlotAxes: no visible global function definition for ‘abline’
plotDegenerateConic: no visible global function definition for ‘points’
plotDegenerateConic: no visible global function definition for ‘abline’
plotEllipsis: no visible global function definition for ‘lines’
plotEllipsis: no visible global function definition for ‘points’
plotHyperbola: no visible global function definition for ‘lines’
plotHyperbola: no visible global function definition for ‘points’
plotParabola: no visible global function definition for ‘lines’
Undefined global functions or variables:
  abline lines palette points
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "abline", "lines", "points")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
'library' or 'require' call to ‘parallel’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘Rmpi’ ‘snow’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ConjointChecks: no visible global function definition for ‘makeCluster’
ConjointChecks: no visible global function definition for
  ‘clusterSetRNGStream’
ConjointChecks: no visible global function definition for
  ‘clusterApply’
ConjointChecks: no visible global function definition for ‘stopCluster’
omni.check: no visible global function definition for ‘runif’
omni.check: no visible global function definition for ‘quantile’
plot.checks: no visible global function definition for ‘mtext’
plot.checks: no visible global function definition for ‘text’
Undefined global functions or variables:
  clusterApply clusterSetRNGStream makeCluster mtext quantile runif
  stopCluster text
Consider adding
  importFrom("graphics", "mtext", "text")
  importFrom("stats", "quantile", "runif")
to your NAMESPACE file.
Found the following files/directories:
  ‘design_names.csv’ ‘design_numbers.csv’
  ‘encoded_orthogonal_factorial_design.csv’
  ‘orthogonal_factorial_design.csv’
Namespace in Imports field not imported from: ‘reshape’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘geosphere’ ‘igraph’ ‘methods’ ‘rgdal’ ‘sf’
  All declared Imports should be used.
Running examples in ‘contact-Ex.R’ failed
The error most likely occurred in:

> ### Name: contactDur.all
> ### Title: Identify Inter-animal Contacts
> ### Aliases: contactDur.all
> ### Keywords: contact data-processing
> 
> ### ** Examples
> 
> 
> data(calves)
> 
> calves.dateTime<-datetime.append(calves, date = calves$date, time =
+     calves$time) #create a dataframe with dateTime identifiers for location foxes
>     
> calves.agg<-tempAggregate(calves.dateTime, id = calves.dateTime$calftag,
+     dateTime = calves.dateTime$dateTime, point.x = calves.dateTime$x,
+     point.y = calves.dateTime$y, secondAgg = 300, extrapolate.left = FALSE,
+     extrapolate.right = FALSE, resolutionLevel = "reduced", parallel = FALSE,
+     na.rm = TRUE, smooth.type = 1) #smooth locations to 5-min fix intervals.
> 
> calves.dist<-dist2All_df(x = calves.agg, parallel = FALSE, dataType = "Point",
+     lonlat = FALSE) #calculate distance between all individuals at each timepoint
>     
> calves.contact.block<-contactDur.all(x = calves.dist, dist.threshold=1,
+     sec.threshold=10, blocking = TRUE, blockUnit = "hours", blockLength = 1,
+     equidistant.time = FALSE, parallel = FALSE, reportParameters = TRUE)
Error in UseMethod("droplevels") : 
  no applicable method for 'droplevels' applied to an object of class "character"
Calls: contactDur.all ... data.frame -> <Anonymous> -> apply -> FUN -> droplevels
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Using_the_contact_package_v1.0.1.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 222-230 (Using_the_contact_package_v1.0.1.Rmd) 
Error: processing vignette 'Using_the_contact_package_v1.0.1.Rmd' failed with diagnostics:
invalid color name 'feed'
--- failed re-building ‘Using_the_contact_package_v1.0.1.Rmd’

SUMMARY: processing the following file failed:
  ‘Using_the_contact_package_v1.0.1.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘MASS’ ‘geepack’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘contrast.Rnw’ using Sweave
Loading required package: rms
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: ‘Hmisc’

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

    format.pval, units

Loading required package: SparseM

Attaching package: ‘SparseM’

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

    backsolve


Error: processing vignette 'contrast.Rnw' failed with diagnostics:
 chunk 8 (label = eachTest) 
Error in eval(predvars, data, env) : object 'diet' not found

--- failed re-building 'contrast.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Note: found 3 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘devtools’ ‘formattable’ ‘gridExtra’ ‘kableExtra’ ‘knitr’ ‘magrittr’
  ‘readr’ ‘readxl’ ‘tidyverse’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Package suggested but not available for checking: ‘MonetDBLite’
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Running examples in ‘cooccurNet-Ex.R’ failed
The error most likely occurred in:

> ### Name: coocnet
> ### Title: coocnet
> ### Aliases: coocnet
> 
> ### ** Examples
> 
> cooccurNetwork  = coocnet(dataFile=getexample(dataType="protein"), dataType="protein")
reading file......
completed. (10,329)
preprocess file......Error in if (pred >= memsize * alpha || ncol > 150 || (nrow > 30000 &  : 
  missing value where TRUE/FALSE needed
Calls: coocnet ... cooccur.dataprepreprocess.preprocess -> inmemoryflag
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Extending-cooccurNet.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 176-178 (Extending-cooccurNet.Rmd) 
Error: processing vignette 'Extending-cooccurNet.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building ‘Extending-cooccurNet.Rmd’

SUMMARY: processing the following file failed:
  ‘Extending-cooccurNet.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘memory.limits’
maCooperative: no visible global function definition for ‘points’
maCooperative: no visible global function definition for ‘legend’
maPessimistic: no visible global function definition for ‘combn’
maRules: no visible global function definition for ‘capture.output’
mstCooperative: no visible global function definition for ‘points’
mstCooperative: no visible global function definition for ‘legend’
mstOptimistic: no visible global function definition for ‘combn’
mstPessimistic: no visible global function definition for ‘combn’
mstRules: no visible global function definition for ‘capture.output’
plotCoreSet: no visible global function definition for ‘points’
plotCoreSet: no visible global function definition for ‘polygon’
plotImputationSet: no visible global function definition for ‘par’
plotImputationSet: no visible global function definition for ‘box’
plotImputationSet: no visible global function definition for ‘polygon’
plotImputationSet: no visible global function definition for ‘text’
shapleyValue: no visible global function definition for ‘combn’
Undefined global functions or variables:
  box capture.output combn legend par points polygon text
Consider adding
  importFrom("graphics", "box", "legend", "par", "points", "polygon",
             "text")
  importFrom("utils", "capture.output", "combn")
to your NAMESPACE file.
Package suggested but not available for checking: ‘cec2005benchmark’
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    R     2.4Mb
    doc   5.9Mb
Namespace in Imports field not imported from: ‘mcc’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
Note: found 26 marked UTF-8 strings
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
advanceRNG: no visible global function definition for ‘runif’
randomEventMoves: no visible global function definition for ‘runif’
randomRescaledEventMoves: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
coreTDT_geneset: no visible global function definition for
  ‘write.table’
pvalue_calculator: no visible global function definition for ‘dbinom’
Undefined global functions or variables:
  dbinom write.table
Consider adding
  importFrom("stats", "dbinom")
  importFrom("utils", "write.table")
to your NAMESPACE file.
compute.llh: no visible global function definition for ‘dnorm’
compute.u.hat.simple: no visible global function definition for ‘dnorm’
fit.CLM.1u.simple.start: no visible global function definition for
  ‘kmeans’
fit.CLMM.simple.start: no visible global function definition for
  ‘kmeans’
fit.CLMM.simple.start.NA: no visible global function definition for
  ‘kmeans’
Undefined global functions or variables:
  dnorm kmeans
Consider adding
  importFrom("stats", "dnorm", "kmeans")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘ggplot2’ ‘rmarkdown’ ‘shinyWidgets’ ‘shinydashboard’
  ‘shinyjs’
  All declared Imports should be used.
Note: found 1187 marked UTF-8 strings
Note: found 578 marked UTF-8 strings
Running examples in ‘corpus-Ex.R’ failed
The error most likely occurred in:

> ### Name: text_locate
> ### Title: Searching for Terms
> ### Aliases: text_count text_detect text_locate text_match text_sample
> ###   text_subset
> 
> ### ** Examples
> 
> text <- c("Rose is a rose is a rose is a rose.",
+           "A rose by any other name would smell as sweet.",
+           "Snow White and Rose Red")
> 
> text_count(text, "rose")
[1] 4 1 1
> text_detect(text, "rose")
[1] TRUE TRUE TRUE
> text_locate(text, "rose")
Error in sum(colwidths) : invalid 'type' (list) of argument
Calls: <Anonymous> ... print.corpus_text_locate -> format.corpus_text_locate
Execution halted
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Running ‘testthat.R’ [14s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(corpus)
  > 
  > test_check("corpus")
  -- 1. Error: 'text_locate' prints results correctly (@test-text_locate.R#161
  invalid 'type' (list) of argument
  Backtrace:
    1. base::strsplit(capture_output(print(loc), width = 76), "\n")
    9. corpus:::print.corpus_text_locate(loc)
   10. corpus:::format.corpus_text_locate(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 581 | SKIPPED: 12 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: 'text_locate' prints results correctly (@test-text_locate.R#161) 
  
  Error: testthat unit tests failed
  Execution halted
Note: found 532 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘profr’ ‘xtable’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
Note: found 2 marked Latin-1 strings
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    help   1.8Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
corr.Qmatrix: no visible global function definition for ‘cor’
corr.Qmatrix: no visible global function definition for ‘cor.test’
summarise.Fst: no visible global function definition for ‘cor’
summarise.Fst: no visible global function definition for ‘sd’
summarise.lnPD: no visible global function definition for ‘sd’
Undefined global functions or variables:
  cor cor.test sd
Consider adding
  importFrom("stats", "cor", "cor.test", "sd")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
dist: no visible global function definition for ‘quantile’
edgecount: no visible global function definition for ‘reshape’
edgecutoff: no visible global function definition for ‘boxplot’
edgecutoff: no visible global function definition for ‘sd’
edgecutoff: no visible global function definition for ‘median’
edgecutoff: no visible global function definition for ‘IQR’
Undefined global functions or variables:
  IQR boxplot median quantile reshape sd
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "IQR", "median", "quantile", "reshape", "sd")
to your NAMESPACE file.
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.
GA_search : subset_score: no visible global function definition for
  ‘combn’
choose_lambda : subset_score: no visible global function definition for
  ‘combn’
cond.fyx: no visible global function definition for ‘var’
cond.fyx: no visible global function definition for ‘cor’
diff_gen_PPI: no visible global function definition for ‘cov’
diff_gen_PPI: no visible global function definition for ‘sd’
f.test: no visible binding for global variable ‘var’
get_quantiles : node_edge: no visible global function definition for
  ‘combn’
score_scaling: no visible global function definition for ‘hist’
score_scaling: no visible global function definition for ‘sd’
Undefined global functions or variables:
  combn cor cov hist sd var
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "cor", "cov", "sd", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
cosinor.lm: no visible binding for global variable ‘na.omit’
cosinor.lm: no visible global function definition for ‘terms’
cosinor.lm: no visible global function definition for ‘as.formula’
cosinor.lm: no visible global function definition for ‘lm’
cosinor_analyzer: no visible binding for global variable ‘vitamind’
cosinor_analyzer : <anonymous>: no visible global function definition
  for ‘as.formula’
ggplot.cosinor.lm: no visible global function definition for ‘predict’
predict.cosinor.lm: no visible global function definition for ‘fitted’
predict.cosinor.lm: no visible global function definition for ‘predict’
simulate_cosinor: no visible global function definition for ‘runif’
simulate_cosinor: no visible global function definition for ‘rbinom’
simulate_cosinor: no visible global function definition for ‘rnorm’
summary.cosinor.lm: no visible global function definition for ‘vcov’
summary.cosinor.lm: no visible global function definition for ‘qnorm’
summary.cosinor.lm: no visible global function definition for ‘pnorm’
test_cosinor: no visible global function definition for ‘pchisq’
test_cosinor: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as.formula fitted lm na.omit pchisq pnorm predict qnorm rbinom rnorm
  runif terms vcov vitamind
Consider adding
  importFrom("stats", "as.formula", "fitted", "lm", "na.omit", "pchisq",
             "pnorm", "predict", "qnorm", "rbinom", "rnorm", "runif",
             "terms", "vcov")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
D.M: no visible global function definition for ‘integrate’
lookbackTime: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
Running examples in ‘CoSMoS-Ex.R’ failed
The error most likely occurred in:

> ### Name: acs
> ### Title: AutoCorrelation Structure
> ### Aliases: acs
> 
> ### ** Examples
> 
> 
> library(CoSMoS); library(ggplot2)
> 
> ## specify lag
> t <- 0:10
> 
> ## get the ACS
> f <- acs('fgn', t = t, H = .75)
> b <- acs('burrXII', t = t, scale = 1, shape1 = .6, shape2 = .4)
> w <- acs('weibull', t = t, scale = 2, shape = 0.8)
> p <- acs('paretoII', t = t, scale = 3, shape = 0.3)
> 
> ## visualize the ACS
> dta <- data.frame(t, f, b, w, p)
> 
> m.dta <- melt(dta, id.vars = 't')
Error in value[[3L]](cond) : 
  The melt generic in data.table has been passed a data.frame, but data.table::melt currently only has a method for data.tables. Please confirm your input is a data.table, with setDT(dta) or as.data.table(dta). If you intend to use a method from reshape2, try installing that package first, but do note that reshape2 is deprecated and you should be migrating your code away from using it.
Calls: melt ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  ‘Rglpk’ ‘glmnet’ ‘parallel’ ‘quadprog’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespace in Imports field not imported from: ‘jpeg’
  All declared Imports should be used.
Note: found 190294 marked UTF-8 strings
Namespace in Imports field not imported from: ‘maps’
  All declared Imports should be used.
Note: found 1 marked UTF-8 string
Namespace in Imports field not imported from: ‘gstat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘dplyr’ ‘ggridges’ ‘markdown’ ‘shinyjs’ ‘tidyr’
  All declared Imports should be used.
Found the following files/directories:
  ‘covfefe_inauguration.txt’
'library' or 'require' calls to packages already attached by Depends:
  ‘Matrix’ ‘mlogit’ ‘poLCA’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Matrix’ ‘mlogit’ ‘poLCA’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
covLCA: no visible global function definition for ‘model.response’
covLCA: no visible global function definition for ‘model.frame’
covLCA: no visible global function definition for ‘model.matrix’
covLCA: no visible global function definition for ‘rnorm’
covLCA: no visible global function definition for ‘flush.console’
covLCA: no visible global function definition for ‘ginv’
covLCA.initialAlphaGamma: no visible global function definition for
  ‘as.formula’
covLCA.initialAlphaGamma: no visible global function definition for
  ‘mlogit.data’
covLCA.initialAlphaGamma: no visible global function definition for
  ‘mlogit’
covLCA.initialBeta: no visible global function definition for
  ‘as.formula’
covLCA.initialBeta: no visible global function definition for ‘poLCA’
covLCA.initialBeta: no visible global function definition for
  ‘mlogit.data’
covLCA.initialBeta: no visible global function definition for ‘mlogit’
covLCA.paramVariance: no visible global function definition for ‘ginv’
covLCA.varianceFirst: no visible global function definition for ‘bdiag’
Undefined global functions or variables:
  as.formula bdiag flush.console ginv mlogit mlogit.data model.frame
  model.matrix model.response poLCA rnorm
Consider adding
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response", "rnorm")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
covreg.mcmc: no visible global function definition for ‘model.frame’
covreg.mcmc: no visible global function definition for ‘model.matrix’
covreg.mcmc: no visible global function definition for ‘model.response’
covreg.mcmc: no visible global function definition for ‘lm’
covreg.mcmc: no visible global function definition for ‘rnorm’
covreg.mcmc: no visible global function definition for ‘cov’
rmn: no visible global function definition for ‘rnorm’
rwish: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  cov lm model.frame model.matrix model.response rnorm
Consider adding
  importFrom("stats", "cov", "lm", "model.frame", "model.matrix",
             "model.response", "rnorm")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘misc3d’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls in package code:
  ‘parallel’ ‘snowfall’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Matrix’ ‘prodlim’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CoxBoost: no visible global function definition for ‘Matrix’
CoxBoost: no visible binding for global variable ‘sd’
CoxBoost: no visible global function definition for ‘predict’
cv.CoxBoost : eval.fold: no visible global function definition for
  ‘predict’
cv.CoxBoost: no visible global function definition for ‘mclapply’
cv.CoxBoost: no visible binding for global variable ‘sd’
estimPVal: no visible global function definition for ‘mclapply’
iCoxBoost: no visible global function definition for ‘terms’
iCoxBoost: no visible global function definition for ‘model.response’
iCoxBoost: no visible global function definition for ‘model.frame’
iCoxBoost: no visible global function definition for ‘model.matrix’
iCoxBoost: no visible global function definition for ‘Matrix’
plot.CoxBoost: no visible global function definition for ‘lines’
plot.CoxBoost: no visible global function definition for ‘text’
predict.iCoxBoost: no visible global function definition for
  ‘model.response’
predict.iCoxBoost: no visible global function definition for
  ‘model.frame’
predict.iCoxBoost: no visible global function definition for
  ‘model.matrix’
Undefined global functions or variables:
  Matrix lines mclapply model.frame model.matrix model.response predict
  sd terms text
Consider adding
  importFrom("graphics", "lines", "text")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "predict", "sd", "terms")
to your NAMESPACE file.
coxaalen: no visible global function definition for ‘terms’
coxaalen: no visible global function definition for ‘model.matrix’
coxaalen: no visible binding for global variable ‘frame’
coxaalen: no visible global function definition for ‘update.formula’
coxaalen: no visible global function definition for ‘capture.output’
coxdual: no visible global function definition for ‘terms’
coxdual: no visible global function definition for ‘model.matrix’
coxdual: no visible binding for global variable ‘frame’
coxdual: no visible global function definition for ‘update.formula’
coxdual: no visible global function definition for ‘as.formula’
coxdual: no visible global function definition for ‘capture.output’
frame.assign: no visible global function definition for ‘model.matrix’
linapprox: no visible global function definition for ‘approx’
print.coxinterval: no visible global function definition for ‘pchisq’
print.summary.coxinterval : f: no visible global function definition
  for ‘printCoefmat’
step2stepfun : f: no visible global function definition for ‘stepfun’
summary.coxinterval : f: no visible global function definition for
  ‘pchisq’
summary.coxinterval : f: no visible global function definition for
  ‘qnorm’
Undefined global functions or variables:
  approx as.formula capture.output frame model.matrix pchisq
  printCoefmat qnorm stepfun terms update.formula
Consider adding
  importFrom("graphics", "frame")
  importFrom("stats", "approx", "as.formula", "model.matrix", "pchisq",
             "printCoefmat", "qnorm", "stepfun", "terms",
             "update.formula")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Package required but not available: ‘SNPRelate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
comp.graph: no visible global function definition for ‘qnorm’
comp.graph: no visible global function definition for ‘polygon’
comp.graph: no visible global function definition for ‘lines’
cox.ridge: no visible global function definition for ‘terms’
cox.ridge: no visible global function definition for ‘model.extract’
cox.ridge: no visible global function definition for ‘model.matrix’
cox.ridge: no visible binding for global variable ‘hat’
Undefined global functions or variables:
  hat lines model.extract model.matrix polygon qnorm terms
Consider adding
  importFrom("graphics", "lines", "polygon")
  importFrom("stats", "hat", "model.extract", "model.matrix", "qnorm",
             "terms")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
coxr: no visible global function definition for ‘model.extract’
coxr: no visible global function definition for ‘model.matrix’
coxr.draw: no visible global function definition for ‘lines’
coxr.draw: no visible global function definition for ‘points’
coxr.fit: no visible global function definition for ‘quantile’
gen_data: no visible global function definition for ‘rnorm’
gen_data: no visible global function definition for ‘rexp’
plot.coxr: no visible global function definition for ‘quantile’
plot.coxr: no visible global function definition for ‘par’
plot.coxr: no visible global function definition for ‘mtext’
plot.coxr: no visible global function definition for ‘title’
plot.coxr: no visible global function definition for ‘split.screen’
plot.coxr: no visible global function definition for ‘screen’
plot.coxr: no visible global function definition for ‘close.screen’
print.coxr: no visible global function definition for ‘pnorm’
print.coxr: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  close.screen lines model.extract model.matrix mtext par pchisq pnorm
  points quantile rexp rnorm screen split.screen title
Consider adding
  importFrom("graphics", "close.screen", "lines", "mtext", "par",
             "points", "screen", "split.screen", "title")
  importFrom("stats", "model.extract", "model.matrix", "pchisq", "pnorm",
             "quantile", "rexp", "rnorm")
to your NAMESPACE file.
Package 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.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘grDevices’
  All declared Imports should be used.
Found the following files/directories:
  ‘rs1234.pdf’
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘cents’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RcppProgress’
  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 399-421 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
QR.cd: no visible global function definition for ‘quantile’
QR.lasso.cd: no visible global function definition for ‘quantile’
cqr.cd: no visible global function definition for ‘quantile’
cqr.lasso.cd: no visible global function definition for ‘quantile’
cqr.lasso.mm: no visible global function definition for ‘quantile’
cqr.mm: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Running examples in ‘cr17-Ex.R’ failed
The error most likely occurred in:

