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130 checked out of 130 dependencies

afex (0.15-2)

Maintainer: Henrik Singmann

OK

agRee (0.4-0)

Maintainer: Dai Feng

checking Rd cross-references ... NOTE
Packages unavailable to check Rd xrefs: ‘epiR’, ‘cccrm’, ‘Agreement’

DONE
Status: 1 NOTE

agridat (1.12)

Maintainer: Kevin Wright
Bug reports: https://github.com/kwstat/agridat/issues

OK

AICcmodavg (2.0-3)

Maintainer: Marc J. Mazerolle

checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  AICc.mult AICc.unmarked aictab.clm aictab.clmm aictab.coxph
  aictab.glm aictab.gls aictab.lm aictab.lme aictab.mer aictab.merMod
  aictab.mult aictab.nlme aictab.nls aictab.polr aictab.rlm
  aictab.unmarked dictab.bugs dictab.rjags modavg.clm modavg.clmm
  modavg.coxph modavg.effect modavg.effect.glm modavg.effect.gls
  modavg.effect.lme modavg.effect.mer modavg.effect.merMod
  modavg.effect.rlm modavg.effect.unmarked modavg.glm modavg.gls
  modavg.lme modavg.mer modavg.merMod modavg.mult modavg.polr
  modavg.rlm modavg.shrink modavg.shrink.clm modavg.shrink.clmm
  modavg.shrink.coxph modavg.shrink.glm modavg.shrink.gls
  modavg.shrink.lme modavg.shrink.mer modavg.shrink.merMod
  modavg.shrink.mult modavg.shrink.polr modavg.shrink.rlm
  modavg.shrink.unmarked modavg.unmarked predictSE.zip
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.

checking R code for possible problems ... NOTE
mb.gof.test.unmarkedFitColExt: no visible global function definition
  for ‘par’
Undefined global functions or variables:
  par
Consider adding
  importFrom("graphics", "par")
to your NAMESPACE.

DONE
Status: 2 NOTEs

ANOM (0.4.2)

Maintainer: Philip Pallmann

checking examples ... ERROR
Running examples in ‘ANOM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ANOM
> ### Title: ANOM Decision Charts
> ### Aliases: ANOM
> ### Keywords: ~dplot
> 
> ### ** Examples
> ## No test: 
> ###############################################
> ### Standard ANOM (Gaussian, homoscedastic) ###
> ###############################################
> 
> ### Devices of which brand filter bacteria significantly worse?
> head(waterfilter)
  brand colonies
1     1       69
2     1      122
3     1       95
4     2      118
5     2      154
6     2      102
> str(waterfilter)
'data.frame':   19 obs. of  2 variables:
 $ brand   : Factor w/ 7 levels "1","2","3","4",..: 1 1 1 2 2 2 3 3 3 4 ...
 $ colonies: int  69 122 95 118 154 102 171 132 182 122 ...
 - attr(*, "na.action")=Class 'omit'  Named int [1:2] 12 21
  .. ..- attr(*, "names")= chr [1:2] "12" "21"
> 
> library(multcomp)
Loading required package: mvtnorm
Loading required package: survival
Loading required package: TH.data
Loading required package: MASS

Attaching package: ‘TH.data’

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

    geyser

> model <- lm(colonies ~ brand, waterfilter)
> hom <- glht(model, mcp(brand="GrandMean"), alternative="less")
> ANOM(hom)
> 
> ############################
> ### Heteroscedastic ANOM ###
> ############################
> 
> ## With sandwich covariance matrix estimate (Herberich et al. 2010)
> 
> library(multcomp)
> library(sandwich)
> het1 <- glht(model, mcp(brand="GrandMean"), alternative="less", vcov=vcovHC)
> ANOM(het1)
Warning in RET$pfunction("adjusted", ...) :
  Completion with error > abseps
Warning in RET$pfunction("adjusted", ...) :
  Completion with error > abseps
Warning in RET$pfunction("adjusted", ...) :
  Completion with error > abseps
> 
> ## With multiple degrees of freedom (Hasler and Hothorn 2008)
> 
> library(SimComp)
> het2 <- SimCiDiff(data=waterfilter, grp="brand", resp="colonies",
+                   type="GrandMean", alternative="less", covar.equal=FALSE)
Error in checkmvArgs(lower = lower, upper = upper, mean = delta, corr = corr,  : 
  ‘lower’ not specified or contains NA
Calls: SimCiDiff ... get_quant_loclin -> lapply -> FUN -> func -> pmvt -> checkmvArgs
Execution halted

DONE
Status: 1 ERROR

aod (1.3)

Maintainer: Renaud Lancelot

checking dependencies in R code ... NOTE
'library' or 'require' call to ‘boot’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.

checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  print.wald.test
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.

checking R code for possible problems ... NOTE
varbin: no visible global function definition for ‘boot’
Undefined global functions or variables:
  boot

checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘dispmod’

DONE
Status: 4 NOTEs

aods3 (0.4-1)

Maintainer: Renaud Lancelot

checking dependencies in R code ... NOTE
'library' or 'require' call to ‘boot’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘boot’ ‘lme4’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.

checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  AIC.aodml anova.aodml anova.aodql coef.aodml coef.aodql
  deviance.aodml deviance.aodql df.residual.aodml df.residual.aodql
  fitted.aodml fitted.aodql logLik.aodml logLik.aodql predict.aodml
  predict.aodql print.anova.aodml print.aodml print.aodql print.drs
  print.gof print.iccbin print.summary.aodml print.varbin
  print.wald.test residuals.aodml residuals.aodql summary.aodml
  summary.aodql vcov.aodml vcov.aodql
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.

checking R code for possible problems ... NOTE
AIC.aodml: no visible binding for global variable ‘logLik’
anova.aodml: no visible global function definition for ‘AIC’
anova.aodml: no visible global function definition for ‘df.residual’
anova.aodml: no visible global function definition for ‘pchisq’
anova.aodql: no visible global function definition for ‘anova’
aodml: no visible global function definition for ‘update.formula’
aodml: no visible global function definition for ‘model.frame’
aodml: no visible global function definition for ‘model.response’
aodml: no visible global function definition for ‘model.offset’
aodml: no visible global function definition for ‘model.matrix’
aodml: no visible global function definition for ‘glm’
aodml: no visible global function definition for ‘coef’
aodml : m.logL: no visible global function definition for ‘dnbinom’
aodml: no visible global function definition for ‘optim’
aodml: no visible global function definition for ‘dnbinom’
aodql: no visible global function definition for ‘model.frame’
aodql: no visible global function definition for ‘model.response’
aodql: no visible global function definition for ‘glm’
aodql: no visible global function definition for ‘residuals’
aodql: no visible global function definition for ‘deviance’
aodql: no visible global function definition for ‘df.residual’
aodql: no visible global function definition for ‘logLik’
coef.aodql: no visible global function definition for ‘coef’
deviance.aodql: no visible global function definition for ‘deviance’
df.residual.aodql: no visible global function definition for
  ‘df.residual’
drs: no visible global function definition for ‘model.frame’
drs: no visible global function definition for ‘model.response’
drs: no visible global function definition for ‘terms’
fitted.aodql: no visible global function definition for ‘fitted’
gof: no visible global function definition for ‘deviance’
gof: no visible global function definition for ‘residuals’
gof: no visible global function definition for ‘df.residual’
iccbin: no visible binding for global variable ‘binomial’
iccbin: no visible global function definition for ‘rnorm’
iccbin: no visible global function definition for ‘var’
iccbin: no visible global function definition for ‘lm’
iccbin: no visible global function definition for ‘anova’
invlink: no visible global function definition for ‘plogis’
invlink: no visible global function definition for ‘pnorm’
link: no visible global function definition for ‘qlogis’
link: no visible global function definition for ‘qnorm’
logLik.aodql: no visible global function definition for ‘logLik’
predict.aodml: no visible global function definition for ‘model.matrix’
predict.aodml: no visible global function definition for ‘model.frame’
predict.aodml: no visible global function definition for ‘model.offset’
predict.aodml: no visible global function definition for ‘vcov’
predict.aodml: no visible global function definition for ‘dnorm’
predict.aodql: no visible global function definition for ‘predict’
print.drs: no visible global function definition for ‘pchisq’
print.gof: no visible global function definition for ‘pchisq’
print.summary.aodml: no visible global function definition for ‘AIC’
print.summary.aodml: no visible global function definition for
  ‘df.residual’
print.summary.aodml: no visible global function definition for
  ‘deviance’
residuals.aodml: no visible global function definition for ‘fitted’
residuals.aodql: no visible global function definition for ‘residuals’
splitbin : splitbin.w: no visible global function definition for
  ‘model.frame’
splitbin : splitbin.w: no visible global function definition for
  ‘model.response’
summary.aodml: no visible global function definition for ‘coef’
summary.aodml: no visible global function definition for ‘pnorm’
varbin: no visible global function definition for ‘var’
varbin: no visible global function definition for ‘boot’
varbin: no visible global function definition for ‘qnorm’
vcov.aodml: no visible global function definition for ‘coef’
vcov.aodql: no visible global function definition for ‘vcov’
wald.test: no visible global function definition for ‘pchisq’
wald.test: no visible global function definition for ‘pf’
Undefined global functions or variables:
  AIC anova binomial boot coef deviance df.residual dnbinom dnorm
  fitted glm lm logLik model.frame model.matrix model.offset
  model.response optim pchisq pf plogis pnorm predict qlogis qnorm
  residuals rnorm terms update.formula var vcov
Consider adding
  importFrom("stats", "AIC", "anova", "binomial", "coef", "deviance",
             "df.residual", "dnbinom", "dnorm", "fitted", "glm", "lm",
             "logLik", "model.frame", "model.matrix", "model.offset",
             "model.response", "optim", "pchisq", "pf", "plogis",
             "pnorm", "predict", "qlogis", "qnorm", "residuals", "rnorm",
             "terms", "update.formula", "var", "vcov")
to your NAMESPACE.

DONE
Status: 3 NOTEs

ArfimaMLM (1.3)

Maintainer: Patrick Kraft

checking R code for possible problems ... NOTE
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.

DONE
Status: 1 NOTE

arm (1.8-6)

Maintainer: Yu-Sung Su

checking whether the namespace can be loaded with stated dependencies ... NOTE
Warning: no function found corresponding to methods exports from ‘arm’ 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.

checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘Matching’

DONE
Status: 2 NOTEs

ARTool (0.10.0)

Maintainer: Matthew Kay
Bug reports: https://github.com/mjskay/ARTool/issues/new

OK

bapred (0.3)

Maintainer: Roman Hornung

checking package dependencies ... ERROR
Package required but not available: ‘sva’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

DONE
Status: 1 ERROR

BayesFactor (0.9.12-2)

Maintainer: Richard D. Morey
Bug reports: https://github.com/richarddmorey/BayesFactor/issues

OK

Bayesthresh (2.0.1)

Maintainer: Fabio Mathias Correa

checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘lme4’ ‘MASS’ ‘VGAM’ ‘mvtnorm’ ‘matrixcalc’ ‘coda’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘MASS’ ‘VGAM’ ‘coda’ ‘lme4’ ‘matrixcalc’ ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.

checking R code for possible problems ... NOTE
ACGaussian : <anonymous>: no visible global function definition for
  ‘qnorm’
ACGaussian : <anonymous>: no visible global function definition for
  ‘pnorm’
ACGaussian : <anonymous>: no visible global function definition for
  ‘runif’
ACGaussian: no visible global function definition for ‘ginv’
ACGaussian: no visible global function definition for ‘runif’
ACGaussian: no visible global function definition for ‘rmvnorm’
ACt: no visible global function definition for ‘qnorm’
ACt: no visible global function definition for ‘pnorm’
ACt: no visible global function definition for ‘runif’
ACt: no visible global function definition for ‘ginv’
ACt: no visible global function definition for ‘rmvnorm’
ACt: no visible global function definition for ‘rpois’
ACt: no visible global function definition for ‘dpois’
Bayesthresh: no visible global function definition for ‘as.formula’
Bayesthresh: no visible binding for global variable ‘contrasts’
MCGaussian: no visible global function definition for ‘qnorm’
MCGaussian: no visible global function definition for ‘pnorm’
MCGaussian: no visible global function definition for ‘runif’
MCGaussian: no visible global function definition for ‘ginv’
MCGaussian: no visible global function definition for ‘rmvnorm’
MCGaussian: no visible global function definition for ‘vec’
MCGaussian: no visible global function definition for ‘sd’
MCt: no visible global function definition for ‘qnorm’
MCt: no visible global function definition for ‘pnorm’
MCt: no visible global function definition for ‘runif’
MCt: no visible global function definition for ‘ginv’
MCt: no visible global function definition for ‘rmvnorm’
MCt: no visible global function definition for ‘vec’
MCt: no visible global function definition for ‘rpois’
MCt: no visible global function definition for ‘dpois’
MCt: no visible global function definition for ‘sd’
NCGaussian: no visible global function definition for ‘qnorm’
NCGaussian: no visible global function definition for ‘pnorm’
NCGaussian: no visible global function definition for ‘runif’
NCGaussian: no visible global function definition for ‘ginv’
NCGaussian: no visible global function definition for ‘rmvnorm’
NCGaussian: no visible global function definition for ‘rgamma’
NCGaussian: no visible global function definition for ‘rdiric’
NCt: no visible global function definition for ‘qnorm’
NCt: no visible global function definition for ‘pnorm’
NCt: no visible global function definition for ‘runif’
NCt: no visible global function definition for ‘ginv’
NCt: no visible global function definition for ‘rmvnorm’
NCt: no visible global function definition for ‘rgamma’
NCt: no visible global function definition for ‘rpois’
NCt: no visible global function definition for ‘dpois’
NCt: no visible global function definition for ‘rdiric’
UniComp: no visible global function definition for ‘rgamma’
VecFromNames: no visible global function definition for ‘as’
coef.Bayesthresh: no visible global function definition for ‘mcmc’
createCm: no visible global function definition for ‘is’
createCm: no visible global function definition for ‘as’
createCm: no visible global function definition for ‘new’
isNested: no visible global function definition for ‘as’
isNested: no visible global function definition for ‘new’
lmerFactorList : <anonymous>: no visible global function definition for
  ‘as’
lmerFactorList : <anonymous>: no visible global function definition for
  ‘validObject’
lmerFactorList : <anonymous>: no visible global function definition for
  ‘model.matrix’
lmerFactorList : <anonymous>: no visible binding for global variable
  ‘rBind’
lmerFactorList : <anonymous>: no visible global function definition for
  ‘drop0’
lmerFrames: no visible global function definition for ‘model.response’
lmerFrames: no visible global function definition for ‘is.empty.model’
lmerFrames: no visible global function definition for ‘model.matrix’
lmerFrames: no visible global function definition for ‘model.weights’
lmerFrames: no visible global function definition for ‘model.offset’
mkZt: no visible binding for global variable ‘rBind’
plot.random.effects: no visible global function definition for ‘gray’
plot.random.effects: no visible global function definition for ‘plot’
plot.random.effects: no visible global function definition for ‘axis’
plot.random.effects: no visible global function definition for
  ‘segments’
plot.random.effects: no visible global function definition for ‘box’
plot.random.effects: no visible global function definition for ‘qnorm’
predict.Bayesthresh: no visible global function definition for ‘coef’
predict.Bayesthresh: no visible global function definition for ‘pnorm’
predict.Bayesthresh: no visible global function definition for
  ‘rankMatrix’
predict.Bayesthresh: no visible global function definition for ‘pt’
random.effects: no visible global function definition for ‘coef’
random.effects: no visible global function definition for ‘mcmc’
Undefined global functions or variables:
  as as.formula axis box coef contrasts dpois drop0 ginv gray is
  is.empty.model mcmc model.matrix model.offset model.response
  model.weights new plot pnorm pt qnorm rBind rankMatrix rdiric rgamma
  rmvnorm rpois runif sd segments validObject vec
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "axis", "box", "plot", "segments")
  importFrom("methods", "as", "is", "new", "validObject")
  importFrom("stats", "as.formula", "coef", "contrasts", "dpois",
             "is.empty.model", "model.matrix", "model.offset",
             "model.response", "model.weights", "pnorm", "pt", "qnorm",
             "rgamma", "rpois", "runif", "sd")
to your NAMESPACE (and ensure that your DESCRIPTION Imports field
contains 'methods').