> ### Name: fitCuminc
> ### Title: Cumulative Incidences Curves
> ### Aliases: fitCuminc
> 
> ### ** Examples
> 
> fitCuminc(time = LUAD$time, risk = LUAD$event, group = LUAD$gender, cens = "alive")
19 cases omitted due to missing values
Warning in cuminc(ftime = time, fstatus = risk, group = group, cencode = cens) :
  NAs introduced by coercion
Error in cuminc(ftime = time, fstatus = risk, group = group, cencode = cens) : 
  NAs in foreign function call (arg 3)
Calls: fitCuminc -> cuminc
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in cuminc(ftime = time, fstatus = risk, group = group, cencode = cens) :
  NAs introduced by coercion
Quitting from lines 176-180 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
NAs in foreign function call (arg 3)
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
distance.comoving: no visible global function definition for
  ‘integrate’
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   8.0Mb
Note: found 11 marked Latin-1 strings
  Note: found 57 marked UTF-8 strings
Malformed Description field: should contain one or more complete sentences.
crantastic.submitInstalledPackages: no visible global function
  definition for ‘installed.packages’
postData: no visible global function definition for ‘make.socket’
postData: no visible global function definition for ‘write.socket’
postData: no visible global function definition for ‘read.socket’
postData: no visible global function definition for ‘close.socket’
Undefined global functions or variables:
  close.socket installed.packages make.socket read.socket write.socket
Consider adding
  importFrom("utils", "close.socket", "installed.packages",
             "make.socket", "read.socket", "write.socket")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘gdistance’ ‘raster’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
cm.CVaR: no visible global function definition for ‘quantile’
cm.hist: no visible global function definition for ‘hist’
cm.quantile: no visible global function definition for ‘qnorm’
cm.rnorm: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  hist qnorm quantile rnorm
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "qnorm", "quantile", "rnorm")
to your NAMESPACE file.
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
'library' or 'require' call to ‘RCurl’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RCurl’ ‘chron’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
collateDaily: no visible global function definition for ‘read.table’
collateDaily: no visible global function definition for ‘write.table’
collateHourly: no visible global function definition for ‘read.table’
collateHourly: no visible global function definition for ‘write.table’
downloadCRN: no visible global function definition for ‘download.file’
getUrlsCRN: no visible global function definition for ‘getURL’
writeDataset: no visible global function definition for ‘read.table’
writeDataset: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  download.file getURL read.table write.table
Consider adding
  importFrom("utils", "download.file", "read.table", "write.table")
to your NAMESPACE file.
Note: found 3 marked UTF-8 strings
Found the following files/directories:
  ‘core’ ‘crop.eps’ ‘crop.pdf’ ‘crop.png’ ‘crop.ps’
Namespace in Imports field not imported from: ‘glue’
  All declared Imports should be used.
get.plan: no visible global function definition for ‘menu’
Undefined global functions or variables:
  menu
Consider adding
  importFrom("utils", "menu")
to your NAMESPACE file.
Package in Depends field not imported from: ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
crossmatchtest: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
BootC : BSs: no visible global function definition for ‘lm’
BootC : BSs: no visible global function definition for ‘vcov’
BootC: no visible global function definition for ‘boot’
BootC: no visible global function definition for ‘boot.ci’
DeltaC: no visible global function definition for ‘lm’
DeltaC: no visible global function definition for ‘vcov’
FiellerC: no visible global function definition for ‘lm’
FiellerC: no visible global function definition for ‘vcov’
nonLinearC: no visible global function definition for ‘nls’
Undefined global functions or variables:
  boot boot.ci lm nls vcov
Consider adding
  importFrom("stats", "lm", "nls", "vcov")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘R6’ ‘dplyr’ ‘r6extended’
  All declared Imports should be used.
Warning: no function found corresponding to methods exports from ‘CR’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
curerate : cr: no visible global function definition for ‘rbinom’
curerate : cr: no visible global function definition for ‘rexp’
curerate : cr: no visible global function definition for ‘runif’
curerate: no visible global function definition for ‘new’
showcr: no visible global function definition for ‘show’
Undefined global functions or variables:
  new rbinom rexp runif show
Consider adding
  importFrom("methods", "new", "show")
  importFrom("stats", "rbinom", "rexp", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
crrp: no visible global function definition for ‘approx’
gcrrp: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx
Consider adding
  importFrom("stats", "approx")
to your NAMESPACE file.
crrc: no visible binding for global variable ‘na.omit’
crrs: no visible binding for global variable ‘na.omit’
mycrr: no visible binding for global variable ‘na.omit’
mycrr.test: no visible binding for global variable ‘na.omit’
print.crrs: no visible global function definition for ‘pnorm’
psh.test: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  na.omit pchisq pnorm
Consider adding
  importFrom("stats", "na.omit", "pchisq", "pnorm")
to your NAMESPACE file.
crrstep : crr.makecov1: no visible global function definition for
  ‘model.matrix’
crrstep : crr.dropterm: no visible global function definition for
  ‘terms’
crrstep : crr.dropterm: no visible global function definition for
  ‘as.formula’
crrstep : crr.addterm: no visible global function definition for
  ‘terms’
crrstep : crr.addterm: no visible global function definition for
  ‘as.formula’
crrstep: no visible global function definition for ‘as.formula’
crrstep: no visible global function definition for ‘terms’
crrstep: no visible global function definition for ‘model.frame’
crrstep: no visible binding for global variable ‘na.pass’
crrstep: no visible global function definition for ‘update’
crrstep: no visible global function definition for ‘drop.terms’
Undefined global functions or variables:
  as.formula drop.terms model.frame model.matrix na.pass terms update
Consider adding
  importFrom("stats", "as.formula", "drop.terms", "model.frame",
             "model.matrix", "na.pass", "terms", "update")
to your NAMESPACE file.
Note: found 500 marked UTF-8 strings
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   5.1Mb
Namespace in Imports field not imported from: ‘survminer’
  All declared Imports should be used.
Running examples in ‘crypto-Ex.R’ failed
The error most likely occurred in:

> ### Name: crypto_prices
> ### Title: Get current crypto currency prices
> ### Aliases: crypto_prices
> 
> ### ** Examples
> 
> {
+ kin_price <- crypto_prices('kin')
+ }
Error: 
Execution halted
Namespace in Imports field not imported from: ‘qte’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    shp   7.8Mb
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/csp.Rcheck/00install.out’ for details.
pielou: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Package in Depends field not imported from: ‘compiler’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
csSAM: no visible binding for global variable ‘quantile’
csSAM: no visible global function definition for ‘median’
csfit: no visible global function definition for ‘lsfit’
csfit: no visible global function definition for ‘ls.diag’
plotCsSAM: no visible global function definition for ‘pdf’
plotCsSAM: no visible global function definition for ‘par’
plotCsSAM: no visible global function definition for ‘title’
plotCsSAM: no visible global function definition for ‘dev.off’
runSAM: no visible binding for global variable ‘median’
runSAM: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  dev.off ls.diag lsfit median par pdf quantile title
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par", "title")
  importFrom("stats", "ls.diag", "lsfit", "median", "quantile")
to your NAMESPACE file.
Found the following files/directories:
  ‘Example File.pdf’
Malformed Title field: should not end in a period.
cstar: no visible global function definition for ‘vcov’
cstar : utility: no visible global function definition for ‘dt’
cstar : maximand: no visible global function definition for ‘integrate’
cstar: no visible global function definition for ‘uniroot’
cstari : utility: no visible global function definition for ‘dt’
cstari : maximand: no visible global function definition for
  ‘integrate’
cstari: no visible global function definition for ‘uniroot’
cstarme : utility: no visible global function definition for ‘density’
cstarme : maximand: no visible global function definition for
  ‘integrate’
cstarme : maximand: no visible global function definition for ‘sd’
cstarme: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  density dt integrate sd uniroot vcov
Consider adding
  importFrom("stats", "density", "dt", "integrate", "sd", "uniroot",
             "vcov")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘epitools’ ‘rpivotTable’ ‘shinyMatrix’
  All declared Imports should be used.
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/ctsem.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘dplyr’ ‘e1071’ ‘party’ ‘rhandsontable’ ‘rpart’
  ‘rpart.plot’ ‘shiny’
  All declared Imports should be used.
Found the following files/directories:
  ‘Hello.csv’
GNU make is a SystemRequirements.
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
File ‘curl/libs/curl.so’:
  Found non-API call to R: ‘R_new_custom_connection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
cci.nostrat: no visible global function definition for ‘quantile’
cci.nostrat: no visible global function definition for ‘axis’
cci.nostrat: no visible global function definition for ‘lines’
cci.nostrat: no visible global function definition for ‘legend’
cci.strat: no visible global function definition for ‘axis’
cci.strat: no visible global function definition for ‘lines’
cci.strat: no visible global function definition for ‘legend’
clfs.nostrat: no visible global function definition for ‘quantile’
clfs.nostrat: no visible global function definition for ‘axis’
clfs.nostrat: no visible global function definition for ‘lines’
clfs.nostrat: no visible global function definition for ‘legend’
clfs.strat: no visible global function definition for ‘axis’
clfs.strat: no visible global function definition for ‘lines’
clfs.strat: no visible global function definition for ‘legend’
pvals.2cat: no visible global function definition for ‘pchisq’
pvals.cat: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  axis legend lines pchisq quantile
Consider adding
  importFrom("graphics", "axis", "legend", "lines")
  importFrom("stats", "pchisq", "quantile")
to your NAMESPACE file.
Found the following files/directories:
  ‘Adjusted_p_values.pdf’ ‘Effect_Size_Curves.pdf’
  ‘Mean_Difference_Curves.pdf’
Namespaces in Imports field not imported from:
  ‘rlang’ ‘tidyselect’
  All declared Imports should be used.
Cut: no visible global function definition for ‘cor’
MissSimulation: no visible global function definition for ‘rbinom’
cutoff: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor rbinom
Consider adding
  importFrom("stats", "cor", "rbinom")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
delta.glm: no visible global function definition for ‘glm’
delta.glm: no visible global function definition for ‘residuals’
delta.glm: no visible global function definition for ‘fitted’
delta.glm: no visible global function definition for ‘predict.glm’
two.stage.model.outputs: no visible global function definition for ‘sd’
Undefined global functions or variables:
  fitted glm predict.glm residuals sd
Consider adding
  importFrom("stats", "fitted", "glm", "predict.glm", "residuals", "sd")
to your NAMESPACE file.
ci.cvAUC: no visible global function definition for ‘qnorm’
ci.pooled.cvAUC: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
calfun: no visible global function definition for ‘optim’
calfun: no visible global function definition for ‘cov’
calfun: no visible global function definition for ‘var’
Undefined global functions or variables:
  cov optim var
Consider adding
  importFrom("stats", "cov", "optim", "var")
to your NAMESPACE file.
Found the following files/directories:
  ‘dickinson_constrained.csv’ ‘dickinson_cov_constrained.csv’
Namespace in Imports field not imported from: ‘lattice’
  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.
func.constructRegressionFormula: no visible global function definition
  for ‘as.formula’
func.crossValidationAnalysis: no visible global function definition for
  ‘glm’
func.crossValidationAnalysis: no visible global function definition for
  ‘predict’
func.crossValidationAnalysis: no visible global function definition for
  ‘write.table’
func.externalValidationAnalysis: no visible global function definition
  for ‘predict’
func.externalValidationAnalysis: no visible global function definition
  for ‘write.table’
func.linearRegressionAnalysis: no visible global function definition
  for ‘glm’
func.linearRegressionAnalysis: no visible global function definition
  for ‘predict’
func.linearRegressionAnalysis: no visible global function definition
  for ‘write.table’
func.sortDataColumns: no visible global function definition for
  ‘write.table’
mainfunc.q2: no visible global function definition for ‘write.table’
mainfunc.q2: no visible global function definition for ‘new’
mainfunc.stats: no visible global function definition for ‘write.table’
mainfunc.stats: no visible global function definition for ‘new’
Undefined global functions or variables:
  as.formula glm new predict write.table
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "as.formula", "glm", "predict")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
cvimpute.by.wavelet: no visible global function definition for ‘sd’
cvimpute.by.wavelet: no visible global function definition for ‘mad’
cvimpute.image.by.wavelet: no visible global function definition for
  ‘sd’
cvimpute.image.by.wavelet: no visible global function definition for
  ‘mad’
cvwavelet.image.after.impute: no visible global function definition for
  ‘sd’
cvwavelet.image.after.impute: no visible global function definition for
  ‘mad’
Undefined global functions or variables:
  mad sd
Consider adding
  importFrom("stats", "mad", "sd")
to your NAMESPACE file.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’ ‘robustbase’
A package should be listed in only one of these fields.
random.CV: no visible global function definition for ‘var’
regular.CV: no visible global function definition for ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
create_clustering_problem: no visible global function definition for
  ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Found the following Makefile(s) without a final LF:
  src/Makevars
Some ‘make’ programs ignore lines not ending in LF.
Packages suggested but not available for checking:
  'Rmosek', 'gurobi', 'Rcplex', 'rcbc'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      2.8Mb
    doc    1.3Mb
    help   1.1Mb
Running examples in ‘CVXR-Ex.R’ failed
The error most likely occurred in:

> ### Name: diag,Expression-method
> ### Title: Matrix Diagonal
> ### Aliases: diag,Expression-method diag
> 
> ### ** Examples
> 
> C <- Variable(3,3)
> obj <- Maximize(C[1,3])
> constraints <- list(diag(C) == 1, C[1,2] == 0.6, C[2,3] == -0.3, C == Variable(3,3, PSD = TRUE))
> prob <- Problem(obj, constraints)
> result <- solve(prob)

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

Traceback:
 1: scs::scs(A = args$A, b = args$b, obj = args$c, cone = cones,     control = control)
 2: solve_via_data(object@solver, data, warm_start, verbose, feastol,     reltol, abstol, num_iter, solver_opts, problem@.solver_cache)
 3: solve_via_data(object@solver, data, warm_start, verbose, feastol,     reltol, abstol, num_iter, solver_opts, problem@.solver_cache)
 4: reduction_solve_via_data(object@.solving_chain, object, data,     warm_start, verbose, feastol, reltol, abstol, num_iter, list(...))
 5: reduction_solve_via_data(object@.solving_chain, object, data,     warm_start, verbose, feastol, reltol, abstol, num_iter, list(...))
 6: psolve(a, solver = NA, ...)
 7: psolve(a, solver = NA, ...)
 8: solve(prob)
 9: solve(prob)
An irrecoverable exception occurred. R is aborting now ...
Found the following files/directories:
  ‘tex.table.tex’
.mixgauss_init: no visible global function definition for ‘cov’
.mixgauss_init: no visible global function definition for ‘var’
Undefined global functions or variables:
  cov var
Consider adding
  importFrom("stats", "cov", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
cxxfun.from.dll: no visible global function definition for ‘new’
cxxfun.from.dso.bin: no visible global function definition for ‘new’
cxxfunctionplus: no visible global function definition for ‘getPlugin’
cxxfunctionplus: no visible global function definition for
  ‘cxxfunction’
cxxfunctionplus: no visible global function definition for ‘new’
show,cxxdso: no visible global function definition for ‘object.size’
Undefined global functions or variables:
  cxxfunction getPlugin new object.size
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "object.size")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Error(s) in re-building vignettes:
  ...
--- re-building ‘cycling_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 177-179 (cycling_data_analysis.Rmd) 
Error: processing vignette 'cycling_data_analysis.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘cycling_data_analysis.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Package in Depends field not imported from: ‘fda’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
check.for.sequence.endpoint.breaks: no visible global function
  definition for ‘na.omit’
get.breaks.vector: no visible global function definition for ‘na.omit’
get.cycle.breaks: no visible global function definition for ‘na.omit’
get.cycle.counts: no visible global function definition for ‘na.omit’
get.cycle.matrix: no visible global function definition for ‘na.omit’
get.cycle.minimums: no visible global function definition for ‘na.omit’
get.peaks: no visible global function definition for ‘embed’
get.trans: no visible global function definition for
  ‘create.bspline.basis’
get.trans: no visible global function definition for ‘smooth.basis’
get.trans: no visible global function definition for ‘deriv.fd’
get.trans: no visible global function definition for ‘eval.fd’
get.transition.locations: no visible global function definition for
  ‘na.omit’
get.transition.locations.FDiff: no visible global function definition
  for ‘na.omit’
get.window: no visible global function definition for ‘sd’
Undefined global functions or variables:
  create.bspline.basis deriv.fd embed eval.fd na.omit sd smooth.basis
Consider adding
  importFrom("stats", "embed", "na.omit", "sd")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
Malformed Description field: should contain one or more complete sentences.
cytoDiv: no visible global function definition for ‘colorRampPalette’
cytoDiv: no visible global function definition for ‘persp’
Undefined global functions or variables:
  colorRampPalette persp
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "persp")
to your NAMESPACE file.
Found the following files/directories:
  ‘GRCh38_browser’ ‘GRCh38_map’
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 27-38 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    img   4.7Mb
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Running examples in ‘dabestr-Ex.R’ failed
The error most likely occurred in:

> ### Name: dabest
> ### Title: Differences between Groups with Bootstrap Confidence Intervals
> ### Aliases: dabest
> 
> ### ** Examples
> 
> 
> # Performing unpaired (two independent groups) analysis.
> unpaired_mean_diff <- dabest(iris, Species, Petal.Width,
+                              idx = c("setosa", "versicolor"),
+                              paired = FALSE)
> 
> # Display the results in a user-friendly format.
> unpaired_mean_diff
DABEST (Data Analysis with Bootstrap Estimation) v0.2.3
=======================================================

Variable: Petal.Width 

Unpaired mean difference of versicolor (n=50) minus setosa (n=50)
 1.08 [95CI  1.01; 1.14]


5000 bootstrap resamples.
All confidence intervals are bias-corrected and accelerated.

> 
> # Produce an estimation plot.
> plot(unpaired_mean_diff)
Error in loadNamespace(name) : there is no package called ‘plyr’
Calls: plot ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘using-dabestr.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 82-83 (using-dabestr.Rmd) 
Error: processing vignette 'using-dabestr.Rmd' failed with diagnostics:
there is no package called 'plyr'
--- failed re-building ‘using-dabestr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Note: found 4 marked Latin-1 strings
  Note: found 21 marked UTF-8 strings
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘s20x’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
allCombs: no visible global function definition for ‘combn’
brute.search: no visible global function definition for ‘na.omit’
dag.draw: no visible global function definition for ‘text’
dag.init: no visible global function definition for
  ‘installed.packages’
dag.legend: no visible global function definition for ‘text’
dag.letter: no visible global function definition for ‘text’
dag.move: no visible global function definition for ‘identify’
dag.move: no visible global function definition for ‘locator’
dag.sim: no visible global function definition for ‘rnorm’
dag.sim: no visible global function definition for ‘rbinom’
dag.sim : <anonymous>: no visible global function definition for
  ‘rbinom’
garrows: no visible global function definition for ‘arrows’
smoothArc: no visible global function definition for ‘points’
summary_dagRdag: no visible global function definition for ‘na.omit’
viv: no visible global function definition for ‘na.omit’
write.paths: no visible global function definition for ‘text’
Undefined global functions or variables:
  arrows combn identify installed.packages locator na.omit points
  rbinom rnorm text
Consider adding
  importFrom("graphics", "arrows", "identify", "locator", "points",
             "text")
  importFrom("stats", "na.omit", "rbinom", "rnorm")
  importFrom("utils", "combn", "installed.packages")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Package suggested but not available for checking: ‘mljar’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    Pied_Flycatchers_1   2.5Mb
    Pied_Flycatchers_2   1.3Mb
    doc                  1.2Mb
Namespace in Imports field not imported from: ‘expm’
  All declared Imports should be used.
drawAimSpot: no visible global function definition for ‘points’
drawBoard: no visible global function definition for ‘par’
drawBoard: no visible global function definition for ‘points’
drawBoard: no visible global function definition for ‘text’
drawHeatmap: no visible global function definition for ‘heat.colors’
drawHeatmap: no visible global function definition for ‘par’
drawHeatmap: no visible global function definition for ‘image’
drawHeatmap: no visible global function definition for ‘rect’
generalExpScores: no visible global function definition for ‘fft’
simpleExpScores: no visible global function definition for ‘mvfft’
simpleExpScores: no visible global function definition for ‘fft’
Undefined global functions or variables:
  fft heat.colors image mvfft par points rect text
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "image", "par", "points", "rect", "text")
  importFrom("stats", "fft", "mvfft")
to your NAMESPACE file.
dashboard_open: no visible global function definition for ‘write.csv’
dashboard_open: no visible global function definition for
  ‘capture.output’
dctable: no visible global function definition for ‘capture.output’
Undefined global functions or variables:
  capture.output write.csv
Consider adding
  importFrom("utils", "capture.output", "write.csv")
to your NAMESPACE file.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    java   7.8Mb
Namespace in Imports field not imported from: ‘DatabaseConnectorJars’
  All declared Imports should be used.
datadict.profile: no visible global function definition for
  ‘txtProgressBar’
datadict.profile: no visible global function definition for
  ‘setTxtProgressBar’
datadict_profile: no visible global function definition for
  ‘txtProgressBar’
datadict_profile: no visible global function definition for
  ‘setTxtProgressBar’
heatmap.quality: no visible global function definition for
  ‘colorRampPalette’
heatmap.quality: no visible global function definition for ‘heatmap’
heatmap_quality: no visible global function definition for
  ‘colorRampPalette’
heatmap_quality: no visible global function definition for ‘heatmap’
is.oneOf: no visible global function definition for ‘read.csv’
is_one_of: no visible global function definition for ‘read.csv’
pkg.version: no visible global function definition for ‘citation’
pkg_version: no visible global function definition for ‘citation’
ruleCoverage: no visible global function definition for ‘dotchart’
ruleCoverage: no visible global function definition for ‘abline’
rule_coverage: no visible global function definition for ‘dotchart’
rule_coverage: no visible global function definition for ‘abline’
shortSummary: no visible global function definition for ‘sd’
short_summary: no visible global function definition for ‘sd’
Undefined global functions or variables:
  abline citation colorRampPalette dotchart heatmap read.csv sd
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "abline", "dotchart")
  importFrom("stats", "heatmap", "sd")
  importFrom("utils", "citation", "read.csv", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
Package has no Sweave vignette sources and no VignetteBuilder field.
Namespace in Imports field not imported from: ‘miniUI’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘shinyFiles’ ‘shinycssloaders’ ‘shinyjs’ ‘shinythemes’
  All declared Imports should be used.
Package in Depends field not imported from: ‘DBI’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.onLoad : <anonymous>: no visible global function definition for
  ‘read.table’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbConnect’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbListTables’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbExistsTable’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbReadTable’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbWriteTable’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbDisconnect’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbRemoveTable’
Undefined global functions or variables:
  dbConnect dbDisconnect dbExistsTable dbListTables dbReadTable
  dbRemoveTable dbWriteTable read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘get_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 26-34 (get_started.Rmd) 
Error: processing vignette 'get_started.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘get_started.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘my new data set.rds’
Namespaces in Imports field not imported from:
  ‘future’ ‘iterators’ ‘readr’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
License components which are templates and need '+ file LICENSE':
  MIT
checkDataQuality: no visible binding for global variable ‘quantile’
checkDataQuality: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  quantile write.csv
Consider adding
  importFrom("stats", "quantile")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   5.7Mb
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   2.8Mb
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘applications.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 ‘applications.Rmd’