checking Rd line widths ... NOTE
Rd file 'Bayesthresh.Rd':
  \examples lines wider than 100 characters:
                                                                                                                                             ... [TRUNCATED]

Rd file 'MCMCsample.Rd':
  \examples lines wider than 100 characters:
                                                                                                                                             ... [TRUNCATED]

Rd file 'coef.Bayesthresh.Rd':
  \examples lines wider than 100 characters:
                                                                                                                                             ... [TRUNCATED]
                                                                                                                                             ... [TRUNCATED]

Rd file 'compVar.Rd':
  \examples lines wider than 100 characters:
                                                                                                                                             ... [TRUNCATED]

Rd file 'plot.random.effects.Rd':
  \usage lines wider than 90 characters:
                                           xlim = NULL, ylim = NULL, pch=19, col.points='red', col.seg=gray(0.5), ...)
  \examples lines wider than 100 characters:
                                                                                                                                             ... [TRUNCATED]

Rd file 'predict.Bayesthresh.Rd':
  \examples lines wider than 100 characters:
                                                                                                                                             ... [TRUNCATED]

Rd file 'random.effects.Rd':
  \examples lines wider than 100 characters:
                                                                                                                                             ... [TRUNCATED]

These lines will be truncated in the PDF manual.

DONE
Status: 4 NOTEs

BBRecapture (0.1)

Maintainer: Danilo Alunni Fegatelli

checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.

checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘HI’ ‘lme4’ ‘locfit’ ‘secr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.

checking R code for possible problems ... NOTE
BBRecap: no visible global function definition for ‘optimize’
BBRecap: no visible global function definition for ‘arms’
BBRecap: no visible global function definition for ‘median’
BBRecap : HPD.interval: no visible global function definition for
  ‘density’
BBRecap : HPD.interval: no visible global function definition for
  ‘quantile’
BBRecap.custom.part: no visible global function definition for
  ‘optimize’
LBRecap: no visible global function definition for ‘findbars’
LBRecap: no visible global function definition for ‘as.formula’
LBRecap: no visible global function definition for ‘glm’
LBRecap: no visible global function definition for ‘binomial’
LBRecap: no visible global function definition for ‘glmer’
LBRecap: no visible global function definition for ‘logLik’
LBRecap: no visible global function definition for ‘coef’
LBRecap: no visible global function definition for ‘na.omit’
LBRecap: no visible global function definition for ‘fixef’
LBRecap: no visible global function definition for ‘ranef’
LBRecap: no visible global function definition for ‘qnorm’
LBRecap: no visible global function definition for ‘plot’
LBRecap: no visible global function definition for ‘points’
LBRecap: no visible global function definition for ‘axis’
LBRecap: no visible global function definition for ‘abline’
LBRecap.custom.part: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  abline arms as.formula axis binomial coef density findbars fixef glm
  glmer logLik median na.omit optimize plot points qnorm quantile ranef
Consider adding
  importFrom("graphics", "abline", "axis", "plot", "points")
  importFrom("stats", "as.formula", "binomial", "coef", "density", "glm",
             "logLik", "median", "na.omit", "optimize", "qnorm",
             "quantile")
to your NAMESPACE.

DONE
Status: 3 NOTEs

benchmark (0.3-6)

Maintainer: Manuel J. A. Eugster

checking dependencies in R code ... NOTE
'library' or 'require' call to ‘multcomp’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.

checking R code for possible problems ... NOTE
as.dataset: no visible global function definition for ‘terms’
as.dataset: no visible global function definition for ‘as.formula’
as.psychobench: no visible global function definition for ‘is’
as.psychobench: no visible global function definition for ‘reshape’
benchmark: no visible global function definition for ‘as.formula’
benchmark: no visible global function definition for ‘predict’
benchmark: no visible global function definition for ‘na.omit’
beplot0.AlgorithmPerformance : <anonymous>: no visible global function
  definition for ‘legend’
beplot0.matrix : <anonymous>: no visible global function definition for
  ‘legend’
beplot0.matrix : <anonymous>: no visible global function definition for
  ‘col2rgb’
beplot0.matrix : <anonymous>: no visible global function definition for
  ‘rgb’
beplot0.matrix: no visible global function definition for ‘par’
beplot0.matrix: no visible global function definition for ‘layout’
beplot0.matrix: no visible global function definition for ‘axis’
beplot0.matrix: no visible global function definition for ‘box’
beplot0.matrix: no visible global function definition for ‘abline’
beplot0.matrix : linesegments: no visible global function definition
  for ‘segments’
beplot0.matrix: no visible binding for global variable ‘points’
beplot0.matrix: no visible global function definition for ‘barplot’
boxplot.AlgorithmPerformance: no visible binding for global variable
  ‘median’
boxplot.AlgorithmPerformance: no visible binding for global variable
  ‘algorithms’
boxplot.AlgorithmPerformance: no visible binding for global variable
  ‘value’
boxplot.AlgorithmPerformance: no visible binding for global variable
  ‘samples’
bsgraph0.dist: no visible global function definition for ‘gray’
bsgraph0.dist: no visible global function definition for ‘new’
bsgraph0.dist: no visible global function definition for ‘addEdge’
bsgraph0.graphNEL: no visible global function definition for
  ‘getDefaultAttrs’
bsgraph0.graphNEL: no visible global function definition for ‘agopen’
bsgraph0.graphNEL: no visible global function definition for ‘par’
bsplot0.matrix: no visible global function definition for ‘axis’
bsplot0.matrix: no visible global function definition for ‘mtext’
bsplot0.matrix: no visible global function definition for ‘box’
bsplot0.matrix: no visible global function definition for ‘rect’
bsplot0.matrix : <anonymous>: no visible global function definition for
  ‘lines’
characterize: no visible global function definition for ‘is’
densityplot.AlgorithmPerformance: no visible binding for global
  variable ‘value’
densityplot.AlgorithmPerformance: no visible binding for global
  variable ‘algorithms’
fcc: no visible global function definition for ‘cancor’
frac1: no visible global function definition for ‘cancor’
mac : <anonymous>: no visible global function definition for ‘lm’
map.dataset: no visible global function definition for ‘is’
map.dataset : traverse.tree : <anonymous>: no visible global function
  definition for ‘is’
mi: no visible global function definition for ‘mi.plugin’
order.algorithms.by: no visible global function definition for
  ‘na.omit’
patch.relation_class_ids: no visible global function definition for
  ‘relation_is_strict_weak_order’
plot.DatasetCharacterization: no visible global function definition for
  ‘gray’
plot.DatasetCharacterization: no visible binding for global variable
  ‘characteristics’
plot.DatasetCharacterization: no visible binding for global variable
  ‘value’
plot.DatasetCharacterization: no visible binding for global variable
  ‘samples’
plot.DatasetCharacterization: no visible global function definition for
  ‘theme_text’
plot.TestResult: no visible binding for global variable ‘samples’
plot.TestResult: no visible binding for global variable ‘value’
reduce.mapped.dataset: no visible global function definition for ‘is’
reduce.mapped.dataset : traverse.tree : <anonymous>: no visible global
  function definition for ‘is’
stripchart.AlgorithmPerformance: no visible binding for global variable
  ‘median’
stripchart.AlgorithmPerformance: no visible binding for global variable
  ‘algorithms’
stripchart.AlgorithmPerformance: no visible binding for global variable
  ‘value’
stripchart.AlgorithmPerformance: no visible binding for global variable
  ‘samples’
Undefined global functions or variables:
  abline addEdge agopen algorithms as.formula axis barplot box cancor
  characteristics col2rgb getDefaultAttrs gray is layout legend lines
  lm median mi.plugin mtext na.omit new par points predict rect
  relation_is_strict_weak_order reshape rgb samples segments terms
  theme_text value
Consider adding
  importFrom("grDevices", "col2rgb", "gray", "rgb")
  importFrom("graphics", "abline", "axis", "barplot", "box", "layout",
             "legend", "lines", "mtext", "par", "points", "rect",
             "segments")
  importFrom("methods", "is", "new")
  importFrom("stats", "as.formula", "cancor", "lm", "median", "na.omit",
             "predict", "reshape", "terms")
to your NAMESPACE (and ensure that your DESCRIPTION Imports field
contains 'methods').

DONE
Status: 2 NOTEs

BIFIEsurvey (1.8-0)

Maintainer: Alexander Robitzsch

OK

blmeco (1.1)

Maintainer: Fraenzi Korner-Nievergelt

OK

blme (1.0-4)

Maintainer: Vincent Dorie
Bug reports: https://github.com/vdorie/blme/issues

checking R code for possible problems ... NOTE
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.

DONE
Status: 1 NOTE

BradleyTerry2 (1.0-6)