--- re-building ‘data.tree.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 513-516 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘data.tree.Rmd’

SUMMARY: processing the following file failed:
  ‘data.tree.Rmd’

Error: Vignette re-building failed.
Execution halted
Malformed Title field: should not end in a period.
'library' or 'require' calls to packages already attached by Depends:
  ‘RMySQL’ ‘gWidgets’
  Please remove these calls from your code.
Malformed Description field: should contain one or more complete sentences.
dbEmpLikeGOF: no visible global function definition for ‘runif’
dbEmpLikeGOF: no visible global function definition for ‘var’
dbEmpLikeGOF: no visible global function definition for ‘rnorm’
emplikeGOFinternal: no visible global function definition for ‘var’
getCutoff: no visible binding for global variable ‘unifCut’
getCutoff: no visible binding for global variable ‘normCut’
getCutoff: no visible global function definition for ‘lm’
getCutoff: no visible binding for global variable ‘distEqCut’
getPval: no visible binding for global variable ‘unifCut’
getPval: no visible binding for global variable ‘normCut’
getPval: no visible global function definition for ‘lm’
getPval: no visible binding for global variable ‘distEqCut’
helperPval: no visible global function definition for ‘lm’
returnCutoff: no visible global function definition for ‘quantile’
testfun2: no visible global function definition for ‘runif’
testfun2: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  distEqCut lm normCut quantile rnorm runif unifCut var
Consider adding
  importFrom("stats", "lm", "quantile", "rnorm", "runif", "var")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
computePval: no visible global function definition for ‘lm’
computeQhat: no visible global function definition for ‘pnorm’
dbELnorm: no visible global function definition for ‘rnorm’
getCutoffTableThree: no visible global function definition for ‘lm’
getCutoffTableTwo: no visible global function definition for ‘lm’
getCutoffValue: no visible global function definition for ‘lm’
helperGetTstat: no visible global function definition for ‘rnorm’
returnCutoffValue: no visible global function definition for ‘rnorm’
returnCutoffValue: no visible global function definition for ‘quantile’
varianceEstimator: no visible global function definition for ‘density’
varianceEstimator: no visible global function definition for ‘ecdf’
Undefined global functions or variables:
  density ecdf lm pnorm quantile rnorm
Consider adding
  importFrom("stats", "density", "ecdf", "lm", "pnorm", "quantile",
             "rnorm")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
'library' or 'require' call to ‘fdrtool’ which was already attached by Depends.
  Please remove these calls from your code.
avelinkdis: no visible global function definition for ‘sd’
avelinkdis: no visible global function definition for ‘dist’
centdis: no visible global function definition for ‘sd’
centdis: no visible global function definition for ‘dist’
distable: no visible global function definition for ‘write.table’
functionall: no visible global function definition for ‘read.table’
randdis: no visible global function definition for ‘write.table’
valuep: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  dist read.table sd write.csv write.table
Consider adding
  importFrom("stats", "dist", "sd")
  importFrom("utils", "read.table", "write.csv", "write.table")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘dplyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘RPostgres’
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Found the following files/directories:
  ‘LFC.d.jpeg’ ‘LFC.s.jpeg’ ‘TF_bridged_DCL.pdf’
  ‘TF_bridged_DCL_int.pdf’
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
Package suggested but not available for checking: ‘BRugs’
Packages in Depends field not imported from:
  ‘lattice’ ‘latticeExtra’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: ‘INLA’
Note: found 2 marked Latin-1 strings
Namespace in Imports field not imported from: ‘CDM’
  All declared Imports should be used.
GNU make is a SystemRequirements.
test.LM: no visible global function definition for ‘lm’
Undefined global functions or variables:
  lm
Consider adding
  importFrom("stats", "lm")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    sample_data   3.6Mb
ifft: no visible global function definition for ‘fft’
lines.deamer: no visible global function definition for ‘lines’
rlaplace: no visible global function definition for ‘runif’
Undefined global functions or variables:
  fft lines runif
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "fft", "runif")
to your NAMESPACE file.
compare.relimp: no visible global function definition for ‘qchisq’
compare.relimp: no visible global function definition for ‘pchisq’
plot_transition: no visible global function definition for ‘dnorm’
plot_transition: no visible global function definition for ‘par’
plot_transition: no visible global function definition for ‘lines’
plot_transition: no visible global function definition for ‘plogis’
plot_transition: no visible global function definition for ‘axis’
plot_transition: no visible global function definition for ‘mtext’
relative.importance: no visible global function definition for ‘glm’
relative.importance: no visible global function definition for ‘sd’
relative.importance : tr.pr: no visible global function definition for
  ‘pnorm’
relative.importance: no visible global function definition for ‘vcov’
Undefined global functions or variables:
  axis dnorm glm lines mtext par pchisq plogis pnorm qchisq sd vcov
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "par")
  importFrom("stats", "dnorm", "glm", "pchisq", "plogis", "pnorm",
             "qchisq", "sd", "vcov")
to your NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘RC_units.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 ‘RC_units.Rmd’

--- re-building ‘decoder.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 ‘decoder.Rmd’

--- re-building ‘sjukhus.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.
Joining, by = "key"
Joining, by = "key"
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 102-122 (sjukhus.Rmd) 
Error: processing vignette 'sjukhus.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘sjukhus.Rmd’

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

Error: Vignette re-building failed.
Execution halted
DeconCPdf: no visible global function definition for ‘bw.nrd0’
DeconCPdf: no visible global function definition for ‘bw.nrd’
DeconCPdf: no visible global function definition for ‘bw.ucv’
DeconCPdf: no visible global function definition for ‘bw.bcv’
DeconCPdf: no visible global function definition for ‘bw.SJ’
DeconCPdf: no visible global function definition for ‘density’
DeconCPdf: no visible global function definition for ‘dnorm’
bw.dboot2 : suppL2: no visible global function definition for ‘density’
bw.dboot2 : suppL2: no visible global function definition for ‘rnorm’
bw.dboot2 : gaussL2: no visible global function definition for
  ‘density’
bw.dboot2 : gaussL2: no visible global function definition for ‘rnorm’
bw.dmise: no visible global function definition for ‘var’
plot.Decon: no visible global function definition for ‘plot.default’
plot.Decon: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline bw.SJ bw.bcv bw.nrd bw.nrd0 bw.ucv density dnorm plot.default
  rnorm var
Consider adding
  importFrom("graphics", "abline", "plot.default")
  importFrom("stats", "bw.SJ", "bw.bcv", "bw.nrd", "bw.nrd0", "bw.ucv",
             "density", "dnorm", "rnorm", "var")
to your NAMESPACE file.
Package in Depends field not imported from: ‘Deducer’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Depends: includes the non-default packages:
  'Deducer', 'psych', 'GPArotation', 'mvnormtest', 'irr', 'klaR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' call to ‘klaR’ which was already attached by Depends.
  Please remove these calls from your code.
.makeICCDialog: no visible global function definition for ‘J’
.makeICCDialog: no visible global function definition for ‘new’
.makeICCDialog: no visible global function definition for ‘.jnull’
.makeNewFactorAnalysisDialog: no visible global function definition for
  ‘new’
.makeNewFactorAnalysisDialog: no visible global function definition for
  ‘J’
.makeNewFactorAnalysisDialog: no visible global function definition for
  ‘toJava’
.makeNewLDADialog: no visible global function definition for ‘new’
.makeNewLDADialog: no visible global function definition for ‘J’
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for ‘new’
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for ‘toJava’
.makeNewLDADialog: no visible global function definition for ‘toJava’
.makeNewReliabilityDialog: no visible global function definition for
  ‘new’
.makeNewReliabilityDialog: no visible global function definition for
  ‘toJava’
.onLoad: no visible global function definition for ‘.jnull’
.onLoad: no visible global function definition for ‘jgr.getMenuNames’
.onLoad: no visible global function definition for ‘jgr.insertMenu’
.onLoad: no visible global function definition for ‘jgr.addMenu’
.onLoad: no visible global function definition for ‘jgr.addMenuItem’
Undefined global functions or variables:
  .jnull J jgr.addMenu jgr.addMenuItem jgr.getMenuNames jgr.insertMenu
  new toJava
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Depends: includes the non-default packages:
  'JavaGD', 'Deducer', 'sp', 'maptools', 'OpenStreetMap', 'scales',
  'rgdal'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘UScensus2010’
A package should be listed in only one of these fields.
'library' or 'require' call to ‘UScensus2010’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘UScensus2010’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘JavaGD’ ‘OpenStreetMap’ ‘maptools’ ‘rgdal’ ‘scales’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘Deducer’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Malformed Description field: should contain one or more complete sentences.
.makeQuickWordcloud: no visible global function definition for ‘J’
.makeQuickWordcloud: no visible global function definition for ‘new’
.makeQuickWordcloud: no visible global function definition for ‘.jnull’
.makeTextPlot: no visible global function definition for ‘J’
.makeTextPlot: no visible global function definition for ‘new’
.makeTextPlot: no visible global function definition for ‘.jnull’
.onLoad: no visible global function definition for ‘.jpackage’
.onLoad: no visible global function definition for ‘.jnew’
.onLoad: no visible global function definition for ‘J’
make.color.scale: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  .jnew .jnull .jpackage J new rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
binary.state: no visible global function definition for ‘runif’
dbn.dnn.train: no visible global function definition for ‘runif’
dropout.mask: no visible global function definition for ‘runif’
nn.train: no visible global function definition for ‘runif’
rbm.train: no visible global function definition for ‘runif’
sae.dnn.train: no visible global function definition for ‘runif’
show.digit: no visible global function definition for ‘gray’
show.digit: no visible global function definition for ‘image’
Undefined global functions or variables:
  gray image runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "image")
  importFrom("stats", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
DEEPR : perm_function: no visible global function definition for ‘head’
DEEPR : perm_function: no visible global function definition for ‘tail’
simCophy: no visible global function definition for ‘rpois’
simCophy: no visible global function definition for ‘rmultinom’
Undefined global functions or variables:
  head rmultinom rpois tail
Consider adding
  importFrom("stats", "rmultinom", "rpois")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘assertthat’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘delayed.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 97-98 (delayed.Rmd) 
Error: processing vignette 'delayed.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘delayed.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Namespace in Imports field not imported from: ‘lattice’
  All declared Imports should be used.
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘res.pdf’ ‘res1.jpg’
Found an obsolete/platform-specific call in the following function:
  ‘dr_df’
Found the platform-specific device:
  ‘x11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
bootbagg: no visible global function definition for ‘runif’
bootworpl: no visible global function definition for ‘runif’
des12: no visible global function definition for ‘rnorm’
des12: no visible global function definition for ‘runif’
eval.stage.gauss: no visible global function definition for ‘var’
plotparti: no visible global function definition for ‘lines’
plotpartilev: no visible global function definition for ‘polygon’
plotpartilev: no visible global function definition for ‘points’
simesi: no visible global function definition for ‘runif’
simesi3d: no visible global function definition for ‘runif’
simfssk: no visible global function definition for ‘rnorm’
simfssk: no visible global function definition for ‘runif’
simmix.delt: no visible global function definition for ‘rnorm’
simmix.delt: no visible global function definition for ‘runif’
simpp: no visible global function definition for ‘rnorm’
simpp: no visible global function definition for ‘runif’
simutree: no visible global function definition for ‘runif’
stage.gaussR: no visible global function definition for ‘var’
unidis: no visible global function definition for ‘runif’
Undefined global functions or variables:
  lines points polygon rnorm runif var
Consider adding
  importFrom("graphics", "lines", "points", "polygon")
  importFrom("stats", "rnorm", "runif", "var")
to your NAMESPACE file.
Found the following files/directories:
  ‘smd_table.docx’
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Malformed Description field: should contain one or more complete sentences.
DendSer: no visible global function definition for ‘getFromNamespace’
crit2cost : <anonymous>: no visible global function definition for
  ‘as.dist’
dser.dist: no visible global function definition for ‘hclust’
dser.matrix: no visible global function definition for ‘dist’
plotAsColor: no visible global function definition for ‘image’
plotAsColor: no visible global function definition for ‘box’
plotAsColor: no visible global function definition for ‘axis’
seriation_method_dist_dser: no visible global function definition for
  ‘hclust’
seriation_method_dist_dser: no visible global function definition for
  ‘modifyList’
seriation_method_leafsort: no visible global function definition for
  ‘modifyList’
Undefined global functions or variables:
  as.dist axis box dist getFromNamespace hclust image modifyList
Consider adding
  importFrom("graphics", "axis", "box", "image")
  importFrom("stats", "as.dist", "dist", "hclust")
  importFrom("utils", "getFromNamespace", "modifyList")
to your NAMESPACE file.
Package suggested but not available for checking: ‘gapmap’
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       5.0Mb
    extdata   2.3Mb
Package suggested but not available for checking: ‘Rdonlp2’
Package suggested but not available for checking: ‘Rdonlp2’
MBD: no visible global function definition for ‘par’
MBD: no visible global function definition for ‘gray’
MBD: no visible global function definition for ‘matplot’
MBD: no visible global function definition for ‘polygon’
MBD: no visible global function definition for ‘lines’
MBD: no visible global function definition for ‘legend’
MBD: no visible global function definition for ‘matlines’
R.test: no visible global function definition for ‘runif’
R.test: no visible global function definition for ‘wilcox.test’
centralPlot: no visible global function definition for ‘par’
centralPlot: no visible global function definition for
  ‘colorRampPalette’
centralPlot: no visible global function definition for ‘matplot’
centralPlot: no visible global function definition for ‘matlines’
centralPlot: no visible global function definition for ‘legend’
scalecurve: no visible global function definition for ‘lines’
scalecurve: no visible global function definition for ‘legend’
tmean: no visible global function definition for ‘matplot’
tmean: no visible global function definition for ‘matlines’
tmean: no visible global function definition for ‘lines’
tmean: no visible global function definition for ‘legend’
tmean: no visible global function definition for ‘colorRampPalette’
Undefined global functions or variables:
  colorRampPalette gray legend lines matlines matplot par polygon runif
  wilcox.test
Consider adding
  importFrom("grDevices", "colorRampPalette", "gray")
  importFrom("graphics", "legend", "lines", "matlines", "matplot", "par",
             "polygon")
  importFrom("stats", "runif", "wilcox.test")
to your NAMESPACE file.
Note: found 5764 marked UTF-8 strings
Found the following files/directories:
  ‘x.R’ ‘x.sps’ ‘x.txt’
Namespace in Imports field not imported from: ‘datasets’
  All declared Imports should be used.
Package suggested but not available for checking: ‘RDCOMClient’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.0Mb
    help   1.6Mb
ds: no visible global function definition for ‘is.ts’
ds: no visible global function definition for ‘frequency’
getds: no visible global function definition for ‘resid’
getds: no visible global function definition for ‘lm.fit’
getds: no visible global function definition for ‘sd’
getds: no visible global function definition for ‘var’
getds: no visible global function definition for ‘fitted’
Undefined global functions or variables:
  fitted frequency is.ts lm.fit resid sd var
Consider adding
  importFrom("stats", "fitted", "frequency", "is.ts", "lm.fit", "resid",
             "sd", "var")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
arrayUpdate : pairUpdate: no visible global function definition for
  ‘runif’
conditionUpdate: no visible global function definition for ‘runif’
designGG: no visible global function definition for ‘runif’
experimentDesignTable: no visible global function definition for
  ‘write.csv’
plotAllScores: no visible global function definition for ‘png’
plotAllScores: no visible global function definition for ‘par’
plotAllScores: no visible global function definition for ‘text’
plotAllScores: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off par png runif text write.csv
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "par", "text")
  importFrom("stats", "runif")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Found the following files/directories:
  ‘myDesignGGSAplot.png’ ‘myDesignGG_arrayDesign.csv’
  ‘myDesignGG_conditionDesign.csv’
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'Rmosek', 'Rsymphony'
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
fs.agreement.part: no visible global function definition for ‘as.dist’
fs.agreement.part: no visible global function definition for ‘cor’
fs.leave.k.out.combn: no visible global function definition for ‘sd’
fs.leave.k.out.sample: no visible global function definition for ‘sd’
fs.rd: no visible global function definition for ‘pchisq’
fs.selection: no visible global function definition for ‘p.adjust’
plot.FIT: no visible global function definition for ‘qchisq’
plot.FIT: no visible global function definition for ‘ppoints’
plot.FIT: no visible global function definition for ‘points’
plot.FIT: no visible global function definition for ‘abline’
plotJn: no visible global function definition for ‘points’
robust.distance.signed: no visible global function definition for
  ‘mahalanobis’
snowball: no visible global function definition for ‘is’
snowball: no visible global function definition for ‘median’
weight.sd: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  abline as.dist cor is mahalanobis median p.adjust pchisq points
  ppoints qchisq sd
Consider adding
  importFrom("graphics", "abline", "points")
  importFrom("methods", "is")
  importFrom("stats", "as.dist", "cor", "mahalanobis", "median",
             "p.adjust", "pchisq", "ppoints", "qchisq", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package in Depends field not imported from: ‘dplR’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.get’ ‘InteractiveDetrending’ ‘RemoveTrend’
Found the following files/directories:
  ‘data’
GNU make is a SystemRequirements.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘utils’
  All declared Imports should be used.
simulate_dataframe : generate_dumb_answer: no visible global function
  definition for ‘rbinom’
simulate_dataframe : generate_dumb_answer: no visible global function
  definition for ‘rnorm’
simulate_dataframe : generate_initial: no visible global function
  definition for ‘rbinom’
simulate_dataframe: no visible binding for global variable ‘randu’
simulate_dataframe: no visible global function definition for ‘rbinom’
simulate_dataframe: no visible global function definition for ‘rnorm’
simulate_dataframe: no visible global function definition for ‘rpois’
simulate_dataframe : add_NAs: no visible global function definition for
  ‘rbinom’
Undefined global functions or variables:
  randu rbinom rnorm rpois
Consider adding
  importFrom("datasets", "randu")
  importFrom("stats", "rbinom", "rnorm", "rpois")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
GNU make is a SystemRequirements.
makeAdjMatrix: no visible global function definition for ‘combn’
plotPosteriorN: no visible global function definition for ‘title’
plotPosteriorN: no visible global function definition for ‘lines’
plotPosteriorN: no visible global function definition for ‘legend’
venn3: no visible global function definition for ‘runif’
venn3: no visible global function definition for ‘points’
venn3: no visible global function definition for ‘lines’
venn3: no visible global function definition for ‘text’
venn4: no visible global function definition for ‘lines’
venn4: no visible global function definition for ‘runif’
venn4: no visible global function definition for ‘points’
Undefined global functions or variables:
  combn legend lines points runif text title
Consider adding
  importFrom("graphics", "legend", "lines", "points", "text", "title")
  importFrom("stats", "runif")
  importFrom("utils", "combn")
to your NAMESPACE file.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
cvm.test : cvm.pval.disc: no visible global function definition for
  ‘integrate’
cvm.test : cvm.pval.disc: no visible global function definition for
  ‘dchisq’
cvm.test : cvm.pval.disc: no visible global function definition for
  ‘nlm’
cvm.test : cvm.stat.disc: no visible global function definition for
  ‘knots’
cvm.test : cvm.pval.disc.sim: no visible global function definition for
  ‘knots’
cvm.test : cvm.pval.disc.sim: no visible global function definition for
  ‘runif’
cvm.test: no visible global function definition for ‘is.stepfun’
cvm.test: no visible global function definition for ‘knots’
ks.test : exact.pval : ts.pval: no visible global function definition
  for ‘ecdf’
ks.test : sim.pval: no visible global function definition for ‘runif’
ks.test : sim.pval : getks: no visible global function definition for
  ‘ecdf’
ks.test: no visible global function definition for ‘is.stepfun’
ks.test: no visible global function definition for ‘knots’
ks.test: no visible global function definition for ‘ecdf’
Undefined global functions or variables:
  dchisq ecdf integrate is.stepfun knots nlm runif
Consider adding
  importFrom("stats", "dchisq", "ecdf", "integrate", "is.stepfun",
             "knots", "nlm", "runif")
to your NAMESPACE file.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    1.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘DGVM3D.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: rgl
Loading required namespace: rmarkdown
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 230-234 (DGVM3D.Rmd) 
Error: processing vignette 'DGVM3D.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘DGVM3D.Rmd’

SUMMARY: processing the following file failed:
  ‘DGVM3D.Rmd’

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘mgcv’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rsvg’
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    doc           9.8Mb
    htmlwidgets   6.2Mb
Note: found 1 marked UTF-8 string
dichromat: no visible global function definition for ‘col2rgb’
dichromat: no visible global function definition for ‘predict’
dichromat: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  col2rgb predict rgb
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
  importFrom("stats", "predict")
to your NAMESPACE file.
le.pesquisa: no visible global function definition for ‘txtProgressBar’
le.pesquisa: no visible global function definition for ‘type.convert’
le.pesquisa: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar type.convert
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar",
             "type.convert")
to your NAMESPACE file.
Note: found 2297 marked UTF-8 strings
Malformed Title field: should not end in a period.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
L2eV: no visible binding for global variable ‘constants’
L2w: no visible binding for global variable ‘constants’
dielectric: no visible global function definition for ‘new’
dielectric2plot: no visible global function definition for ‘reshape’
eV2L: no visible binding for global variable ‘constants’
t2eV: no visible binding for global variable ‘constants’
Undefined global functions or variables:
  constants new reshape
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "reshape")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  ‘module_list.txt’ ‘res.txt’
Packages in Depends field not imported from:
  ‘PropCIs’ ‘gee’ ‘rootSolve’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
diffpci: no visible global function definition for ‘diffpropci.Wald.mp’
diffpci: no visible global function definition for ‘diffpropci.mp’
diffpci: no visible global function definition for ‘scoreci.mp’
exact.cond : exactci: no visible global function definition for ‘qf’
exact.midp : binom.midp : f.low: no visible global function definition
  for ‘dbinom’
exact.midp : binom.midp : f.low: no visible global function definition
  for ‘pbinom’
exact.midp : binom.midp : f.up: no visible global function definition
  for ‘dbinom’
exact.midp : binom.midp : f.up: no visible global function definition
  for ‘pbinom’
exact.midp : binom.midp : one.ci: no visible global function definition
  for ‘uniroot’
np.nv: no visible global function definition for ‘qnorm’
np.t: no visible global function definition for ‘qt’
uncond: no visible global function definition for ‘qnorm’
wald.cc: no visible global function definition for ‘qnorm’
wilson: no visible global function definition for ‘qnorm’
wilson: no visible global function definition for ‘uniroot.all’
wilson.cc: no visible global function definition for ‘qnorm’
wilson.cc: no visible global function definition for ‘uniroot.all’
wilson.phi: no visible global function definition for ‘qnorm’
wilson.phi: no visible global function definition for ‘uniroot.all’
Undefined global functions or variables:
  dbinom diffpropci.Wald.mp diffpropci.mp pbinom qf qnorm qt scoreci.mp
  uniroot uniroot.all
Consider adding
  importFrom("stats", "dbinom", "pbinom", "qf", "qnorm", "qt", "uniroot")
to your NAMESPACE file.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc   9.5Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘sf’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gplots’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
'library' or 'require' calls to packages already attached by Depends:
  ‘maptools’ ‘spatstat’ ‘spdep’
  Please remove these calls from your code.
fAssocmatrix : fAssocmatrix1: no visible global function definition for
  ‘coordinates<-’
fAssocplot: no visible global function definition for ‘coordinates’
fAssocplot: no visible global function definition for ‘text’
fAssocplot: no visible global function definition for ‘box’
fDrawfigure: no visible global function definition for ‘slot’
fDrawfigure : <anonymous>: no visible global function definition for
  ‘slot’
fDrawfigure: no visible global function definition for
  ‘SpatialPolygons’
fDrawfigure: no visible global function definition for ‘spsample’
fDrawfigure: no visible global function definition for ‘image’
fDrawfigure: no visible global function definition for
  ‘colorRampPalette’
fDrawfigure: no visible global function definition for ‘points’
fRanXY : <anonymous>: no visible global function definition for ‘slot’
fRanXY : <anonymous>: no visible global function definition for
  ‘spsample’
Undefined global functions or variables:
  SpatialPolygons box colorRampPalette coordinates coordinates<- image
  points slot spsample text
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "box", "image", "points", "text")
  importFrom("methods", "slot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in ‘Digiroo2-Ex.R’ failed
The error most likely occurred in:

> ### Name: fDrawfigure
> ### Title: Plot the location of the random point falling within an
> ###   individual's home range
> ### Aliases: fDrawfigure
> 
> ### ** Examples
> 
> 
> ## Load required packages
> library(adehabitatHR)
Loading required package: deldir
deldir 0.1-25
Loading required package: ade4

Attaching package: ‘ade4’

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

    mstree

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

    disc

Loading required package: adehabitatMA
Loading required package: adehabitatLT
Loading required package: CircStats
Loading required package: MASS

Attaching package: ‘MASS’

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

    area

Loading required package: boot

Attaching package: ‘boot’

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

    envelope

> 
> ## Load study data
> data(StudyArea)
> data(Roos)
> 
> # Subset the data for only 1 individual
> RooSubid <- 'Stripes'
> RooSub <- subset(Roos,Roos$ID==RooSubid)
> RooSub$ID <- as.character(RooSub$ID)
> 
> coordinates(RooSub) <- ~x+y
> 
> ## Estimation of UD and KUD 95% for 1 animal
> ud <- kernelUD(RooSub,h="href",same4all=TRUE)
> ver95 <- getverticeshr(ud,95,unin = c("m"),unout=c("ha"))
> udsgdf <- as(estUDm2spixdf(ud),"SpatialGridDataFrame")
> 
> ## Extract random points falling within animal #1's KUD 95%
> fDrawfigure(1,ver95,RooSub,StudyArea) 
Error in as.double(y) : 
  cannot coerce type 'S4' to vector of type 'double'
Calls: fDrawfigure -> plot -> plot.default -> xy.coords
Execution halted
Malformed Title field: should not end in a period.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘igraph’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: ‘RcppRedis’
aLine: no visible global function definition for ‘lines’
aLine: no visible global function definition for ‘ecdf’
dip.test: no visible global function definition for ‘complete.cases’
dip.test: no visible global function definition for ‘runif’
dip.test: no visible global function definition for ‘approx’
plot.dip: no visible global function definition for ‘par’
plot.dip: no visible global function definition for ‘ecdf’
plot.dip: no visible global function definition for ‘title’
plot.dip: no visible global function definition for ‘abline’
plot.dip: no visible global function definition for ‘axis’
plot.dip: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline approx axis complete.cases ecdf legend lines par runif title
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "title")
  importFrom("stats", "approx", "complete.cases", "ecdf", "runif")
to your NAMESPACE file.
Output for data("exHartigan", package = "diptest"):
  'exHartigan' data is identical to 'statfaculty' and hence deprecated.
   Use the 'statfaculty' instead
Namespace in Imports field not imported from: ‘sandwich’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
nullTest: no visible global function definition for ‘rmultinom’
rdirichlet: no visible global function definition for ‘rgamma’
simPop: no visible global function definition for ‘rnorm’
simPop: no visible global function definition for ‘rmultinom’
Undefined global functions or variables:
  rgamma rmultinom rnorm
Consider adding
  importFrom("stats", "rgamma", "rmultinom", "rnorm")
to your NAMESPACE file.
Package suggested but not available for checking: ‘INLA’
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘rgeos’ ‘splancs’ ‘utils’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
rdisclap: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
p.discrete.adjust : <anonymous>: no visible global function definition
  for ‘stepfun’
Undefined global functions or variables:
  stepfun
Consider adding
  importFrom("stats", "stepfun")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
value: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  qchisq
Consider adding
  importFrom("stats", "qchisq")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Package which this enhances but not available for checking: ‘INLA’
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Note: found 106 marked UTF-8 strings
densest: no visible global function definition for ‘weighted.mean’
diss: no visible global function definition for ‘cov’
neighbors: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov weighted.mean
Consider adding
  importFrom("stats", "cov", "weighted.mean")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘proxy’
  All declared Imports should be used.
Deprecated license: BSD
dist.multiPhylo: no visible global function definition for ‘as.dist’
gromov.hyperbolicity: no visible global function definition for
  ‘as.dist’
mcmc.target.seq: no visible global function definition for ‘runif’
phylo.diff: no visible global function definition for ‘par’
Undefined global functions or variables:
  as.dist par runif
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "as.dist", "runif")
to your NAMESPACE file.
Found the following files/directories:
  ‘csim’ ‘xyz’ ‘xyz.sav’ ‘xyz.sav.comment’
Found the following files/directories:
  ‘csim.mean’ ‘csim.mean.comment’
Malformed Title field: should not end in a period.
prepare_Rd: extract.val.Rd:25-26: Dropping empty section \note
prepare_Rd: extract.val.Rd:27: Dropping empty section \seealso
Package suggested but not available for checking: ‘HWxtest’
'library' or 'require' call to ‘glmnet’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘glmnet’ ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following files/directories:
  ‘new_model.rda’
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    include  15.1Mb
Package suggested but not available for checking: ‘asreml’
'library' or 'require' calls to packages already attached by Depends:
  ‘nlme’ ‘wgaim’
  Please remove these calls from your code.
'library' or 'require' call to ‘asreml’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘ibdreg’ ‘mgcv’ ‘nlme’ ‘qtl’ ‘wgaim’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘qtl:::adjust.rf.ri’
  See the note in ?`:::` about the use of this operator.
Foreign function call to a different package:
  .C(cfunc, ..., PACKAGE = "qtl")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   2.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Running examples in ‘dmdScheme-Ex.R’ failed
The error most likely occurred in:

> ### Name: report
> ### Title: Generic function for creating a report from an object 'x'
> ### Aliases: report report.character report.dmdScheme_validation
> 
> ### ** Examples
> 
> ## Report of `dmdScheme_validation`
> report( scheme_path_xlsx() )
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Running ‘testthat.R’ [32s/78s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(magrittr)
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  > ##
  > library(dmdScheme)
  
  #############################################
  The cache will be in a temporary location and be deleted when you quit R.
  It is located at
     /tmp/RtmpXdayTK/working_dir/RtmpJfa4.x/dmdScheme_2ff72c92732a
  To make it permanent, call
     cache(createPermanent = TRUE)
  and restart R
  and a permanent cache will be created which will survive restarts.
  #############################################
  
  
  trying URL 'https://github.com/Exp-Micro-Ecol-Hub/dmdSchemeRepository/raw/master/schemes/dmdScheme_0.9.5.tar.gz'
  Content type 'application/octet-stream' length 27511 bytes (26 KB)
  ==================================================
  downloaded 26 KB
  
  Scheme definition `/tmp/RtmpXdayTK/working_dir/RtmpJfa4.x/file2ff7633924e1/dmdScheme_0.9.5.tar.gz, installed with
  name:    dmdScheme
  version: 0.9.5
  Theme switched to dmdScheme_0.9.5
  > ##
  > test_check("dmdScheme")
  terminate called after throwing an instance of 'Rcpp::exception'
    what():  Start tag expected, '<' not found [4]
Package suggested but not available for checking: ‘RPostgres’
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
Warning: no function found corresponding to methods exports from ‘DMwR’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
Packages in Depends field not imported from:
  ‘grid’ ‘lattice’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing object imported by a ':::' call: ‘rpart:::rpconvert’
Unexported objects imported by ':::' calls:
  ‘rpart:::rpart.branch’ ‘rpart:::rpartco’
  ‘rpart:::string.bounding.box’
  See the note in ?`:::` about the use of this operator.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘GOstats’ ‘caTools’ ‘fdrtool’
  All declared Imports should be used.
DNMF: no visible global function definition for ‘runif’
NMFpval: no visible global function definition for ‘p.adjust’
ndNMF: no visible global function definition for ‘runif’
rnk: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  p.adjust runif write.table
Consider adding
  importFrom("stats", "p.adjust", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
ppert: no visible global function definition for ‘pbeta’
prepare8pkg: no visible global function definition for ‘glob2rx’
qpert: no visible global function definition for ‘qbeta’
rpert: no visible global function definition for ‘rbeta’
Undefined global functions or variables:
  glob2rx pbeta qbeta rbeta
Consider adding
  importFrom("stats", "pbeta", "qbeta", "rbeta")
  importFrom("utils", "glob2rx")
to your NAMESPACE file.
Found the following files/directories:
  ‘annotation_file.yml’
Running ‘runit.R’ [17s/29s]
  Running ‘testthat.R’ [19s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > running_on_my_machines <- function() {
  +     sys_info <- Sys.info()
  +     r <- sys_info[["nodename"]] %in% c("h6", "h7") &&
  +         sys_info[["effective_user"]] == "qwer" &&
  +         .Platform[["OS.type"]] == "unix"
  +     return(r)
  + }
  > 
  > set_NOT_CRAN  <- function() {
  +     is_unset <- is.na(Sys.getenv("NOT_CRAN", unset = NA))
  +     if (running_on_my_machines() && is_unset)
  +         Sys.setenv("NOT_CRAN" = TRUE)
  + }
  > 
  > set_NOT_CRAN()
  > library("testthat")
  > library("document")
  > test_check("document")
  ── R CMD build ─────────────────────────────────────────────────────────────────
  * checking for file ‘.../DESCRIPTION’ ... OK
  * preparing ‘mini.mal’:
  * checking DESCRIPTION meta-information ... OK
  * checking for LF line-endings in source and make files and shell scripts
  * checking for empty or unneeded directories
  * building ‘mini.mal_2.0.0.tar.gz’
  
  ── 1. Error: (unknown) (@test_basic.R#13)  ─────────────────────────────────────
  Still alive
  Backtrace:
   1. document::document(file_name, check_package = TRUE, runit = TRUE)
   2. document:::check_package(...)
   3. rcmdcheck::rcmdcheck(...)
   4. rcmdcheck:::build_package(...)
   7. proc$get_built_file()
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: (unknown) (@test_basic.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
GNU make is a SystemRequirements.
Found the following files/directories:
  ‘test.html’ ‘test.rda’
Packages which this enhances but not available for checking:
  'gurobi', 'Rmosek'
Running examples in ‘DoE.multi.response-Ex.R’ failed
The error most likely occurred in:

> ### Name: ufccd
> ### Title: This function generates the design matrix for a unique factor
> ###   CCD.
> ### Aliases: ufccd
> 
> ### ** Examples
> 
> #Response 1 is related to factors 1, 2, and 3
> #Response 2 is related to factors 2, 3, and 4
> #Response 3 is related to factors 1, 3, and 5
> #Response 4 is related to factors 1 and 4
> x<-matrix(c(1,1,1,0,0,
+             0,1,1,1,0,
+             1,0,1,0,1,
+             1,0,0,1,0), nrow = 4,byrow = TRUE)
> ufccd(x)
full factorial design needed
creating full factorial with 16 runs ...

Error in punkt1 + 1 : non-numeric argument to binary operator
Calls: ufccd ... ccd.augment -> add.center -> sapply -> lapply -> substr
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DoE.multi.response)
  Loading required package: DoE.wrapper
  Loading required package: FrF2
  Loading required package: DoE.base
  Loading required package: grid
  Loading required package: conf.design
  
  Attaching package: 'DoE.base'
  
  The following objects are masked from 'package:stats':
  
      aov, lm
  
  The following object is masked from 'package:graphics':
  
      plot.design
  
  The following object is masked from 'package:base':
  
      lengths
  
  Loading required package: rsm
  
  Attaching package: 'DoE.wrapper'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  > 
  > test_check("DoE.multi.response")
  ── 1. Error: (unknown) (@testufccd.R#8)  ───────────────────────────────────────
  non-numeric argument to binary operator
  Backtrace:
   1. DoE.multi.response::ufccd(x)
   2. DoE.wrapper::ccd.design(...)
   3. DoE.wrapper::ccd.augment(...)
   4. FrF2::add.center(cube, ncenter[1])
   7. base::substr(rostdrplev, punkt1 + 1, 999)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 23 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@testufccd.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
dostats: no visible binding for global variable ‘na.fail’
first: no visible global function definition for ‘head’
last: no visible global function definition for ‘tail’
pval.default: no visible global function definition for ‘.hasSlot’
pval.lm: no visible global function definition for ‘anova’
Undefined global functions or variables:
  .hasSlot anova head na.fail tail
Consider adding
  importFrom("methods", ".hasSlot")
  importFrom("stats", "anova", "na.fail")
  importFrom("utils", "head", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  ‘myfile.ps’ ‘myfile.svg’
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘parallel’ ‘rgdal’ ‘sp’ ‘tensorflow’
  All declared Imports should be used.
Found the following files/directories:
  ‘ansic_gram.c’
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.
Quitting from lines 359-375 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
graphical parameter "col.axis" has the wrong length
--- failed re-building ‘overview.Rmd’

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

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

> ### Name: ccf.series.rwl
> ### Title: Cross-Correlation between a Series and a Master Chronology
> ### Aliases: ccf.series.rwl
> ### Keywords: manip
> 
> ### ** Examples
> 
> library(utils)
> data(co021)
> dat <- co021
> ## Create a missing ring by deleting a year of growth in a random series
> flagged <- dat$"641143"
> flagged <- c(NA, flagged[-325])
> names(flagged) <- rownames(dat)
> dat$"641143" <- NULL
> ccf.100 <- ccf.series.rwl(rwl = dat, series = flagged, seg.length = 100)
NB: With series.x = FALSE (default), negative lags indicate missing rings in seriesError in limits.and.aspect(default.prepanel, prepanel = prepanel, have.xlim = have.xlim,  : 
  need at least one panel
Calls: ccf.series.rwl -> xyplot -> xyplot.formula -> limits.and.aspect
Execution halted
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Error(s) in re-building vignettes:
  ...
--- re-building ‘chron-dplR.Rnw’ using Sweave
--- finished re-building 'chron-dplR.Rnw'

--- re-building ‘intro-dplR.Rnw’ using Sweave
Warning in detrend.series(y = series, y.name = "CAM011", verbose = TRUE) :
  Ar fit is not all positive
--- finished re-building 'intro-dplR.Rnw'

--- re-building ‘timeseries-dplR.Rnw’ using Sweave
Loading required package: forecast
Loading required package: waveslim

waveslim: Wavelet Method for 1/2/3D Signals (version = 1.8.2)

--- finished re-building 'timeseries-dplR.Rnw'

--- re-building ‘xdate-dplR.Rnw’ using Sweave
Warning in RNGkind("Mersenne-Twister", "Inversion", "Rounding") :
  non-uniform 'Rounding' sampler used

Error: processing vignette 'xdate-dplR.Rnw' failed with diagnostics:
 chunk 8 (label = d) 
Error in limits.and.aspect(default.prepanel, prepanel = prepanel, have.xlim = have.xlim,  : 
  need at least one panel

--- failed re-building 'xdate-dplR.Rnw'

SUMMARY: processing the following file failed:
  ‘xdate-dplR.Rnw’

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   2.6Mb
Note: found 4 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘bit64’ ‘rstudioapi’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘tools’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘broom’ ‘colorspace’ ‘colourpicker’ ‘cowplot’
  ‘igraph’ ‘magrittr’ ‘shinyBS’ ‘shinyWidgets’ ‘shinydashboard’
  ‘shinythemes’ ‘tidyverse’ ‘visNetwork’
  All declared Imports should be used.
Found the following files/directories:
  ‘drawBox.pdf’ ‘drawCircle.pdf’ ‘drawCurve.pdf’ ‘drawLine.pdf’
  ‘drawPoint.pdf’ ‘drawSettingsExample.pdf’ ‘drawText.pdf’ ‘export.pdf’
DRaWR: no visible global function definition for ‘write.table’
DRaWR: no visible global function definition for ‘read.table’
DRaWR: no visible global function definition for ‘aggregate’
DRaWR: no visible global function definition for ‘slot’
Undefined global functions or variables:
  aggregate read.table slot write.table
Consider adding
  importFrom("methods", "slot")
  importFrom("stats", "aggregate")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  ‘output_sample.uni.sample.undir.weight.type.50.1e-04.0.7.base’
  ‘output_sample.uni.sample.undir.weight.type.50.1e-04.1.1.0.7.sample.setlist.stats’
cdfDRM: no visible global function definition for ‘tail’
densityDRM: no visible binding for global variable ‘density’
drmdel: no visible binding for global variable ‘optim’
drmdel: no visible global function definition for ‘pchisq’
quantEst: no visible global function definition for ‘tail’
quantileCompWald: no visible global function definition for ‘pchisq’
quantileCompWald: no visible global function definition for ‘p.adjust’
quantileDRM: no visible global function definition for ‘tail’
quantileDRM: no visible global function definition for ‘density’
Undefined global functions or variables:
  density optim p.adjust pchisq tail
Consider adding
  importFrom("stats", "density", "optim", "p.adjust", "pchisq")
  importFrom("utils", "tail")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    DRomics-shiny   1.8Mb
    extdata         3.1Mb
compute_xsq: no visible global function definition for ‘chisq.test’
Undefined global functions or variables:
  chisq.test
Consider adding
  importFrom("stats", "chisq.test")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘userGuide.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.
Using constraints: b = 1
Using constraints: b = 1
Running default monotherapy fitting. Note that if constraints are needed, run mono fitting manually first
Using constraints: b = 1
Using constraints: b = 1
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]="webshotbc6538300b.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotbc6538300b.png': No such file or directory
Quitting from lines 357-358 (userGuide.Rmd) 
Error: processing vignette 'userGuide.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘userGuide.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘readr’ ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    appinformation   4.2Mb
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
Namespaces in Imports field not imported from:
  ‘rJava’ ‘tools’ ‘xtable’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘dsa-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 37-38 (dsa-vignette.Rmd) 
Error: processing vignette 'dsa-vignette.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
--- failed re-building ‘dsa-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘out.html’
DSBayes: no visible global function definition for ‘qnorm’
DSBayes: no visible global function definition for ‘coef’
DSBayes: no visible global function definition for ‘vcov’
DSBayes : MLE: no visible global function definition for ‘qnorm’
DSBayes: no visible global function definition for ‘integrate’
DSBayes : qfunc.numer : <anonymous>: no visible global function
  definition for ‘dnorm’
DSBayes : ds.numer: no visible global function definition for
  ‘integrate’
DSBayes : lower: no visible global function definition for ‘qlogis’
DSBayes : lower: no visible global function definition for ‘integrate’
DSBayes : upper: no visible global function definition for ‘qlogis’
DSBayes : upper: no visible global function definition for ‘integrate’
DSBayes: no visible global function definition for ‘optimize’
DSBayes: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  coef dnorm integrate optimize qlogis qnorm uniroot vcov
Consider adding
  importFrom("stats", "coef", "dnorm", "integrate", "optimize", "qlogis",
             "qnorm", "uniroot", "vcov")
to your NAMESPACE file.
Note: found 3 marked UTF-8 strings
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
Note: found 4891 marked UTF-8 strings
Running examples in ‘dsmodels-Ex.R’ failed
The error most likely occurred in:

> ### Name: dscurve
> ### Title: Parametric curves or a graph of functions
> ### Aliases: dscurve
> 
> ### ** Examples
> 
> library(dsmodels)
> 
> fun <- function(X,Y) {
+   list(
+     X/exp(Y),
+     Y/exp(X)
+   )
+ }
> 
> model <- dsmodel(fun, title = "Points on a One-Dimensional Curve")
> range <- dsrange(-2:2,-2:2, discretize = 0.5)
> 
> # Add the graph of a function and its image in blue.
> graphcrv <- dscurve(function(x) x^2,
+                     col = "orange",
+                     image = "blue",
+                     discretize = TRUE,
+                     xlim = c(-2,2))
> model + range +	graphcrv
Error in -rid : invalid argument to unary operator
Calls: +.dsproto ... <Anonymous> -> f -> <Anonymous> -> f -> <Anonymous> -> f
Execution halted
AIC.dspat: no visible global function definition for ‘coef’
LTDataFrame: no visible global function definition for ‘as.formula’
coef.dspat: no visible global function definition for ‘coef’
integrate.intensity: no visible global function definition for ‘coef’
integrate.intensity: no visible global function definition for
  ‘predict’
integrate.intensity: no visible global function definition for
  ‘model.matrix’
integrate.intensity: no visible global function definition for ‘vcov’
integrate.intensity: no visible global function definition for ‘fitted’
lgcp.correction: no visible global function definition for ‘predict’
lgcp.correction: no visible global function definition for
  ‘model.matrix’
lgcp.correction: no visible global function definition for ‘fitted’
lgcp.correction: no visible global function definition for ‘var’
lines_to_strips : line_to_strip: no visible global function definition
  for ‘as’
owin.gpc.poly: no visible global function definition for ‘as’
sample.points : sample.points.from.line: no visible global function
  definition for ‘runif’
sample.points: no visible global function definition for ‘model.matrix’
simCovariates: no visible global function definition for ‘quantile’
simPts: no visible global function definition for ‘model.matrix’
transect.intensity: no visible global function definition for ‘predict’
transect.intensity: no visible global function definition for ‘hist’
Undefined global functions or variables:
  as as.formula coef fitted hist model.matrix predict quantile runif
  var vcov
Consider adding
  importFrom("graphics", "hist")
  importFrom("methods", "as")
  importFrom("stats", "as.formula", "coef", "fitted", "model.matrix",
             "predict", "quantile", "runif", "var", "vcov")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
DStree: no visible global function definition for ‘model.frame’
DStree: no visible global function definition for ‘model.matrix’
DStree: no visible global function definition for ‘model.response’
DStree: no visible global function definition for ‘as.formula’
bag: no visible global function definition for ‘model.frame’
bag: no visible global function definition for ‘model.response’
plot.DStree: no visible global function definition for ‘par’
plot.DStree: no visible global function definition for ‘rainbow’
plot.DStree: no visible global function definition for ‘lines’
plot.DStree: no visible global function definition for ‘legend’
predict.DStree: no visible global function definition for ‘predict’
print.DStree: no visible global function definition for ‘naprint’
prune.DStree: no visible global function definition for ‘median’
prune.DStree: no visible global function definition for ‘predict’
prune.DStree: no visible binding for global variable ‘var’
summ.MAE: no visible global function definition for ‘predict’
summary.DStree: no visible global function definition for ‘naprint’
Undefined global functions or variables:
  as.formula legend lines median model.frame model.matrix
  model.response naprint par predict rainbow var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend", "lines", "par")
  importFrom("stats", "as.formula", "median", "model.frame",
             "model.matrix", "model.response", "naprint", "predict",
             "var")
to your NAMESPACE file.
DCEA: no visible global function definition for ‘p.adjust’
DS: no visible global function definition for ‘p.adjust’
DS: no visible global function definition for ‘pdf’
DS: no visible global function definition for ‘dev.off’
LFC: no visible global function definition for ‘glm’
LFC: no visible global function definition for ‘predict’
PartialCor: no visible global function definition for ‘na.omit’
comDCGLplot: no visible global function definition for ‘pdf’
comDCGLplot: no visible global function definition for ‘dev.off’
percentLinkfilter: no visible global function definition for ‘cor’
qLinkfilter: no visible global function definition for ‘cor’
qLinkfilter: no visible global function definition for ‘pt’
qLinkfilter: no visible global function definition for ‘p.adjust’
rLinkfilter: no visible global function definition for ‘cor’
varianceBasedfilter: no visible binding for global variable ‘var’
varianceBasedfilter: no visible global function definition for ‘median’
varianceBasedfilter: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  cor dev.off glm median na.omit p.adjust pchisq pdf predict pt var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("stats", "cor", "glm", "median", "na.omit", "p.adjust",
             "pchisq", "predict", "pt", "var")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Designing-33PC.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 163-164 (Designing-33PC.Rmd) 
Error: processing vignette 'Designing-33PC.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Designing-33PC.Rmd’

SUMMARY: processing the following file failed:
  ‘Designing-33PC.Rmd’

Error: Vignette re-building failed.
Execution halted
DLR: no visible global function definition for ‘formula’
DLR: no visible global function definition for ‘terms’
DLR: no visible global function definition for ‘model.matrix’
DLR: no visible global function definition for ‘as.formula’
DLR: no visible binding for global variable ‘binomial’
DLR: no visible global function definition for ‘coef’
DLR: no visible global function definition for ‘pnorm’
DLR: no visible global function definition for ‘qnorm’
acc.1test: no visible global function definition for ‘qnorm’
pv.gs: no visible global function definition for ‘pchisq’
pv.rpv: no visible global function definition for ‘qnorm’
pv.rpv: no visible global function definition for ‘pnorm’
pv.wgs: no visible global function definition for ‘pchisq’
sesp.diff.ci: no visible global function definition for ‘qnorm’
sesp.mcnemar: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  as.formula binomial coef formula model.matrix pchisq pnorm qnorm
  terms
Consider adding
  importFrom("stats", "as.formula", "binomial", "coef", "formula",
             "model.matrix", "pchisq", "pnorm", "qnorm", "terms")
to your NAMESPACE file.
DTK.plot: no visible global function definition for ‘axis’
DTK.plot: no visible global function definition for ‘title’
DTK.plot: no visible global function definition for ‘lines’
DTK.plot: no visible global function definition for ‘points’
DTK.test: no visible binding for global variable ‘sd’
DTK.test: no visible global function definition for ‘qtukey’
TK.test: no visible global function definition for ‘TukeyHSD’
TK.test: no visible global function definition for ‘aov’
Undefined global functions or variables:
  TukeyHSD aov axis lines points qtukey sd title
Consider adding
  importFrom("graphics", "axis", "lines", "points", "title")
  importFrom("stats", "TukeyHSD", "aov", "qtukey", "sd")
to your NAMESPACE file.
DTMC: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
GNU make is a SystemRequirements.
Namespaces in Imports field not imported from:
  ‘digest’ ‘dplyr’
  All declared Imports should be used.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
dummy: no visible global function definition for ‘model.matrix’
dummy: no visible global function definition for ‘model.frame’
Undefined global functions or variables:
  model.frame model.matrix
Consider adding
  importFrom("stats", "model.frame", "model.matrix")
to your NAMESPACE file.
Note: found 2854 marked UTF-8 strings
cvSDDT: no visible global function definition for ‘qt’
cvSDDT : Cj_SD.fun: no visible global function definition for ‘combn’
cvSDDT: no visible global function definition for ‘uniroot’
cvSUDT: no visible global function definition for ‘rnorm’
cvSUDT: no visible global function definition for ‘rchisq’
cvSUDT : psi.fun: no visible global function definition for ‘pnorm’
cvSUDT: no visible global function definition for ‘qt’
cvSUDT: no visible global function definition for ‘uniroot’
cvSUDT: no visible global function definition for ‘combn’
nvDT : samplesize: no visible global function definition for ‘rnorm’
nvDT : samplesize: no visible global function definition for ‘rchisq’
nvDT : samplesize: no visible global function definition for ‘pnorm’
nvDT : ssBonf: no visible global function definition for ‘qnorm’
nvDT : ssBonf: no visible global function definition for ‘qt’
nvDT : ssBonf: no visible global function definition for ‘rnorm’
nvDT : ssBonf: no visible global function definition for ‘rchisq’
nvDT : ssBonf: no visible global function definition for ‘pnorm’
nvDT: no visible global function definition for ‘uniroot’
powDT: no visible global function definition for ‘rnorm’
powDT: no visible global function definition for ‘rchisq’
powDT: no visible global function definition for ‘pnorm’
qvSDDT: no visible global function definition for ‘pt’
qvSUDT: no visible global function definition for ‘rnorm’
qvSUDT: no visible global function definition for ‘rchisq’
qvSUDT : psi.fun: no visible global function definition for ‘pnorm’
qvSUDT: no visible global function definition for ‘pt’
qvSUDT : Pj.fun: no visible global function definition for ‘qt’
qvSUDT : Pj.fun: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  combn pnorm pt qnorm qt rchisq rnorm uniroot
Consider adding
  importFrom("stats", "pnorm", "pt", "qnorm", "qt", "rchisq", "rnorm",
             "uniroot")
  importFrom("utils", "combn")
to your NAMESPACE file.
Clough: no visible global function definition for ‘dgamma’
computePosterior,Counts: no visible global function definition for
  ‘dnbinom’
getPosteriorParam,Counts: no visible global function definition for
  ‘qgamma’
getPosteriorParam,Counts: no visible global function definition for
  ‘dgamma’
getPosteriorParam,Counts: no visible global function definition for
  ‘pgamma’
plotPosterior,Counts: no visible global function definition for ‘axis’
plotPosterior,Counts: no visible global function definition for
  ‘abline’
plotPosterior,Counts: no visible global function definition for ‘lines’
plotPosterior,Counts: no visible global function definition for ‘rect’
plotPosterior,Counts: no visible global function definition for ‘curve’
plotPosterior,Counts: no visible global function definition for
  ‘dgamma’
plotPosterior,Counts: no visible global function definition for
  ‘legend’
show,Counts: no visible global function definition for ‘head’
show,Counts: no visible global function definition for ‘tail’
Undefined global functions or variables:
  abline axis curve dgamma dnbinom head legend lines pgamma qgamma rect
  tail
Consider adding
  importFrom("graphics", "abline", "axis", "curve", "legend", "lines",
             "rect")
  importFrom("stats", "dgamma", "dnbinom", "pgamma", "qgamma")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls to packages already attached by Depends:
  ‘ggm’ ‘tcltk’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘ggm’ ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    doc    1.8Mb
    libs   2.3Mb
Namespaces in Imports field not imported from:
  ‘maptools’ ‘tools’
  All declared Imports should be used.
MultiTestH0 : MultiTestOneColumn: no visible global function definition
  for ‘pchisq’
RunClustering : CheckClusterNew: no visible global function definition
  for ‘qchisq’
RunClustering: no visible global function definition for ‘qchisq’
RunDenoising: no visible binding for global variable ‘var’
RunDenoising: no visible global function definition for ‘qchisq’
RunDenoising: no visible binding for global variable ‘median’
RunDenoising: no visible global function definition for ‘var’
RunDenoising : buildEstimate: no visible global function definition for
  ‘qchisq’
Undefined global functions or variables:
  median pchisq qchisq var
Consider adding
  importFrom("stats", "median", "pchisq", "qchisq", "var")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
GetIntMod: no visible global function definition for ‘arima’
GetLikeDI: no visible global function definition for ‘arima’
GetLikeDI: no visible global function definition for ‘logLik’
GetPV: no visible global function definition for ‘optimize’
GetPV: no visible global function definition for ‘pchisq’
fitdi: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  arima logLik optimize pchisq
Consider adding
  importFrom("stats", "arima", "logLik", "optimize", "pchisq")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.8Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘desc’
  All declared Imports should be used.
Running ‘testthat.R’ [74s/75s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("dynutils")
  Loading required package: dynutils
  
  Attaching package: 'dynutils'
  
  The following object is masked from 'package:testthat':
  
      has_names
  
  ── 1. Error: write_h5 and read_h5 works (@test-h5.R#11)  ───────────────────────
  HDF5-API H5T.c in H5Tget_class(): line 1876: not a datatype
          class: HDF5
          major: Invalid arguments to routine
          minor: Inappropriate type
  Backtrace:
   1. dynutils::read_h5(file)
   2. dynutils::read_h5_(file_h5)
   3. hdf5r::h5attr(file_h5, "object_class")
   4. attr_obj$read()
   5. hdf5r:::H5ToR_Pre(mem_type, nelem)
  
  ❌ Unable to read hdf5 files
  ── 2. Error: test_h5_installation works (@test-h5.R#17)  ───────────────────────
  HDF5-API H5T.c in H5Tget_class(): line 1876: not a datatype
          class: HDF5
          major: Invalid arguments to routine
          minor: Inappropriate type
  Backtrace:
   1. testthat::expect_true(test_h5_installation())
   4. dynutils::test_h5_installation()
   5. dynutils:::test_h5_installation_read(detailed, file)
   6. base::tryCatch(...)
   7. base:::tryCatchList(expr, classes, parentenv, handlers)
   8. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   9. value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 402 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 2 ]
  1. Error: write_h5 and read_h5 works (@test-h5.R#11) 
  2. Error: test_h5_installation works (@test-h5.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘FNN’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
Namespace in Imports field not imported from: ‘hms’
  All declared Imports should be used.
GNU make is a SystemRequirements.
File ‘eaf/libs/eaf.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
    Objects: ‘eaf/eaf.o’, ‘eaf/io.o’, ‘mo-tools/hv.o’, ‘Repsilon.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
Found the following files/directories:
  ‘example_table1.csv’ ‘example_table1.txt’ ‘example_table2.csv’
  ‘example_table2.txt’ ‘example_table3.csv’ ‘example_table3.txt’
  ‘table1.csv’ ‘table2.csv’ ‘table2.txt’ ‘table3.txt’ ‘table4.txt’
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’ ‘scales’ ‘xtable’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘base64enc’ ‘knitr’ ‘markdown’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.file_attachment: no visible global function definition for
  ‘base64encode’
.plot_attachment: no visible global function definition for ‘dev.off’
.update_list: no visible global function definition for ‘modifyList’
easyHtmlReport: no visible global function definition for ‘knit’
easyHtmlReport: no visible global function definition for
  ‘markdownToHTML’
mime_part.data.frame: no visible global function definition for
  ‘write.table’
mime_part.ggplot: no visible binding for global variable ‘pdf’
mime_part.matrix: no visible global function definition for
  ‘write.table’
mime_part.trellis: no visible binding for global variable ‘pdf’
simpleHtmlReport : <anonymous>: no visible global function definition
  for ‘write.table’
Undefined global functions or variables:
  base64encode dev.off knit markdownToHTML modifyList pdf write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "modifyList", "write.table")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
MARK.MCMC : Model.Creator: no visible global function definition for
  ‘combn’
MARK.MCMC : formula.Maker: no visible global function definition for
  ‘combn’
Simulate.CH: no visible global function definition for ‘rnorm’
Simulate.CH: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  combn rbinom rnorm
Consider adding
  importFrom("stats", "rbinom", "rnorm")
  importFrom("utils", "combn")
to your NAMESPACE file.
eb: no visible global function definition for ‘optimize’
ebalance: no visible global function definition for ‘var’
Undefined global functions or variables:
  optimize var
Consider adding
  importFrom("stats", "optimize", "var")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘methods’ ‘mgcv’ ‘rappdirs’ ‘rgdal’ ‘scales’ ‘tools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
ebSNP: no visible global function definition for ‘optim’
Undefined global functions or variables:
  optim
Consider adding
  importFrom("stats", "optim")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
Note: found 8 marked UTF-8 strings
dilution: no visible global function definition for ‘grey’
dilution: no visible global function definition for ‘lines’
dilution: no visible global function definition for ‘rect’
dilution: no visible global function definition for ‘segments’
dilution: no visible global function definition for ‘text’
dilution: no visible global function definition for ‘arrows’
pricefit: no visible global function definition for ‘runif’
Undefined global functions or variables:
  arrows grey lines rect runif segments text
Consider adding
  importFrom("grDevices", "grey")
  importFrom("graphics", "arrows", "lines", "rect", "segments", "text")
  importFrom("stats", "runif")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘tnet’
  All declared Imports should be used.
Found the following files/directories:
  ‘ecosim_example_plot1.pdf’ ‘ecosim_example_plot2.pdf’
  ‘ecosim_example_plot3.pdf’
GNU make is a SystemRequirements.
plot.ETdiagnosis: no visible global function definition for ‘par’
plot.ETdiagnosis: no visible global function definition for ‘lines’
plot.ETdiagnosis: no visible global function definition for ‘legend’
plot.ETmain: no visible global function definition for ‘par’
plot.ETmain: no visible global function definition for ‘polygon’
plot.ETmain: no visible global function definition for ‘axis’
plot.ETmain: no visible global function definition for ‘legend’
plot.ETmain: no visible global function definition for ‘lines’
plot.Transpose: no visible global function definition for ‘par’
plot.Transpose: no visible global function definition for ‘polygon’
plot.Transpose: no visible global function definition for ‘axis’
plot.Transpose: no visible global function definition for ‘legend’
plot.smooth: no visible global function definition for ‘lines’
plot_ETdiagnosis_isopleth: no visible global function definition for
  ‘par’
plot_ETdiagnosis_isopleth: no visible global function definition for
  ‘rainbow’
plot_ETdiagnosis_isopleth: no visible global function definition for
  ‘filled.contour’
regPB: no visible global function definition for ‘coef’
regPB: no visible global function definition for ‘lm’
regPB.ac: no visible global function definition for ‘coef’
regPB.ac: no visible global function definition for ‘lm’
regPB.ctsa: no visible global function definition for ‘coef’
regPB.ctsa: no visible global function definition for ‘lm’
Undefined global functions or variables:
  axis coef filled.contour legend lines lm par polygon rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "filled.contour", "legend", "lines",
             "par", "polygon")
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
Note: found 8 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘dae’ ‘dplyr’
  All declared Imports should be used.
Package in Depends field not imported from: ‘spc’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following files/directories:
  ‘tmplp.dat’
UCexactTest: no visible global function definition for ‘is’
UCexactTest: no visible global function definition for ‘new’
pvalue: no visible global function definition for ‘dnbinom’
pvalue: no visible global function definition for ‘pnbinom’
sup.mu: no visible global function definition for ‘predict’
Undefined global functions or variables:
  dnbinom is new pnbinom predict
Consider adding
  importFrom("methods", "is", "new")
  importFrom("stats", "dnbinom", "pnbinom", "predict")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in ‘eDMA-Ex.R’ failed
The error most likely occurred in:

> ### Name: BacktestDMA
> ### Title: Backtest measures for Dynamic Model Averaging and comparison
> ###   with Dynamic Model Selection
> ### Aliases: BacktestDMA
> 
> ### ** Examples
> 
> 
> library(eDMA)
> 
> ## load data
> data("USData")
> 
> ## do DMA, keep the first three predictors fixed and the intercept
> Fit <- DMA(GDPDEF ~ Lag(GDPDEF, 1) + Lag(GDPDEF, 2) + Lag(GDPDEF, 3) +
+             Lag(ROUTP, 1) + Lag(UNEMP, 1), data = USData, vDelta = c(0.9, 0.95, 0.99),
+             vKeep = c(1, 2, 3))