Maintainer: Heather Turner

checking R code for possible problems ... NOTE
BTabilities: no visible global function definition for ‘model.matrix’
BTabilities: no visible global function definition for ‘terms’
BTabilities: no visible global function definition for ‘reformulate’
BTabilities: no visible global function definition for ‘model.frame’
BTabilities: no visible binding for global variable ‘na.pass’
BTabilities: no visible global function definition for ‘model.offset’
BTabilities: no visible global function definition for ‘vcov’
BTabilities: no visible global function definition for ‘na.exclude’
BTabilities: no visible global function definition for ‘C’
BTabilities: no visible global function definition for ‘relevel’
BTabilities: no visible global function definition for ‘contrasts’
BTm: no visible binding for global variable ‘binomial’
BTm.setup: no visible global function definition for ‘reformulate’
Diff: no visible global function definition for ‘reformulate’
Diff: no visible global function definition for ‘is.empty.model’
Diff: no visible global function definition for ‘terms’
Diff: no visible global function definition for ‘model.frame’
Diff: no visible binding for global variable ‘na.pass’
Diff: no visible global function definition for ‘relevel’
Diff: no visible global function definition for ‘model.offset’
Diff : recode: no visible global function definition for ‘relevel’
Diff: no visible global function definition for ‘model.matrix’
Diff: no visible global function definition for ‘na.omit’
GenDavidson : <anonymous>: no visible global function definition for
  ‘runif’
GenDavidsonTie: no visible binding for global variable ‘coef’
GenDavidsonTie: no visible global function definition for ‘plogis’
add1.BTm: no visible global function definition for ‘formula’
add1.BTm: no visible global function definition for ‘update.formula’
add1.BTm: no visible global function definition for ‘add.scope’
add1.BTm: no visible global function definition for ‘terms’
add1.BTm: no visible global function definition for ‘reformulate’
add1.BTm: no visible global function definition for ‘update’
add1.BTm: no visible binding for global variable ‘model.frame’
add1.BTm: no visible global function definition for ‘model.response’
add1.BTm: no visible global function definition for ‘model.weights’
add1.BTm: no visible global function definition for ‘model.offset’
add1.BTm: no visible global function definition for ‘coef’
add1.BTm: no visible global function definition for ‘vcov’
add1.BTm: no visible global function definition for ‘pchisq’
add1.BTm: no visible global function definition for ‘pf’
anova.BTm : <anonymous>: no visible global function definition for
  ‘formula’
anova.BTm: no visible global function definition for ‘model.matrix’
anova.BTm: no visible global function definition for ‘coef’
anova.BTm: no visible global function definition for ‘vcov’
anova.BTm: no visible global function definition for ‘formula’
anova.BTm: no visible global function definition for ‘pchisq’
anova.BTm: no visible global function definition for ‘pf’
anova.BTmlist : <anonymous>: no visible global function definition for
  ‘formula’
anova.BTmlist : <anonymous>: no visible global function definition for
  ‘terms’
anova.BTmlist : <anonymous>: no visible global function definition for
  ‘fitted’
anova.BTmlist : <anonymous>: no visible global function definition for
  ‘na.omit’
anova.BTmlist : <anonymous>: no visible global function definition for
  ‘coef’
anova.BTmlist: no visible global function definition for ‘coef’
anova.BTmlist: no visible global function definition for ‘vcov’
anova.BTmlist: no visible global function definition for ‘pchisq’
anova.BTmlist: no visible global function definition for ‘pf’
drop1.BTm: no visible global function definition for ‘model.matrix’
drop1.BTm: no visible global function definition for ‘terms’
drop1.BTm: no visible global function definition for ‘formula’
drop1.BTm: no visible global function definition for ‘drop.scope’
drop1.BTm: no visible global function definition for ‘update.formula’
drop1.BTm: no visible global function definition for ‘coef’
drop1.BTm: no visible global function definition for ‘vcov’
drop1.BTm: no visible global function definition for ‘pchisq’
drop1.BTm: no visible global function definition for ‘pf’
glmmPQL: no visible binding for global variable ‘binomial’
glmmPQL: no visible global function definition for ‘terms’
glmmPQL: no visible binding for global variable ‘model.frame’
glmmPQL: no visible global function definition for ‘model.response’
glmmPQL: no visible global function definition for ‘model.weights’
glmmPQL: no visible global function definition for ‘model.offset’
glmmPQL: no visible global function definition for ‘is.empty.model’
glmmPQL: no visible global function definition for ‘model.matrix’
glmmPQL: no visible global function definition for ‘glm.fit’
glmmPQL: no visible global function definition for ‘.getXlevels’
glmmPQL.fit: no visible global function definition for ‘gaussian’
glmmPQL.fit: no visible global function definition for ‘flush.console’
glmmPQL.fit: no visible global function definition for ‘optimize’
model.frame.BTm: no visible binding for global variable ‘model.frame’
plotProportions: no visible global function definition for ‘plot’
plotProportions: no visible global function definition for ‘points’
plotProportions: no visible global function definition for ‘curve’
plotProportions: no visible global function definition for ‘na.omit’
predict.BTglmmPQL: no visible binding for global variable ‘na.pass’
predict.BTglmmPQL: no visible global function definition for
  ‘delete.response’
predict.BTglmmPQL: no visible global function definition for
  ‘model.frame’
predict.BTglmmPQL: no visible global function definition for
  ‘.checkMFClasses’
predict.BTglmmPQL: no visible global function definition for
  ‘model.matrix’
predict.BTglmmPQL: no visible global function definition for
  ‘napredict’
predict.BTglmmPQL: no visible global function definition for ‘family’
predict.BTglmmPQL: no visible global function definition for
  ‘na.exclude’
predict.BTm: no visible binding for global variable ‘na.pass’
predict.BTm: no visible global function definition for ‘model.matrix’
predict.BTm: no visible global function definition for ‘reformulate’
print.BTglmmPQL: no visible global function definition for ‘coef’
print.BTglmmPQL: no visible global function definition for ‘naprint’
print.summary.BTglmmPQL: no visible global function definition for
  ‘printCoefmat’
print.summary.BTglmmPQL: no visible global function definition for
  ‘naprint’
print.summary.BTglmmPQL: no visible global function definition for
  ‘symnum’
residuals.BTm: no visible global function definition for ‘as.formula’
residuals.BTm: no visible global function definition for ‘terms’
residuals.BTm: no visible global function definition for ‘model.frame’
residuals.BTm: no visible global function definition for ‘model.matrix’
summary.BTglmmPQL: no visible global function definition for ‘coef’
summary.BTglmmPQL: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  .checkMFClasses .getXlevels C add.scope as.formula binomial coef
  contrasts curve delete.response drop.scope family fitted
  flush.console formula gaussian glm.fit is.empty.model model.frame
  model.matrix model.offset model.response model.weights na.exclude
  na.omit na.pass napredict naprint optimize pchisq pf plogis plot
  pnorm points printCoefmat reformulate relevel runif symnum terms
  update update.formula vcov
Consider adding
  importFrom("graphics", "curve", "plot", "points")
  importFrom("stats", ".checkMFClasses", ".getXlevels", "C", "add.scope",
             "as.formula", "binomial", "coef", "contrasts",
             "delete.response", "drop.scope", "family", "fitted",
             "formula", "gaussian", "glm.fit", "is.empty.model",
             "model.frame", "model.matrix", "model.offset",
             "model.response", "model.weights", "na.exclude", "na.omit",
             "na.pass", "napredict", "naprint", "optimize", "pchisq",
             "pf", "plogis", "pnorm", "printCoefmat", "reformulate",
             "relevel", "runif", "symnum", "terms", "update",
             "update.formula", "vcov")
  importFrom("utils", "flush.console")
to your NAMESPACE.