error: sort(): detected NaN
Error in funcEstimate_Eff_par(vY, mF, vDelta, dAlpha, vKeep, dBeta, bZellnerPrior,  : 
  sort(): detected NaN
Calls: DMA -> funcEstimate_Eff_par
Execution halted
geteegdata: no visible global function definition for ‘untar’
geteegdata: no visible global function definition for ‘read.table’
geteegdata: no visible global function definition for ‘write.csv’
geteegdata: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  read.table untar write.csv write.table
Consider adding
  importFrom("utils", "read.table", "untar", "write.csv", "write.table")
to your NAMESPACE file.
Running ‘test-all.R’ [23s/76s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(eeptools)
  Loading required package: ggplot2
  > 
  > test_check("eeptools")
  ── 1. Failure: moves_calc gets the correct results (@test-calculators.R#210)  ──
  `moves` not equal to `correct_result`.
  Component "sid": Modes: character, numeric
  Component "sid": Attributes: < target is NULL, current is list >
  Component "sid": target is character, current is factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 509 | SKIPPED: 0 | WARNINGS: 29 | FAILED: 1 ]
  1. Failure: moves_calc gets the correct results (@test-calculators.R#210) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘rmarkdown’
  All declared Imports should be used.
Malformed Title field: should not end in a period.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(effsize)
  > 
  > test_check("effsize")
  ── 1. Failure: double factor (@testCliff.R#101)  ───────────────────────────────
  resf$estimate not equal to -0.44.
  1/1 mismatches
  [1] -0.167 - -0.44 == 0.273
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 146 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: double factor (@testCliff.R#101) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following files/directories:
  ‘eval_test_LG_ROC.pdf’ ‘test.pdf’
Package suggested but not available for checking: ‘eggCountsExtra’
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
GNU make is a SystemRequirements.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc       5.3Mb
    extdata   5.3Mb
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘EHRtemporalVariability.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: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Joining, by = "diagcode1"
Warning: Column `diagcode1` joining factor and character vector, coercing into character vector
# Missing values: 0 cases ( 0%)
# External causes codes: 0 cases ( 0%)
# V codes not mapped: 74330 cases ( 22.82%)
# Total ICD9-CM codes mapped: 146262 cases ( 44.9%)
# Unique ICD9-CM codes mapped: 3020
# Total PheWAS codes: 757
# ICD9 codes not mapped: 105180 cases ( 32.29%)
Quitting from lines 317-322 (EHRtemporalVariability.Rmd) 
Error: processing vignette 'EHRtemporalVariability.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘EHRtemporalVariability.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘canda~ black.pdf’
eiginv: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
boot_pr_comp: no visible global function definition for ‘cov’
boot_pr_comp: no visible global function definition for ‘quantile’
boot_pr_comp: no visible global function definition for ‘segments’
boot_pr_comp: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline cov quantile segments
Consider adding
  importFrom("graphics", "abline", "segments")
  importFrom("stats", "cov", "quantile")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  ‘class’ ‘quantreg’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cluster.segment: no visible global function definition for ‘kmeans’
cluster.segment: no visible global function definition for ‘knn’
comp.anc.dist: no visible global function definition for ‘wilcox.test’
eila: no visible global function definition for ‘hasArg’
get.prob.score: no visible global function definition for ‘glm’
get.prob.score: no visible global function definition for ‘binomial’
get.prob.score: no visible binding for global variable ‘logit’
get.prob.score: no visible global function definition for ‘predict’
quantreg.est: no visible global function definition for ‘rnorm’
quantreg.est: no visible global function definition for ‘rq.fit.fnb’
Undefined global functions or variables:
  binomial glm hasArg kmeans knn logit predict rnorm rq.fit.fnb
  wilcox.test
Consider adding
  importFrom("methods", "hasArg")
  importFrom("stats", "binomial", "glm", "kmeans", "predict", "rnorm",
             "wilcox.test")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Namespaces in Imports field not imported from:
  ‘MASS’ ‘eco’
  All declared Imports should be used.
comPlot: no visible global function definition for ‘lines’
convertEiData: no visible global function definition for ‘model.frame’
plot.eiwild: no visible global function definition for ‘par’
plotResult: no visible global function definition for ‘grey’
plotResult: no visible global function definition for
  ‘colorRampPalette’
plotResult: no visible global function definition for ‘plot.new’
plotResult: no visible global function definition for ‘plot.window’
prioriPlot: no visible global function definition for ‘par’
prioriPlot : <anonymous> : <anonymous>: no visible global function
  definition for ‘rgamma’
prioriPlot : <anonymous>: no visible global function definition for
  ‘rbeta’
prioriPlot: no visible global function definition for ‘hist’
prioriPlot : <anonymous>: no visible global function definition for
  ‘rgamma’
prioriPlot : <anonymous> : <anonymous>: no visible global function
  definition for ‘rexp’
prioriPlot : <anonymous>: no visible global function definition for
  ‘rexp’
runMBayes: no visible global function definition for ‘runif’
runMBayes: no visible global function definition for ‘rgamma’
runMBayes: no visible global function definition for ‘rexp’
str0: no visible global function definition for ‘str’
tuneVars: no visible global function definition for ‘sd’
Undefined global functions or variables:
  colorRampPalette grey hist lines model.frame par plot.new plot.window
  rbeta rexp rgamma runif sd str
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey")
  importFrom("graphics", "hist", "lines", "par", "plot.new",
             "plot.window")
  importFrom("stats", "model.frame", "rbeta", "rexp", "rgamma", "runif",
             "sd")
  importFrom("utils", "str")
to your NAMESPACE file.
Package suggested but not available for checking: ‘lightgbm’
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘tidyr’
  All declared Imports should be used.
Found the following files/directories:
  ‘MM.csv’ ‘Simul.csv’ ‘catalytic.csv’ ‘combined.csv’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    examples   4.2Mb
Package in Depends field not imported from: ‘elec’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
BaB: no visible binding for global variable ‘calc.pairwise.e_p’
BaB: no visible global function definition for ‘weight.function’
BaB: no visible global function definition for ‘compute.stark.t’
LKPBound: no visible binding for global variable ‘calc.pairwise.e_p’
LKPBound: no visible global function definition for ‘weight.function’
LKPBound: no visible global function definition for ‘compute.stark.t’
eqValBound: no visible binding for global variable ‘calc.pairwise.e_p’
eqValBound: no visible global function definition for ‘weight.function’
eqValBound: no visible global function definition for ‘compute.stark.t’
getEbsMargin: no visible global function definition for ‘is.elec.data’
getEbsMargin: no visible global function definition for
  ‘maximumMarginBound’
makeStratObj: no visible global function definition for ‘is.elec.data’
makeStratObj: no visible global function definition for
  ‘maximumMarginBound’
strat.elec.data: no visible global function definition for ‘elec.data’
takeOutZeroMMB: no visible global function definition for
  ‘maximumMarginBound’
withReplaceBound: no visible binding for global variable
  ‘calc.pairwise.e_p’
withReplaceBound: no visible global function definition for
  ‘weight.function’
withReplaceBound: no visible global function definition for
  ‘compute.stark.t’
Undefined global functions or variables:
  calc.pairwise.e_p compute.stark.t elec.data is.elec.data
  maximumMarginBound weight.function
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Malformed Description field: should contain one or more complete sentences.
Package in Depends field not imported from: ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Likelihood: no visible global function definition for
  ‘makePSOCKcluster’
Likelihood: no visible global function definition for ‘clusterExport’
Likelihood: no visible global function definition for ‘makeForkCluster’
Likelihood.first.run: no visible global function definition for
  ‘clusterApply’
Likelihood.next.runs: no visible global function definition for
  ‘clusterApply’
es.stopCluster: no visible global function definition for ‘stopCluster’
plot.es.pedigree: no visible global function definition for ‘hasArg’
Undefined global functions or variables:
  clusterApply clusterExport hasArg makeForkCluster makePSOCKcluster
  stopCluster
Consider adding
  importFrom("methods", "hasArg")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package suggested but not available for checking: ‘lumi’
Namespaces in Imports field not imported from:
  ‘AER’ ‘pROC’ ‘pander’
  All declared Imports should be used.
Running examples in ‘emax.glm-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot.em.glm.summary
> ### Title: Error bar plot of coefficients and errors to inspect class
> ###   overlap.
> ### Aliases: plot.em.glm.summary
> 
> ### ** Examples
> 
> x <- model.matrix(~ factor(wool) + factor(tension), warpbreaks)
> y <- warpbreaks$breaks
> 
> m <- em.glm(x = x, y = y, K = 2, b.init = "random")
> m.sum <- summary(m)
> 
> plot(m.sum)
Warning in xy.coords(x, y, xlabel, ylabel, log) :
  NAs introduced by coercion
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in plot.window(...) : need finite 'ylim' values
Calls: plot ... plot2 -> plot -> plot.default -> localWindow -> plot.window
Execution halted
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘Rtsne’ ‘uwot’
  All declared Imports should be used.
Note: found 5 marked UTF-8 strings
Malformed Description field: should contain one or more complete sentences.
Packages in Depends field not imported from:
  ‘MASS’ ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespaces in Imports field not imported from:
  ‘graphics’ ‘maptools’ ‘rgeos’
  All declared Imports should be used.
Note: found 24 marked Latin-1 strings
License components which are templates and need '+ file LICENSE':
  MIT
Found the following files/directories:
  ‘EmiStatR_output’ ‘Temporal aggregation of precipitation P1 (res =
  120 min).pdf’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    xsd   4.1Mb
'library' or 'require' calls to packages already attached by Depends:
  ‘clusterSim’ ‘earth’
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘clusterSim’ ‘earth’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
distance: no visible global function definition for
  ‘data.Normalization’
emmatn: no visible global function definition for ‘runif’
estimateModel: no visible global function definition for ‘as.formula’
estimateModel: no visible global function definition for ‘earth’
estimateModel: no visible global function definition for ‘plotmo’
estimateModel: no visible global function definition for ‘predict’
mutation: no visible global function definition for ‘runif’
plot.emma: no visible global function definition for ‘colorRampPalette’
plot.emma: no visible global function definition for ‘par’
plot.emma: no visible global function definition for ‘persp’
plot.emma: no visible global function definition for ‘points’
plot.emma: no visible global function definition for ‘trans3d’
Undefined global functions or variables:
  as.formula colorRampPalette data.Normalization earth par persp plotmo
  points predict runif trans3d
Consider adding
  importFrom("grDevices", "colorRampPalette", "trans3d")
  importFrom("graphics", "par", "persp", "points")
  importFrom("stats", "as.formula", "predict", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘reshape’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
MFFetch: no visible global function definition for ‘melt’
Undefined global functions or variables:
  melt
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.6Mb
empiricalFDR: no visible global function definition for ‘axis’
empiricalFDR: no visible global function definition for ‘loess’
empiricalFDR: no visible global function definition for ‘predict’
empiricalFDR: no visible global function definition for ‘lines’
empiricalFDR: no visible global function definition for ‘abline’
fdrBiCurve: no visible global function definition for ‘axis’
fdrBiCurve: no visible global function definition for ‘lines’
fdrBiCurve: no visible global function definition for ‘abline’
fdrBiCurve: no visible global function definition for ‘legend’
simulateCounts: no visible global function definition for
  ‘txtProgressBar’
simulateCounts: no visible global function definition for
  ‘setTxtProgressBar’
simulateCounts: no visible global function definition for ‘rnorm’
simulateCounts: no visible global function definition for ‘hist’
simulateCounts: no visible global function definition for ‘colData’
Undefined global functions or variables:
  abline axis colData hist legend lines loess predict rnorm
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "abline", "axis", "hist", "legend", "lines")
  importFrom("stats", "loess", "predict", "rnorm")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Note: found 23639 marked Latin-1 strings
Running examples in ‘ems-Ex.R’ failed
The error most likely occurred in:

> ### Name: funnel
> ### Title: Funnel plot for benchmarking health units
> ### Aliases: funnel print.funnel plot.funnel rateFunnel changeRateFunnel
> ###   propFunnel changePropFunnel
> 
> ### ** Examples
> 
> # Loading data
> data(icu)
> 
> # Some edition
> icu$Saps3DeathProbabilityStandardEquation <- icu$Saps3DeathProbabilityStandardEquation / 100
> icu <- icu[-which(icu$Unit == "F"),]
> icu$myunits <- ifelse(icu$Unit == "A",1,0) #my units
> icu <- droplevels(icu)
> 
> # Getting the cross-sectional arguments to use in funnel
> x <- SMR.table(data = icu, group.var = "Unit",
+               obs.var = "UnitDischargeName", pred.var = "Saps3DeathProbabilityStandardEquation")
> myunit_names <- unique(icu$Unit[which(icu$myunits == 1)])
> x$myunits <- ifelse(x$Levels %in% myunit_names, 1,0)
> 
> # Analysis of proportions
> f1 <- funnel(unit = x$Levels[-1], o = x[-1,]$Observed, theta = x$Observed[1] / x$N[1],
+             n = x[-1,]$N, method = "exact", myunits = x$myunits[-1], option = "prop", plot = FALSE)
Error in propFunnel(unit = unit, o = o, n = n, theta = theta, p = p, method = method,  : 
  Unit must be a factor.
Calls: funnel -> propFunnel
Execution halted
ExactMultinomialTest: no visible global function definition for
  ‘dmultinom’
ExactMultinomialTest : <anonymous>: no visible global function
  definition for ‘dmultinom’
ExactMultinomialTestChisquare : <anonymous>: no visible global function
  definition for ‘dmultinom’
MonteCarloMultinomialTest: no visible global function definition for
  ‘rmultinom’
MonteCarloMultinomialTest: no visible global function definition for
  ‘flush.console’
MonteCarloMultinomialTestChisquare: no visible global function
  definition for ‘rmultinom’
MonteCarloMultinomialTestChisquare: no visible global function
  definition for ‘flush.console’
multinomial.test: no visible global function definition for
  ‘flush.console’
plotMultinom: no visible global function definition for ‘barplot’
plotMultinom: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  barplot dmultinom flush.console mtext rmultinom
Consider adding
  importFrom("graphics", "barplot", "mtext")
  importFrom("stats", "dmultinom", "rmultinom")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Found the following files/directories:
  ‘file.path(temp_dir, gp2.csv)’
Running examples in ‘eNetXplorer-Ex.R’ failed
The error most likely occurred in:

> ### Name: plotContingency
> ### Title: generates plot of response vs out-of-bag predictions across
> ###   classes
> ### Aliases: plotContingency
> 
> ### ** Examples
> 
> ## Don't show: 
> set.seed(123)
> fit = eNetXplorer(x=matrix(rnorm(120),ncol=4),y=c(rep(0,15),rep(1,15)),
+ family="binomial",n_run=5, n_perm_null=4,alpha=c(0.5,1))
Error during execution of alpha =  0.5 
> plot(x=fit,plot.type="contingency")
Error in if (x$family %in% c("binomial", "multinomial")) { : 
  argument is of length zero
Calls: plot -> plot.eNetXplorer
Execution halted
'library' or 'require' call to ‘RColorBrewer’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘Rcmdr’ ‘gWidgets’ ‘gWidgetstcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Hmisc’ ‘RColorBrewer’ ‘vcd’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following files/directories:
  ‘somefile’
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘bitops’ ‘rjson’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘SPECIES’ ‘ade4’
  All declared Imports should be used.
diffcv: no visible global function definition for ‘sd’
diffcvall: no visible global function definition for ‘sd’
diffcvall: no visible global function definition for ‘fligner.test’
diffcvall: no visible global function definition for ‘p.adjust’
diffcvpFK: no visible global function definition for ‘fligner.test’
diffcvpFK: no visible global function definition for ‘p.adjust’
diffexp: no visible global function definition for ‘var’
diffexp: no visible global function definition for ‘t.test’
diffexp: no visible global function definition for ‘p.adjust’
diffexp2: no visible global function definition for ‘var’
diffexp2: no visible global function definition for ‘t.test’
diffexp2: no visible global function definition for ‘p.adjust’
diffnsepperm: no visible global function definition for ‘p.adjust’
diffseall: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  fligner.test p.adjust sd t.test var
Consider adding
  importFrom("stats", "fligner.test", "p.adjust", "sd", "t.test", "var")
to your NAMESPACE file.
Found the following files/directories:
  ‘Environmental variables.csv’ ‘Inf.txt’ ‘List of species.csv’ ‘Mean
  overlap among taxa.csv’ ‘Overlap among taxa.csv’ ‘Pointsize.dat’
  ‘Polar coordinates.csv’
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    doc    3.4Mb
    help   3.4Mb
'library' or 'require' call to ‘plotrix’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘Hmisc’ ‘survival’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘plotrix’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘a.alpha.ade’ ‘a.coladd.ade’ ‘a.getcol.ade’ ‘a.glc’
Package suggested but not available for checking: ‘epanet2toolkit’
Found the following files/directories:
  ‘Net1-fromR.inp’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
Namespaces in Imports field not imported from:
  ‘readr’ ‘tidyverse’
  All declared Imports should be used.
Note: found 122 marked UTF-8 strings
Namespace in Imports field not imported from: ‘colorspace’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘epicontacts.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 150-151 (epicontacts.Rmd) 
Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘epicontacts.Rmd’

--- re-building ‘epicontacts_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.
--- finished re-building ‘epicontacts_class.Rmd’

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

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

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

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

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘htmlwidgets’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘epiflows-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.
--- finished re-building ‘epiflows-class.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 117-120 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘epidict’
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘graphics’ ‘knitr’ ‘rmarkdown’ ‘utils’
  All declared Imports should be used.
Found the following files/directories:
  ‘AnnualEpidemiologicalReport_SALM2016.docx’ ‘Empty_AER_template.docx’
Found the following files/directories:
  ‘episcan_1geno_cc.txt’ ‘episcan_1geno_quant.txt’
  ‘episcan_2geno_cc.txt’ ‘episcan_2geno_quant.txt’
Namespaces in Imports field not imported from:
  ‘DT’ ‘ggplot2’ ‘knitr’ ‘pander’
  All declared Imports should be used.
Running examples in ‘EpiSignalDetection-Ex.R’ failed
The error most likely occurred in:

> ### Name: runEpiSDReport
> ### Title: Run the EpiSignalDetection report (HTML markdown)
> ### Aliases: runEpiSDReport
> 
> ### ** Examples
> 
> #---> OR
> 
> #-- First setting the parameters to run the report for
> input <- list(
+ disease = "Salmonellosis",
+ country = "Portugal",
+ indicator = "Reported cases",
+ stratification = "Confirmed cases",
+ unit = "Month",
+ daterange = c("2011-01-01", "2016-12-31"),
+ algo = "FarringtonFlexible",
+ testingperiod = 6
+ )
> 
> #-- Second running the report based on the EpiSignalDetection::SignalData dataset
> #-- and store it in a temporary folder
> runEpiSDReport(input = input)
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
plot.episplineDensity: no visible global function definition for
  ‘points’
postproc: no visible global function definition for ‘points’
preprocess.data: no visible global function definition for ‘sd’
Undefined global functions or variables:
  points sd
Consider adding
  importFrom("graphics", "points")
  importFrom("stats", "sd")
to your NAMESPACE file.
Documented arguments not in \usage in documentation object 'oddsratio':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
FCIplot: no visible global function definition for ‘na.omit’
FCIplot: no visible global function definition for ‘tail’
FCIplot: no visible global function definition for ‘grid’
FCIplot: no visible global function definition for ‘polygon’
FCIplot: no visible global function definition for ‘rgb’
linpred: no visible global function definition for ‘lm’
mplott: no visible global function definition for ‘par’
mplott: no visible global function definition for ‘na.omit’
mplott: no visible global function definition for ‘lines’
mplott: no visible global function definition for ‘legend’
mplott: no visible global function definition for ‘grid’
plott: no visible global function definition for ‘lines’
plott: no visible global function definition for ‘par’
plott: no visible global function definition for ‘grid’
tsideplot: no visible global function definition for ‘par’
tsideplot: no visible global function definition for ‘axis’
tsideplot: no visible global function definition for ‘grid’
Undefined global functions or variables:
  axis grid legend lines lm na.omit par polygon rgb tail
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "grid", "legend", "lines", "par",
             "polygon")
  importFrom("stats", "lm", "na.omit")
  importFrom("utils", "tail")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘testthat’ ‘tidyr’
  All declared Imports should be used.
eqs2lavaan: no visible global function definition for ‘ignore.case’
eqs2lavaan: no visible global function definition for ‘str_join’
eqs2lavaan: no visible binding for global variable ‘r’
eqsCorr: no visible global function definition for ‘cov2cor’
plotCov: no visible global function definition for ‘cov2cor’
plotCov: no visible global function definition for ‘par’
plotCov: no visible global function definition for ‘image’
plotCov: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis cov2cor ignore.case image par r str_join
Consider adding
  importFrom("graphics", "axis", "image", "par")
  importFrom("stats", "cov2cor")
to your NAMESPACE file.
'library' or 'require' call to ‘qtl’ which was already attached by Depends.
  Please remove these calls from your code.
Unexported objects imported by ':::' calls:
  ‘qtl:::c.scanone’ ‘qtl:::plot.scanone’
  See the note in ?`:::` about the use of this operator.
Found the following files/directories:
  ‘CATane_4_27_.png’ ‘CATavz_4_37_.png’ ‘CATbaa_4_13_.png’
  ‘CATbko_4_36_.png’ ‘CATbuu_1_45_.png’ ‘CATbuu_4_45_.png’
  ‘CATbuu_5_45_.png’ ‘CATbzp_4_50_.png’ ‘CATbzx_4_29_.png’
  ‘CATdbn_1_18_.png’ ‘CATdbn_3_18_.png’ ‘CATdmq_4_49_.png’
  ‘CATepg_4_44_.png’ ‘CATfgb_4_7_.png’ ‘CATfgb_5_7_.png’
  ‘CATfnu_4_21_.png’ ‘CATfnu_5_21_.png’ ‘CATham_4_14_.png’
  ‘CATham_5_14_.png’ ‘CATipy_4_19_.png’ ‘CATjoj_2_22_.png’
  ‘CATjpz_4_35_.png’ ‘CATjxh_1_31_.png’ ‘CATlbg_4_40_.png’
  ‘CATlkr_4_32_.png’ ‘CATlzh_4_43_.png’ ‘CATntj_4_24_.png’
  ‘CAToti_5_28_.png’ ‘CATppt_4_4_.png’ ‘CATppt_5_4_.png’
  ‘CATpsl_4_23_.png’ ‘CATpyn_4_20_.png’ ‘CATqoq_4_8_.png’
  ‘CATrck_4_26_.png’ ‘CATrjo_4_30_.png’ ‘CATsgu_4_9_.png’
  ‘CATsgu_5_9_.png’ ‘CATtez_4_34_.png’ ‘CATudg_4_16_.png’
  ‘CATuhl_4_39_.png’ ‘CATuhl_5_39_.png’ ‘CATvbb_4_41_.png’
  ‘CATwgo_4_17_.png’ ‘CATwgo_5_17_.png’ ‘CATwrn_4_46_.png’
  ‘CATwwh_4_10_.png’ ‘CATxmc_2_48_.png’ ‘CATxni_5_6_.png’ ‘ID_5_1_.png’
  ‘ae_dotplot_traitxqtl.png’ ‘ae_siplot_traitxqtl.png’
  ‘histogram_controled_etrait.png’ ‘histogram_qtl.png’
  ‘lod_dotplot_traitxqtl.png’ ‘lod_siplot_traitxqtl.png’
The following files contain a license that requires
distribution of original sources:
  ‘upgreek.sty’
Please ensure that you have complied with it.
Namespaces in Imports field not imported from:
  ‘cubature’ ‘rootSolve’
  All declared Imports should be used.
Found the following files/directories:
  ‘aeq3.out’ ‘ste3a.out’
Found the following files/directories:
  ‘Net1’ ‘Net2’
Package suggested but not available for checking: ‘mzR’
Namespace in Imports field not imported from: ‘signal’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘plyr’ ‘sp’
  All declared Imports should be used.
ESA: no visible binding for global variable ‘var’
plot.esabcv: no visible global function definition for ‘points’
plot.esabcv: no visible global function definition for ‘axis’
plot.esabcv: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis points title var
Consider adding
  importFrom("graphics", "axis", "points", "title")
  importFrom("stats", "var")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘colorRamps’ ‘colourpicker’ ‘dichromat’ ‘leaflet’
  ‘lwgeom’ ‘raster’ ‘shinycssloaders’ ‘shinydashboard’ ‘shinyjs’ ‘tmap’
  ‘viridis’ ‘zip’
  All declared Imports should be used.
ESEA.Main: no visible global function definition for ‘rnorm’
ESEA.Main: no visible global function definition for ‘sd’
ESEA.Main: no visible global function definition for ‘p.adjust’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘lines’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘colors’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘points’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘legend’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘text’
PlotPathwayGraph: no visible global function definition for ‘par’
PlotRunEnrichment: no visible global function definition for ‘lines’
PlotRunEnrichment: no visible global function definition for ‘colors’
PlotRunEnrichment: no visible global function definition for ‘text’
SavePathway2File: no visible global function definition for ‘is’
calEdgeCorScore: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  colors is legend lines na.omit p.adjust par points rnorm sd text
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "legend", "lines", "par", "points", "text")
  importFrom("methods", "is")
  importFrom("stats", "na.omit", "p.adjust", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
rAllRisksFactors: no visible global function definition for ‘new’
rAssetDistribution: no visible global function definition for ‘new’
rDefaultSpread: no visible global function definition for ‘new’
rLiquiditySpread: no visible global function definition for ‘new’
rRealEstate: no visible global function definition for ‘new’
rShortRate: no visible global function definition for ‘new’
rStock: no visible global function definition for ‘new’
EuroCall_Stock_PriceDistribution,Scenarios: no visible global function
  definition for ‘pnorm’
EuroCall_ZC_PriceDistribution,Scenarios: no visible global function
  definition for ‘pnorm’
EuroPut_Stock_PriceDistribution,Scenarios: no visible global function
  definition for ‘pnorm’
EuroPut_ZC_PriceDistribution,Scenarios: no visible global function
  definition for ‘pnorm’
MartingaleTest,Scenarios: no visible global function definition for
  ‘lines’
MartingaleTest,Scenarios: no visible global function definition for
  ‘title’
customPathsGeneration,Scenarios: no visible global function definition
  for ‘rnorm’
Undefined global functions or variables:
  lines new pnorm rnorm title
Consider adding
  importFrom("graphics", "lines", "title")
  importFrom("methods", "new")
  importFrom("stats", "pnorm", "rnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Malformed Title field: should not end in a period.
Running examples in ‘ESKNN-Ex.R’ failed
The error most likely occurred in:

> ### Name: Predict.esknnClass
> ### Title: Class predictions from ensemble of subset of k-nearest
> ###   neighbours
> ### Aliases: Predict.esknnClass
> ### Keywords: packages
> 
> ### ** Examples
> 
> # Load the data
> 
>   data(hepatitis)
>   data <- hepatitis
> 
> # Spliting the data into testing and training parts.
> 
>   Class <- data[,names(data)=="Class"]
>   data$Class<-as.factor(as.numeric(Class)-1)
>   train <- data[sample(1:nrow(data),0.7*nrow(data)),]
>   test <- data[-(sample(1:nrow(data),0.7*nrow(data))),]
>   ytrain<-train[,names(train)=="Class"]
>   xtrain<-train[,names(train)!="Class"]
>   xtest<-test[,names(test)!="Class"]
>   ytest <- test[,names(test)=="Class"]
>   
> # Trian esknnClass using training data
> 
> model<-esknnClass(xtrain, ytrain,k=NULL)
Error in order(fBS, decreasing = FALSE) : 
  unimplemented type 'list' in 'orderVector1'
Calls: esknnClass -> order
Execution halted
Malformed Description field: should contain one or more complete sentences.
cv.ES: no visible binding for global variable ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
Documented arguments not in \usage in documentation object 'na.omit_detailed.data.frame':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running ‘sleep.R’
  Comparing ‘sleep.Rout’ to ‘sleep.Rout.save’ ... OK
  Running ‘testthat.R’ [69s/81s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(estimatr)
  > 
  > test_check("estimatr")
  ── 1. Error: FE matches lm_robust with one block (@test-lm-robust-fes.R#528)  ──
  contrasts can be applied only to factors with 2 or more levels
  Backtrace:
   1. estimatr::lm_robust(...)
   2. estimatr::lm_robust_fit(...)
   3. estimatr:::prep_data(...)
   5. stats::model.matrix.default(~0 + ., data = fe_dat)
   6. stats::`contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]])
  
  ── 2. Failure: Handle perfect fits appropriately (@test-lm-robust-fes.R#682)  ──
  tidy(rfo)[rfo$term == "X", ] not equivalent to tidy(ro)[ro$term == "X", ].
  Component "std.error": 'is.NA' value mismatch: 1 in current 0 in target
  Component "statistic": 'is.NA' value mismatch: 1 in current 0 in target
  Component "p.value": 'is.NA' value mismatch: 1 in current 0 in target
  Component "conf.low": 'is.NA' value mismatch: 1 in current 0 in target
  Component "conf.high": 'is.NA' value mismatch: 1 in current 0 in target
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1308 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: FE matches lm_robust with one block (@test-lm-robust-fes.R#528) 
  2. Failure: Handle perfect fits appropriately (@test-lm-robust-fes.R#682) 
  
  Error: testthat unit tests failed
  Execution halted
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘estoutstorage’
descsto: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.Transition: no visible global function definition for ‘rnorm’
.Transition.DC: no visible global function definition for ‘runif’
Simu.Cond.HR: no visible global function definition for ‘rpois’
Simu.Cond.HR: no visible global function definition for ‘runif’
Simu.Cond.HR: no visible global function definition for ‘hist’
Simu.Cond.HR: no visible global function definition for ‘var’
Simu.HR: no visible global function definition for ‘rpois’
Simu.HR: no visible global function definition for ‘runif’
Simu.HR: no visible global function definition for ‘hist’
Simu.HR: no visible global function definition for ‘var’
Undefined global functions or variables:
  hist rnorm rpois runif var
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "rnorm", "rpois", "runif", "var")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘Hmisc’ ‘xtable’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
corr_p_cell: no visible global function definition for ‘cov.wt’
iqr_cell: no visible global function definition for ‘quantile’
iqr_cell: no visible global function definition for ‘wtd.quantile’
mean_sd_cell: no visible global function definition for ‘wtd.mean’
mean_sd_cell: no visible global function definition for ‘wtd.var’
mode_cell: no visible global function definition for ‘wtd.table’
quantile_cell: no visible global function definition for ‘wtd.quantile’
quantile_cell: no visible global function definition for ‘quantile’
stat_cell: no visible global function definition for ‘quantile’
stat_cell: no visible global function definition for ‘wtd.quantile’
stat_cell: no visible global function definition for ‘wtd.mean’
stat_cell: no visible global function definition for ‘wtd.var’
stat_cell: no visible global function definition for ‘mad’
stat_cell: no visible global function definition for ‘wtd.table’
Undefined global functions or variables:
  cov.wt mad quantile wtd.mean wtd.quantile wtd.table wtd.var
Consider adding
  importFrom("stats", "cov.wt", "mad", "quantile")
to your NAMESPACE file.
etc.diff: no visible global function definition for ‘model.frame’
etc.diff: no visible binding for global variable ‘sd’
etc.diff: no visible global function definition for ‘qt’
etc.diff: no visible global function definition for ‘pt’
etc.diff: no visible global function definition for ‘wilcox.test’
etc.rat: no visible global function definition for ‘model.frame’
etc.rat: no visible binding for global variable ‘sd’
etc.rat: no visible global function definition for ‘qt’
etc.rat: no visible global function definition for ‘pt’
Undefined global functions or variables:
  model.frame pt qt sd wilcox.test
Consider adding
  importFrom("stats", "model.frame", "pt", "qt", "sd", "wilcox.test")
to your NAMESPACE file.
Running examples in ‘etm-Ex.R’ failed
The error most likely occurred in:

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

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

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

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

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

Error: Vignette re-building failed.
Execution halted
Undocumented S4 methods:
  generic 'plot' and siglist 'trialDesign_binom_one'
  generic 'plot' and siglist 'trialDesign_binom_two'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
Note: found 1182 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘devtools’ ‘msm’
  All declared Imports should be used.
Found the following files/directories:
  ‘ET_Abtew.csv’ ‘ET_BlaneyCriddle.csv’ ‘ET_BrutsaertStrickler.csv’
  ‘ET_ChapmanAustralian.csv’ ‘ET_GrangerGray.csv’ ‘ET_Hamon.csv’
  ‘ET_HargreavesSamani.csv’ ‘ET_JensenHaise.csv’ ‘ET_Linacre.csv’
  ‘ET_Makkink.csv’ ‘ET_MattShuttleworth.csv’ ‘ET_McGuinnessBordne.csv’
  ‘ET_MortonCRAE.csv’ ‘ET_MortonCRWE.csv’ ‘ET_PenPan.csv’
  ‘ET_Penman.csv’ ‘ET_PenmanMonteith.csv’ ‘ET_PriestleyTaylor.csv’
  ‘ET_Romanenko.csv’ ‘ET_SzilagyiJozsa.csv’ ‘ET_Turc.csv’
Malformed Description field: should contain one or more complete sentences.
powerSet : <anonymous>: no visible global function definition for
  ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
mposterior: no visible global function definition for ‘optim’
rl.pred: no visible global function definition for ‘matplot’
rl.pst: no visible binding for global variable ‘quantile’
rl.pst: no visible global function definition for ‘matplot’
Undefined global functions or variables:
  matplot optim quantile
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "optim", "quantile")
to your NAMESPACE file.
Found the following hidden files and directories:
  .gitignore
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
make_dyads : ff: no visible global function definition for ‘aggregate’
make_scale: no visible global function definition for ‘read.csv’
plot_dyad: no visible global function definition for ‘is’
read_eventdata : read_ed_file: no visible global function definition
  for ‘read.csv’
Undefined global functions or variables:
  aggregate is read.csv
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "aggregate")
  importFrom("utils", "read.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
Namespaces in Imports field not imported from:
  ‘curl’ ‘openxlsx’ ‘stringr’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.1Mb
Found the following files/directories:
  ‘sample .nwk’
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
evolvabilityBetaMCMC : <anonymous>: no visible binding for global
  variable ‘median’
evolvabilityBetaMCMC: no visible binding for global variable ‘median’
evolvabilityBetaMCMC2: no visible binding for global variable ‘median’
evolvabilityMeans: no visible global function definition for ‘var’
evolvabilityMeansMCMC : <anonymous>: no visible global function
  definition for ‘var’
evolvabilityMeansMCMC: no visible binding for global variable ‘median’
randomBeta: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  median rnorm var
Consider adding
  importFrom("stats", "median", "rnorm", "var")
to your NAMESPACE file.
Package in Depends field not imported from: ‘evd’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
DPOT: no visible global function definition for ‘optim’
mop.rho: no visible global function definition for ‘median’
Undefined global functions or variables:
  median optim
Consider adding
  importFrom("stats", "median", "optim")
to your NAMESPACE file.
Found the following files/directories:
  ‘combination_cohort_2.bug’
EW : PhiP : Phi: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
BinomialCIone: no visible global function definition for ‘na.omit’
PairedCIone: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
build.mcx.obj: no visible global function definition for ‘glm’
build.mcx.obj: no visible binding for global variable ‘poisson’
build.mcx.obj: no visible global function definition for ‘fitted’
cab: no visible global function definition for ‘rbinom’
cab: no visible global function definition for ‘runif’
mcexact: no visible global function definition for ‘update’
rounded.tprob: no visible global function definition for ‘pt’
simtable.cab: no visible global function definition for ‘rbinom’
simtable.cab: no visible global function definition for ‘runif’
Undefined global functions or variables:
  fitted glm poisson pt rbinom runif update
Consider adding
  importFrom("stats", "fitted", "glm", "poisson", "pt", "rbinom",
             "runif", "update")
to your NAMESPACE file.
plot.pgrid: no visible global function definition for ‘image’
statistic.cv: no visible global function definition for ‘quantile’
statistic.sim: no visible global function definition for ‘contourLines’
Undefined global functions or variables:
  contourLines image quantile
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "image")
  importFrom("stats", "quantile")
to your NAMESPACE file.
Package suggested but not available for checking: ‘INLA’
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    exiftool  14.5Mb
Namespace in Imports field not imported from: ‘polynom’
  All declared Imports should be used.
print.cdf : numform: warning in formatC(x, dig = digits): partial
  argument match of 'dig' to 'digits'
print.cdf: warning in get("x", env = environment(x)): partial argument
  match of 'env' to 'envir'
print.cdf: warning in get("y", env = environment(x)): partial argument
  match of 'env' to 'envir'
print.ogive : numform: warning in formatC(x, dig = digits): partial
  argument match of 'dig' to 'digits'
print.ogive: warning in get("x", env = environment(x)): partial
  argument match of 'env' to 'envir'
print.ogive: warning in get("y", env = environment(x)): partial
  argument match of 'env' to 'envir'
quantile.expert: warning in formatC(paste(100 * probs, "%", sep = ""),
  format = "fg", wid = 1, digits = dig): partial argument match of
  'wid' to 'width'
MS: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘RColorBrewer’ ‘Rcpp’ ‘e1071’ ‘foreach’ ‘gam’ ‘ggplot2’
  ‘glmnet’ ‘nnet’ ‘polspline’ ‘repmis’ ‘splines’ ‘xgboost’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_genExPrior.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 58-59 (using_genExPrior.Rmd) 
Error: processing vignette 'using_genExPrior.Rmd' failed with diagnostics:
Failed to create the shared library.
--- failed re-building ‘using_genExPrior.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
index.citations: no visible global function definition for
  ‘txtProgressBar’
read.exsic: no visible global function definition for ‘read.csv’
update.pb: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  read.csv setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "read.csv", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Package in Depends field not imported from: ‘rmeta’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
extfunnel: no visible global function definition for ‘qnorm’
extfunnel: no visible global function definition for ‘meta.summaries’
extfunnel: no visible global function definition for ‘flush.console’
extfunnel: no visible global function definition for ‘qt’
extfunnel: no visible global function definition for ‘dev.new’
extfunnel: no visible global function definition for ‘par’
extfunnel: no visible global function definition for ‘polygon’
extfunnel: no visible global function definition for ‘segments’
extfunnel: no visible global function definition for ‘abline’
extfunnel: no visible global function definition for ‘axis’
extfunnel: no visible global function definition for ‘box’
Undefined global functions or variables:
  abline axis box dev.new flush.console meta.summaries par polygon
  qnorm qt segments
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axis", "box", "par", "polygon",
             "segments")
  importFrom("stats", "qnorm", "qt")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
bars: no visible global function definition for ‘segments’
cv.binomial: no visible binding for global variable ‘var’
cv.binomial: no visible global function definition for ‘abline’
cv.normal: no visible binding for global variable ‘var’
cv.normal: no visible global function definition for ‘abline’
cv.poisson: no visible binding for global variable ‘var’
cv.poisson: no visible global function definition for ‘abline’
plot.extlasso: no visible global function definition for ‘matplot’
plot.extlasso: no visible global function definition for ‘axis’
Undefined global functions or variables:
  abline axis matplot segments var
Consider adding
  importFrom("graphics", "abline", "axis", "matplot", "segments")
  importFrom("stats", "var")
to your NAMESPACE file.
exbio: no visible global function definition for ‘as.formula’
exbio: no visible global function definition for ‘glm’
exbio: no visible binding for global variable ‘gaussian’
exbio: no visible global function definition for ‘Gamma’
exbio: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  Gamma as.formula gaussian glm pchisq
Consider adding
  importFrom("stats", "Gamma", "as.formula", "gaussian", "glm", "pchisq")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
font_install: no visible global function definition for
  ‘installed.packages’
font_install: no visible global function definition for
  ‘install.packages’
fonttable_add: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  install.packages installed.packages write.csv
Consider adding
  importFrom("utils", "install.packages", "installed.packages",
             "write.csv")
to your NAMESPACE file.
toJavaMatrix2D: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  ‘temp.Rdata’
bootstrapCMLE: no visible global function definition for ‘qweibull’
bootstrapCMLE: no visible binding for global variable ‘sd’
bootstrapCMLE: no visible global function definition for ‘quantile’
bootstrapCenWbMix: no visible binding for global variable ‘sd’
bootstrapCenWbMix: no visible global function definition for ‘quantile’
cenWeibullMLE: no visible global function definition for ‘sd’
expmx.p2.censor: no visible global function definition for ‘dweibull’
expmx.p2.censor: no visible global function definition for ‘pweibull’
genWbMixIni: no visible global function definition for ‘runif’
log.llh.p2.censor: no visible global function definition for ‘dweibull’
log.llh.p2.censor: no visible global function definition for ‘pweibull’
quanWbMix : t.fun: no visible global function definition for ‘pweibull’
quanWbMix: no visible global function definition for ‘uniroot’
quanWbMix.int : t.fun: no visible global function definition for
  ‘pweibull’
quanWbMix.int: no visible global function definition for ‘uniroot’
simWbMix: no visible global function definition for ‘rbinom’
simWbMix: no visible global function definition for ‘rweibull’
Undefined global functions or variables:
  dweibull pweibull quantile qweibull rbinom runif rweibull sd uniroot
Consider adding
  importFrom("stats", "dweibull", "pweibull", "quantile", "qweibull",
             "rbinom", "runif", "rweibull", "sd", "uniroot")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
BugReports field is not a suitable URL but contains an email address:
   use the Contact field instead
createFormula: no visible global function definition for ‘tail’
createFormula: no visible global function definition for ‘head’
createFormula: no visible global function definition for ‘as.formula’
ezsim: no visible global function definition for ‘runif’
plot.ezsim: no visible global function definition for ‘quantile’
plot.ezsim: no visible global function definition for ‘head’
plot.ezsim: no visible global function definition for ‘tail’
plot.ezsim: no visible binding for global variable ‘dnorm’
plot.ezsim: no visible binding for global variable ‘pdf’
plot.ezsim: no visible global function definition for ‘dev.off’
plot.ezsim : <anonymous>: no visible global function definition for
  ‘dev.new’
plot.summary.ezsim: no visible global function definition for ‘head’
plot.summary.ezsim: no visible global function definition for ‘tail’
plot.summary.ezsim: no visible binding for global variable ‘pdf’
plot.summary.ezsim: no visible global function definition for ‘dev.off’
plot.summary.ezsim : <anonymous>: no visible global function definition
  for ‘dev.new’
Undefined global functions or variables:
  as.formula dev.new dev.off dnorm head pdf quantile runif tail
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("stats", "as.formula", "dnorm", "quantile", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Found the following files/directories:
  ‘facilitationmovie.gif’ ‘ts.gif’
gibbs2: no visible global function definition for ‘rnorm’
gibbs_sampling: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Found the following files/directories:
  ‘test_30iter.RData’ ‘test_50iter.RData’ ‘test_v2_50iter.RData’
Malformed Description field: should contain one or more complete sentences.
fma: no visible global function definition for ‘factanal’
fma: no visible global function definition for ‘runif’
fma: no visible global function definition for ‘kmeans’
fma: no visible global function definition for ‘var’
fma.em.alg: no visible global function definition for ‘var’
misc : q: no visible global function definition for ‘name’
Undefined global functions or variables:
  factanal kmeans name runif var
Consider adding
  importFrom("stats", "factanal", "kmeans", "runif", "var")
to your NAMESPACE file.
Found the following files/directories:
  ‘Bogota.tex’ ‘DogBreeds1.tex’
Running examples in ‘factoextra-Ex.R’ failed
The error most likely occurred in:

> ### Name: fviz_mfa
> ### Title: Visualize Multiple Factor Analysis
> ### Aliases: fviz_mfa fviz_mfa_ind fviz_mfa_quali_biplot fviz_mfa_var
> ###   fviz_mfa_axes
> 
> ### ** Examples
> 
> # Compute Multiple Factor Analysis
> library("FactoMineR")
> data(wine)
> res.mfa <- MFA(wine, group=c(2,5,3,10,9,2), type=c("n",rep("s",5)),
+                ncp=5, name.group=c("orig","olf","vis","olfag","gust","ens"),
+                num.group.sup=c(1,6), graph=FALSE)
>                
> # Eigenvalues/variances of dimensions
> fviz_screeplot(res.mfa)
> # Group of variables
> fviz_mfa_var(res.mfa, "group")
> # Quantitative variables
> fviz_mfa_var(res.mfa, "quanti.var", palette = "jco", 
+   col.var.sup = "violet", repel = TRUE)
Error in `[.data.frame`(X$call$X, rownames(ind), grp, drop = FALSE) : 
  undefined columns selected
Calls: fviz_mfa_var ... .add_ind_groups -> as.data.frame -> [ -> [.data.frame
Execution halted
Namespaces in Imports field not imported from:
  ‘forcats’ ‘formula.tools’
  All declared Imports should be used.
Note: found 5 marked Latin-1 strings
Namespaces in Imports field not imported from:
  ‘R6’ ‘caTools’ ‘httr’ ‘jsonlite’ ‘rlang’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘RCurl’ ‘RJSONIO’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
createFactualConnection: no visible global function definition for
  ‘new’
factualGetSchema: no visible global function definition for ‘fromJSON’
factualRead: no visible global function definition for ‘curlEscape’
factualRead: no visible global function definition for ‘fromJSON’
processFactualReadJSON: no visible global function definition for ‘new’
processFactualSchemaJSON: no visible global function definition for
  ‘new’
Undefined global functions or variables:
  curlEscape fromJSON new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
faisalconjoint: no visible global function definition for ‘barplot’
faisalconjoint: no visible global function definition for ‘text’
faisalconjoint: no visible global function definition for ‘jpeg’
faisalconjoint: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  barplot dev.off jpeg text
Consider adding
  importFrom("grDevices", "dev.off", "jpeg")
  importFrom("graphics", "barplot", "text")
to your NAMESPACE file.
Found the following files/directories:
  ‘FCMgraph.jpg’
File ‘fame/R/windows/zzz.R’:
  .onLoad calls:
    packageStartupMessage("FAME environment variable not set; assuming ",     defaultDir)
    packageStartupMessage("FAME directory ", fameDir, " not found.\n",     "If you have FAME installed, specify it's location ", "via the FAME environment variable.\n",     "Otherwise, this package is pretty useless.\n")