DONE
Status: 1 NOTE

brms (0.7.0)

Maintainer: Paul-Christian Buerkner
Bug reports: http://github.com/paul-buerkner/brms/issues

OK

broom (0.4.0)

Maintainer: David Robinson
Bug reports: http://github.com/dgrtwo/broom/issues

checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘akima’

DONE
Status: 1 NOTE

cAIC4 (0.2)

Maintainer: Benjamin Saefken

checking R code for possible problems ... NOTE
bcMer: no visible global function definition for ‘family’
biasCorrectionBernoulli: no visible global function definition for
  ‘qlogis’
biasCorrectionBernoulli : <anonymous>: no visible global function
  definition for ‘qlogis’
biasCorrectionGaussian: no visible global function definition for
  ‘model.matrix’
cAIC: no visible global function definition for ‘family’
conditionalBootstrap: no visible global function definition for
  ‘simulate’
conditionalBootstrap : <anonymous>: no visible global function
  definition for ‘predict’
conditionalBootstrap: no visible global function definition for ‘sigma’
deleteZeroComponents: no visible global function definition for ‘lm’
deleteZeroComponents: no visible global function definition for
  ‘formula’
deleteZeroComponents: no visible global function definition for
  ‘model.frame’
deleteZeroComponents: no visible global function definition for ‘terms’
deleteZeroComponents: no visible global function definition for
  ‘reformulate’
getcondLL: no visible global function definition for ‘family’
getcondLL: no visible global function definition for ‘dbinom’
getcondLL: no visible global function definition for ‘dpois’
getcondLL: no visible global function definition for ‘dnorm’
getcondLL: no visible global function definition for ‘sigma’
Undefined global functions or variables:
  dbinom dnorm dpois family formula lm model.frame model.matrix predict
  qlogis reformulate sigma simulate terms
Consider adding
  importFrom("stats", "dbinom", "dnorm", "dpois", "family", "formula",
             "lm", "model.frame", "model.matrix", "predict", "qlogis",
             "reformulate", "sigma", "simulate", "terms")
to your NAMESPACE.

DONE
Status: 1 NOTE

carcass (1.5)

Maintainer: Fraenzi Korner-Nievergelt

OK

car (2.1-1)

Maintainer: John Fox

OK

catdata (1.2.1)

Maintainer: Gunther Schauberger

OK

climwin (0.1.2)

Maintainer: Liam D. Bailey

checking dependencies in R code ... NOTE
Error: package or namespace load failed for ‘climwin’
Call sequence:
2: stop(gettextf("package or namespace load failed for %s", sQuote(package)), 
       call. = FALSE, domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted

DONE
Status: 1 NOTE

CLME (2.0-4)

Maintainer: Casey M. Jelsema
Bug reports: https://github.com/jelsema/CLME/issues

OK

clusterPower (0.5)