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 179 marked UTF-8 strings
Package suggested but not available for checking: ‘RWeka’
Package unavailable to check Rd xrefs: ‘RWeka’
Running ‘run-all.R’ [6s/18s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("farff")
  Loading required package: farff
  ── 1. Error: quick test with small arffs (@test_quick.R#6)  ────────────────────
  there is no package called 'RWeka'
  Backtrace:
   1. farff:::compareRWeka(INST_ARFF_DIR, "iris.arff", data.reader = dreader)
   2. RWeka::read.arff /home/ripley/R/packages/tests-devel/farff.Rcheck/tests/helper.R:17:2
   3. base::getExportedValue(pkg, name)
   4. base::asNamespace(ns)
   5. base::getNamespace(ns)
   6. base::loadNamespace(name)
   7. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   8. base:::withOneRestart(expr, restarts[[1L]])
   9. base:::doWithOneRestart(return(expr), restart)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: quick test with small arffs (@test_quick.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following files/directories:
  ‘default5.eps’
Namespace in Imports field not imported from: ‘RobustGaSP’
  All declared Imports should be used.
basis_hica: no visible global function definition for ‘princomp’
energy_hica: no visible global function definition for ‘dev.new’
energy_hica: no visible global function definition for ‘points’
energy_hica: no visible global function definition for ‘legend’
Undefined global functions or variables:
  dev.new legend points princomp
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "points")
  importFrom("stats", "princomp")
to your NAMESPACE file.
Package suggested but not available for checking: ‘coxKM’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
File ‘fastmatch/libs/fastmatch.so’:
  Found non-API call to R: ‘match5’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘mosaicCalc’
Package suggested but not available for checking: ‘Rserve’
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/FastRWeb.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
Namespace in Imports field not imported from: ‘whisker’
  All declared Imports should be used.
FBN.histogramMaxima: no visible global function definition for ‘hist’
FBN.kmeans: no visible global function definition for ‘median’
FBN.kmeans: no visible global function definition for ‘kmeans’
FBNormalization: no visible global function definition for ‘read.table’
FBNormalization: no visible global function definition for ‘median’
FBNormalization: no visible global function definition for ‘hist’
FBNormalization: no visible global function definition for ‘par’
FBNormalization: no visible global function definition for ‘dev.print’
FBNormalization: no visible binding for global variable ‘bmp’
FBNormalization: no visible global function definition for ‘sd’
FBNormalization: no visible global function definition for
  ‘write.table’
medianFilter: no visible global function definition for ‘median’
Undefined global functions or variables:
  bmp dev.print hist kmeans median par read.table sd write.table
Consider adding
  importFrom("grDevices", "bmp", "dev.print")
  importFrom("graphics", "hist", "par")
  importFrom("stats", "kmeans", "median", "sd")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘RCurl’ ‘RJSONIO’ ‘XML’ ‘glmnet’ ‘httr’ ‘speedglm’ ‘tcltk’ ‘xtable’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘MASS’ ‘combinat’ ‘glmnet’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fcd.cluster: no visible global function definition for ‘kmeans’
fcd.start: no visible global function definition for ‘ginv’
fcd.start: no visible global function definition for ‘glmnet’
gen.dcbm: no visible global function definition for ‘rbinom’
gen.sbm: no visible global function definition for ‘rbinom’
mis.cluster: no visible global function definition for ‘permn’
spectral.clustering: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  ginv glmnet kmeans permn rbinom
Consider adding
  importFrom("stats", "kmeans", "rbinom")
to your NAMESPACE file.
PTSingleAssetBarrierOption2: no visible global function definition for
  ‘new’
newton: no visible global function definition for ‘abline’
probInRange: no visible global function definition for ‘pnorm’
shortfall_risk: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline new pnorm
Consider adding
  importFrom("graphics", "abline")
  importFrom("methods", "new")
  importFrom("stats", "pnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  ‘test2delete.txt’ ‘test2delete2_values.txt’ ‘test2delete_values.txt’
Found the following files/directories:
  ‘.Rprofile’
Found the following files/directories:
  ‘fdaMatlabPath.m’
Note: found 76 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘usethis’ ‘utils’
  All declared Imports should be used.
Note: found 1 marked Latin-1 string
Note: found 3 marked Latin-1 strings
  Note: found 3 marked UTF-8 strings
Found the following sources/headers with CR or CRLF line endings:
  inst/include/fDMA.h
Some Unix compilers require LF line endings.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Found the following files/directories:
  ‘vert.txt’
FDRreg: no visible global function definition for ‘dnorm’
colnormalize: no visible global function definition for ‘sd’
efron: no visible global function definition for ‘median’
efron: no visible global function definition for ‘hist’
efron: no visible global function definition for ‘glm’
efron: no visible binding for global variable ‘poisson’
efron: no visible global function definition for ‘qchisq’
efron: no visible global function definition for ‘predict’
efron: no visible global function definition for ‘quantile’
efron: no visible global function definition for ‘lm’
efron: no visible global function definition for ‘coef’
make.bspline.matrix: no visible global function definition for
  ‘quantile’
plotFDR: no visible global function definition for ‘hist’
plotFDR: no visible global function definition for ‘par’
plotFDR: no visible global function definition for ‘axis’
plotFDR: no visible global function definition for ‘lines’
plotFDR: no visible global function definition for ‘legend’
plotFDR: no visible global function definition for ‘rug’
plotFDR: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis coef dnorm glm hist legend lines lm median par poisson predict
  qchisq quantile rug sd title
Consider adding
  importFrom("graphics", "axis", "hist", "legend", "lines", "par", "rug",
             "title")
  importFrom("stats", "coef", "dnorm", "glm", "lm", "median", "poisson",
             "predict", "qchisq", "quantile", "sd")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘latex_fdt.Rnw’ using Sweave

Attaching package: ‘fdth’

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

    sd, var


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

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

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

Error: Vignette re-building failed.
Execution halted
Found the following files/directories:
  ‘treesAll.txt’
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘testthat’
  All declared Imports should be used.
Running examples in ‘febr-Ex.R’ failed
The error most likely occurred in:

> ### Name: febr2spdf
> ### Title: Create an object of class 'SpatialPointsDataFrame'
> ### Aliases: febr2spdf
> 
> ### ** Examples
> 
> res <- observation(dataset = "ctb0003", variable = "taxon", 
+                    progress = FALSE, verbose = FALSE)
> res <- febr2spdf(obj = res)
> sp::spplot(obj = res, zcol = "taxon_sibcs_2009", 
+            auto.key = list(columns = 3), scales = list(draw = TRUE))
Error in create.z(as(obj, "data.frame"), zcol) : 
  no support for variable of this type
Calls: <Anonymous> -> <Anonymous> -> .local -> create.z
Execution halted
Namespaces in Imports field not imported from:
  ‘rvest’ ‘stringi’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘prettycode’
  All declared Imports should be used.
Running examples in ‘ffbase-Ex.R’ failed
The error most likely occurred in:

> ### Name: merge.ffdf
> ### Title: Merge two ffdf by common columns, or do other versions of
> ###   database join operations.
> ### Aliases: merge.ffdf
> 
> ### ** Examples
> 
> authors <- data.frame(
+     surname = c("Tukey", "Venables", "Tierney", "Ripley", "McNeil"),
+     nationality = c("US", "Australia", "US", "UK", "Australia"),
+     deceased = c("yes", rep("no", 4)))
> books <- data.frame(
+     name = c("Tukey", "Venables", "Tierney",
+              "Ripley", "Ripley", "McNeil", "R Core"),
+     title = c("Exploratory Data Analysis",
+               "Modern Applied Statistics ...",
+               "LISP-STAT",
+               "Spatial Statistics", "Stochastic Simulation",
+               "Interactive Data Analysis",
+               "An Introduction to R"),
+     other.author = c(NA, "Ripley", NA, NA, NA, NA,
+                      "Venables & Smith"))
> books <- lapply(1:100, FUN=function(x, books){
+ 	books$price <- rnorm(nrow(books))
+ 	books
+ }, books=books)
> books <- do.call(rbind, books)
> authors <- as.ffdf(authors)                
Error in ff(initdata = initdata, length = length, levels = levels, ordered = ordered,  : 
  vmode 'character' not implemented
Calls: as.ffdf ... do.call -> as.ff -> as.ff.default -> clone.ff -> assign -> ff
Execution halted
'library' or 'require' calls in package code:
  ‘ggplot2’ ‘gridExtra’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
FFieldPtRepDemo: no visible global function definition for ‘ggplot’
FFieldPtRepDemo: no visible binding for global variable ‘mtcars’
FFieldPtRepDemo: no visible global function definition for ‘aes’
FFieldPtRepDemo: no visible binding for global variable ‘mpg’
FFieldPtRepDemo: no visible global function definition for ‘geom_point’
FFieldPtRepDemo: no visible global function definition for ‘geom_text’
FFieldPtRepDemo: no visible global function definition for ‘ggtitle’
FFieldPtRepDemo: no visible global function definition for
  ‘geom_segment’
FFieldPtRepDemo: no visible global function definition for
  ‘grid.arrange’
Undefined global functions or variables:
  aes geom_point geom_segment geom_text ggplot ggtitle grid.arrange mpg
  mtcars
Consider adding
  importFrom("datasets", "mtcars")
to your NAMESPACE file.
Unexported object imported by a ':::' call: ‘bit:::R_bit_as_hi’
  See the note in ?`:::` about the use of this operator.
Running examples in ‘ff-Ex.R’ failed
The error most likely occurred in:

> ### Name: Extract.ffdf
> ### Title: Reading and writing data.frames (ffdf)
> ### Aliases: Extract.ffdf [.ffdf [<-.ffdf [[.ffdf [[<-.ffdf $.ffdf $<-.ffdf
> ### Keywords: IO data
> 
> ### ** Examples
> 
>    d <- data.frame(a=letters, b=rev(letters), c=1:26)
>    x <- as.ffdf(d)
Error in ff(initdata = initdata, length = length, levels = levels, ordered = ordered,  : 
  vmode 'character' not implemented
Calls: as.ffdf ... do.call -> as.ff -> as.ff.default -> clone.ff -> assign -> ff
Execution halted
ftest: no visible global function definition for ‘wilcox.test’
ftest: no visible global function definition for ‘t.test’
Undefined global functions or variables:
  t.test wilcox.test
Consider adding
  importFrom("stats", "t.test", "wilcox.test")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘mvtnorm’ ‘numDeriv’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dmymvnorm: no visible global function definition for ‘dmvnorm’
dmymvt: no visible global function definition for ‘dmvt’
gof.test: no visible global function definition for ‘quantile’
gof.test : ecdf: no visible global function definition for ‘mecdf’
gof.test: no visible global function definition for ‘jacobian’
gof.test: no visible global function definition for ‘var’
gradCdfT: no visible global function definition for ‘dt’
gradCdfT: no visible global function definition for ‘pt’
gradCdfT: no visible global function definition for ‘pmvt’
influFun: no visible global function definition for ‘jacobian’
mult.sim: no visible global function definition for ‘rnorm’
plackettFormula: no visible global function definition for ‘pt’
plackettFormula: no visible global function definition for ‘pmvt’
pmymvnorm: no visible global function definition for ‘GenzBretz’
pmymvnorm: no visible global function definition for ‘TVPACK’
pmymvnorm : <anonymous>: no visible global function definition for
  ‘pmvnorm’
pmymvt: no visible global function definition for ‘GenzBretz’
pmymvt: no visible global function definition for ‘TVPACK’
pmymvt : <anonymous>: no visible global function definition for ‘pmvt’
rmymvnorm: no visible global function definition for ‘rmvnorm’
rmymvt: no visible global function definition for ‘rmvt’
Undefined global functions or variables:
  GenzBretz TVPACK dmvnorm dmvt dt jacobian mecdf pmvnorm pmvt pt
  quantile rmvnorm rmvt rnorm var
Consider adding
  importFrom("stats", "dt", "pt", "quantile", "rnorm", "var")
to your NAMESPACE file.
fgeasy: no visible global function definition for ‘dist’
fgeasy : cor.est: no visible global function definition for ‘cor.test’
fgeasy: no visible binding for global variable ‘var’
fgperm : runrand: no visible global function definition for ‘runif’
fgperm : runrand: no visible global function definition for ‘ave’
fgploc : runrand: no visible global function definition for ‘runif’
fgploc : runrand: no visible global function definition for ‘ave’
fyshuffle: no visible global function definition for ‘runif’
plot.fg: no visible global function definition for ‘par’
plot.fg: no visible global function definition for ‘segments’
plot.fg: no visible binding for global variable ‘quantile’
plot.fg: no visible global function definition for ‘abline’
plot.fg: no visible global function definition for ‘axis’
summary.fg: no visible binding for global variable ‘quantile’
Undefined global functions or variables:
  abline ave axis cor.test dist par quantile runif segments var
Consider adding
  importFrom("graphics", "abline", "axis", "par", "segments")
  importFrom("stats", "ave", "cor.test", "dist", "quantile", "runif",
             "var")
to your NAMESPACE file.
Package suggested but not available for checking: ‘SDMTools’
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
Note: found 5077 marked UTF-8 strings
Namespace in Imports field not imported from: ‘numDeriv’
  All declared Imports should be used.
fieldsim: no visible global function definition for ‘rnorm’
midpoint: no visible global function definition for ‘rnorm’
setAtlas_under: no visible global function definition for ‘runif’
setCovf_under : Ibeta: no visible global function definition for
  ‘pbeta’
visualize: no visible global function definition for ‘colorRampPalette’
Undefined global functions or variables:
  colorRampPalette pbeta rnorm runif
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "pbeta", "rnorm", "runif")
to your NAMESPACE file.
Found the following files/directories:
  ‘dataframe.dump’ ‘list.dump’ ‘myDB’
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘filehash’ ‘DBI’
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  ‘RSQLite’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
createSQLite: no visible global function definition for ‘dbDriver’
createSQLite: no visible global function definition for ‘dbConnect’
createSQLite: no visible global function definition for
  ‘dbUnloadDriver’
createSQLite: no visible global function definition for ‘dbGetQuery’
initializeSQLite: no visible global function definition for ‘dbDriver’
initializeSQLite: no visible global function definition for ‘dbConnect’
initializeSQLite: no visible global function definition for ‘new’
dbDelete,filehashSQLite-character: no visible global function
  definition for ‘dbGetQuery’
dbDisconnect,filehashSQLite: no visible global function definition for
  ‘dbUnloadDriver’
dbFetch,filehashSQLite-character: no visible global function definition
  for ‘dbGetQuery’
dbInsert,filehashSQLite-character: no visible global function
  definition for ‘dbGetQuery’
dbList,filehashSQLite: no visible global function definition for
  ‘dbGetQuery’
dbMultiFetch,filehashSQLite-character: no visible global function
  definition for ‘dbGetQuery’
Undefined global functions or variables:
  dbConnect dbDriver dbGetQuery dbUnloadDriver new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  ‘myTestDB’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
Namespace in Imports field not imported from: ‘rappdirs’
  All declared Imports should be used.
Found the following files/directories:
  ‘AH_genepop.txt’ ‘AH_popname.txt’ ‘JSM_MS_freq.txt’
  ‘JSM_MS_genepop.txt’ ‘JSM_genepop_clipped_both.txt’
  ‘JSM_genepop_clipped_maf.txt’ ‘JSM_genepop_clipped_name.txt’
  ‘JSM_mtDNA_freq.txt’ ‘JSM_popname.txt’ ‘result_DJ.csv’
  ‘result_EBDJ.csv’ ‘result_EBFST.csv’ ‘result_EBFST_mtDNA.csv’
  ‘result_EBGstH.csv’ ‘result_GstH.csv’ ‘result_GstN.csv’
  ‘result_GstNC.csv’ ‘result_thetaWCpair.csv’
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘mapproj’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘quick_charts.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 125-134 (quick_charts.Rmd) 
Error: processing vignette 'quick_charts.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘quick_charts.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘lifeExpectancy.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 76-77 (lifeExpectancy.Rmd) 
Error: processing vignette 'lifeExpectancy.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘lifeExpectancy.Rmd’

--- re-building ‘selectIndicatorsRedRed.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 ‘selectIndicatorsRedRed.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
'library' or 'require' call to ‘tkrplot’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘methods’ ‘tkrplot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
lsmacof: no visible global function definition for ‘cmdscale’
plotInc: no visible global function definition for ‘rainbow’
prepareCalib: no visible global function definition for ‘lm’
Undefined global functions or variables:
  cmdscale lm rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("stats", "cmdscale", "lm")
to your NAMESPACE file.
Note: found 7 marked UTF-8 strings
fishmove : coefs: no visible global function definition for ‘coef’
fishmove : coefs: no visible global function definition for ‘pf’
fishmove: no visible global function definition for ‘lm’
fishmove: no visible global function definition for ‘predict.lm’
fishmove.estimate: no visible global function definition for ‘quantile’
fishmove.estimate : ddoublenorm: no visible global function definition
  for ‘dnorm’
fishmove.query: no visible global function definition for ‘hasArg’
fishmove.query : f: no visible global function definition for ‘pnorm’
fishmove.query: no visible global function definition for ‘uniroot’
pdk: no visible global function definition for ‘hasArg’
pdk : eq: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  coef dnorm hasArg lm pf pnorm predict.lm quantile uniroot
Consider adding
  importFrom("methods", "hasArg")
  importFrom("stats", "coef", "dnorm", "lm", "pf", "pnorm", "predict.lm",
             "quantile", "uniroot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following files/directories:
  ‘converted_AMR_raw.txt’ ‘converted_SMR_raw.txt’ ‘fishresp.txt’
  ‘results.txt’
Namespaces in Imports field not imported from:
  ‘grid’ ‘png’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Depends: includes the non-default packages:
  'gWidgets', 'tcltk', 'tkrplot', 'RGtk2', 'gWidgetsRGtk2',
  'cairoDevice'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' calls to packages already attached by Depends:
  ‘RGtk2’ ‘cairoDevice’ ‘gWidgets’ ‘gWidgetsRGtk2’ ‘tcltk’ ‘tkrplot’
  Please remove these calls from your code.
Package in Depends field not imported from: ‘FitAR’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
FitARMA: no visible global function definition for ‘PacfDL’
FitARMA: no visible global function definition for ‘GetARMeanMLE’
FitARMA: no visible global function definition for
  ‘BackcastResidualsAR’
FitARMA: no visible global function definition for ‘LjungBoxTest’
GetFitARMA: no visible global function definition for ‘LoglikelihoodAR’
GetFitARMA: no visible global function definition for ‘ChampernowneD’
GetFitARMA : EntropyARMA: no visible global function definition for
  ‘PacfToAR’
GetFitARMA : EntropyARMA: no visible global function definition for
  ‘PacfDL’
GetFitARMA : EntropyARMA: no visible global function definition for
  ‘FastLoglikelihoodAR’
GetFitARMA: no visible global function definition for ‘PacfToAR’
InformationMatrixARMA: no visible global function definition for
  ‘InvertibleQ’
TacvfARMA: no visible global function definition for ‘InvertibleQ’
Undefined global functions or variables:
  BackcastResidualsAR ChampernowneD FastLoglikelihoodAR GetARMeanMLE
  InvertibleQ LjungBoxTest LoglikelihoodAR PacfDL PacfToAR
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’ ‘leaps’ ‘ltsa’
A package should be listed in only one of these fields.
Package in Depends field not imported from: ‘bestglm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘XML’ ‘gglasso’ ‘methods’
  All declared Imports should be used.
Found the following files/directories:
  ‘test_modified.fits’
Package suggested but not available for checking: ‘ExtDist’
'library' or 'require' calls in package code:
  ‘devEMF’ ‘doMC’ ‘foreach’ ‘grDevices’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following files/directories:
  ‘modelfile.dat’ ‘plots’ ‘scorefile.dat’
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
Note: found 489 marked UTF-8 strings
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    help   3.2Mb
Malformed Description field: should contain one or more complete sentences.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
Package suggested but not available for checking: ‘multipanelfigure’
Running examples in ‘float-Ex.R’ failed
The error most likely occurred in:

> ### Name: eigen
> ### Title: eigen
> ### Aliases: eigen eigen,float32-method
> 
> ### ** Examples
> 
> library(float)
> 
> s = flrunif(10, 3)
> cp = crossprod(s)
> 
> eigen(cp)
Found the following files/directories:
  ‘core’
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R   6.4Mb
RIind: no visible global function definition for ‘aggregate’
RIind: no visible binding for global variable ‘sd’
RIpop: no visible global function definition for ‘aggregate’
RIpop: no visible binding for global variable ‘sd’
SI: no visible global function definition for ‘sd’
SI2: no visible global function definition for ‘sd’
SI3: no visible global function definition for ‘aggregate’
SI3: no visible global function definition for ‘pairs’
SI3: no visible global function definition for ‘cor’
SI4: no visible global function definition for ‘aggregate’
SI4: no visible global function definition for ‘sd’
fCV: no visible global function definition for ‘sd’
Undefined global functions or variables:
  aggregate cor pairs sd
Consider adding
  importFrom("graphics", "pairs")
  importFrom("stats", "aggregate", "cor", "sd")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
'library' or 'require' call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
GCV: no visible global function definition for ‘lm’
GCV: no visible global function definition for ‘resid’
ffplot: no visible global function definition for ‘par’
ffplot: no visible global function definition for ‘points’
ffplot: no visible global function definition for ‘legend’
flowfield: no visible global function definition for ‘write.table’
gpr: no visible global function definition for ‘quantile’
gpr: no visible global function definition for ‘var’
smoothp: no visible global function definition for ‘lm’
smoothp: no visible global function definition for ‘predict’
smoothp: no visible global function definition for ‘resid’
smoothp: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  legend lm optimize par points predict quantile resid var write.table
Consider adding
  importFrom("graphics", "legend", "par", "points")
  importFrom("stats", "lm", "optimize", "predict", "quantile", "resid",
             "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
GNU make is a SystemRequirements.
Malformed Description field: should contain one or more complete sentences.
prepare_Rd: Flury-package.Rd:37-39: Dropping empty section \examples
prepare_Rd: apples.Rd:19-21: Dropping empty section \details
prepare_Rd: basketball.Rd:28-29: Dropping empty section \references
prepare_Rd: challenger.Rd:18-20: Dropping empty section \details
prepare_Rd: computers.Rd:16-18: Dropping empty section \details
prepare_Rd: cork.Rd:19-20: Dropping empty section \details
prepare_Rd: dead.beetles.Rd:17-19: Dropping empty section \details
prepare_Rd: deer.Rd:14-16: Dropping empty section \details
prepare_Rd: dogwood.Rd:22-24: Dropping empty section \details
prepare_Rd: f.twins.Rd:23-25: Dropping empty section \details
prepare_Rd: flea.beetles.Rd:22-24: Dropping empty section \details
prepare_Rd: ghq.Rd:25-27: Dropping empty section \details
prepare_Rd: lookup.Rd:15-17: Dropping empty section \details
prepare_Rd: lookup.Rd:18-20: Dropping empty section \source
prepare_Rd: m.twins.Rd:24-26: Dropping empty section \details
prepare_Rd: mumps.Rd:14-16: Dropping empty section \details
prepare_Rd: pipits.Rd:17-19: Dropping empty section \details
prepare_Rd: pipits2.Rd:18-19: Dropping empty section \details
prepare_Rd: robustus.Rd:17-19: Dropping empty section \details
prepare_Rd: sibling.heads.Rd:18-20: Dropping empty section \details
prepare_Rd: snailsf.Rd:25-27: Dropping empty section \details
prepare_Rd: steve.Rd:19-20: Dropping empty section \details
prepare_Rd: steve.Rd:26-27: Dropping empty section \references
prepare_Rd: turtles.Rd:19: Dropping empty section \details
prepare_Rd: vasoc.Rd:18-20: Dropping empty section \details
prepare_Rd: wine.sugar.Rd:22-24: Dropping empty section \details
export: no visible global function definition for ‘write.table’
flux.odae : <anonymous>: no visible global function definition for
  ‘combn’
mf.flux: no visible global function definition for ‘runsd’
plot.fluss: no visible global function definition for ‘dev.new’
plot.fluss: no visible global function definition for ‘pdf’
plot.fluss: no visible global function definition for ‘dev.off’
plot.fluxes: no visible global function definition for ‘dev.new’
plot.fluxes: no visible global function definition for ‘devAskNewPage’
plot.fluxes: no visible global function definition for ‘pdf’
plot.fluxes: no visible global function definition for ‘dev.off’
plot.fluxxes: no visible global function definition for ‘dev.new’
plot.fluxxes: no visible global function definition for ‘devAskNewPage’
plot.fluxxes: no visible global function definition for ‘pdf’
plot.fluxxes: no visible global function definition for ‘dev.off’
reco.bulk : get.out: no visible global function definition for
  ‘boxplot.stats’
Undefined global functions or variables:
  boxplot.stats combn dev.new dev.off devAskNewPage pdf runsd
  write.table
Consider adding
  importFrom("grDevices", "boxplot.stats", "dev.new", "dev.off",
             "devAskNewPage", "pdf")
  importFrom("utils", "combn", "write.table")
to your NAMESPACE file.