Maintainer: Nicholas G. Reich

checking R code for possible problems ... NOTE
fixed.effect: no visible global function definition for ‘glm’
fixed.effect: no visible global function definition for ‘qnorm’
fixed.effect.cluster.level: no visible global function definition for
  ‘aggregate’
fixed.effect.cluster.level: no visible global function definition for
  ‘formula’
fixed.effect.cluster.level: no visible global function definition for
  ‘glm’
fixed.effect.cluster.level: no visible global function definition for
  ‘qnorm’
hayes.power.poisson: no visible global function definition for ‘qnorm’
hayes.power.poisson: no visible global function definition for ‘pnorm’
power.sim.binomial: no visible global function definition for ‘rnorm’
power.sim.binomial: no visible global function definition for ‘rbinom’
power.sim.normal: no visible global function definition for ‘rnorm’
power.sim.poisson: no visible global function definition for ‘rnorm’
power.sim.poisson: no visible global function definition for ‘rnbinom’
power.sim.poisson: no visible global function definition for ‘rpois’
random.effect: no visible global function definition for ‘qt’
random.effect: no visible global function definition for ‘coef’
weighted.crossover.cluster.level: no visible global function definition
  for ‘aggregate’
weighted.crossover.cluster.level: no visible global function definition
  for ‘reshape’
weighted.crossover.cluster.level: no visible global function definition
  for ‘lm’
Undefined global functions or variables:
  aggregate coef formula glm lm pnorm qnorm qt rbinom reshape rnbinom
  rnorm rpois
Consider adding
  importFrom("stats", "aggregate", "coef", "formula", "glm", "lm",
             "pnorm", "qnorm", "qt", "rbinom", "reshape", "rnbinom",
             "rnorm", "rpois")
to your NAMESPACE.

DONE
Status: 1 NOTE

DAAG (1.22)

Maintainer: W. John Braun

OK

difR (4.6)

Maintainer: David Magis

checking R code for possible problems ... NOTE
LRT: no visible binding for global variable ‘binomial’
LRT: no visible global function definition for ‘deviance’
Logistik: no visible global function definition for ‘glm’
Logistik: no visible global function definition for ‘deviance’
Logistik: no visible global function definition for ‘coefficients’
breslowDay: no visible global function definition for ‘pchisq’
dichoDif: no visible global function definition for ‘capture.output’
difBD: no visible global function definition for ‘capture.output’
difGMH : internalGMH: no visible global function definition for
  ‘qchisq’
difGMH: no visible global function definition for ‘capture.output’
difGenLogistic : internalGenLog: no visible global function definition
  for ‘qchisq’
difGenLogistic: no visible global function definition for
  ‘capture.output’
difGenLord : internalGLord: no visible global function definition for
  ‘qchisq’
difGenLord: no visible global function definition for ‘capture.output’
difLRT : internalLRT: no visible global function definition for
  ‘qchisq’
difLRT: no visible global function definition for ‘capture.output’
difLogistic : internalLog: no visible global function definition for
  ‘qchisq’
difLogistic: no visible global function definition for ‘capture.output’
difLord : internalLord: no visible global function definition for
  ‘qchisq’
difLord: no visible global function definition for ‘capture.output’
difMH : internalMH: no visible global function definition for ‘qchisq’
difMH : internalMH: no visible global function definition for ‘qnorm’
difMH: no visible global function definition for ‘capture.output’
difRaju : internalRaju: no visible global function definition for
  ‘qnorm’
difRaju: no visible global function definition for ‘capture.output’
difStd: no visible global function definition for ‘capture.output’
difTID: no visible global function definition for ‘capture.output’
genDichoDif: no visible global function definition for ‘capture.output’
genLogistik: no visible global function definition for ‘glm’
genLogistik: no visible global function definition for ‘deviance’
genLogistik: no visible global function definition for ‘coefficients’
itemPar1PL: no visible binding for global variable ‘binomial’
itemPar2PL: no visible global function definition for ‘vcov’
itemPar3PL: no visible global function definition for ‘vcov’
itemPar3PLconst: no visible global function definition for ‘vcov’
itemRescale: no visible global function definition for ‘sd’
mantelHaenszel: no visible global function definition for
  ‘mantelhaen.test’
plot.BD : internalBD: no visible global function definition for
  ‘qchisq’
plot.BD : internalBD: no visible global function definition for ‘plot’
plot.BD : internalBD: no visible global function definition for
  ‘points’
plot.BD : internalBD: no visible global function definition for ‘text’
plot.BD : internalBD: no visible global function definition for ‘lines’
plot.BD: no visible global function definition for ‘pdf’
plot.BD: no visible global function definition for ‘dev.off’
plot.BD: no visible global function definition for ‘jpeg’
plot.GMH : internalGMH: no visible global function definition for
  ‘plot’
plot.GMH : internalGMH: no visible global function definition for
  ‘points’
plot.GMH : internalGMH: no visible global function definition for
  ‘text’
plot.GMH : internalGMH: no visible global function definition for
  ‘abline’
plot.GMH: no visible global function definition for ‘pdf’
plot.GMH: no visible global function definition for ‘dev.off’
plot.GMH: no visible global function definition for ‘jpeg’
plot.GenLord : internalGLord: no visible global function definition for
  ‘points’
plot.GenLord : internalGLord: no visible global function definition for
  ‘text’
plot.GenLord : internalGLord: no visible global function definition for
  ‘abline’
plot.GenLord : internalGLord: no visible global function definition for
  ‘lines’
plot.GenLord : internalGLord: no visible global function definition for
  ‘legend’
plot.GenLord: no visible global function definition for ‘pdf’
plot.GenLord: no visible global function definition for ‘dev.off’
plot.GenLord: no visible global function definition for ‘jpeg’
plot.LRT : internalLRT: no visible global function definition for
  ‘plot’
plot.LRT : internalLRT: no visible global function definition for
  ‘points’
plot.LRT : internalLRT: no visible global function definition for
  ‘text’
plot.LRT : internalLRT: no visible global function definition for
  ‘abline’
plot.LRT: no visible global function definition for ‘pdf’
plot.LRT: no visible global function definition for ‘dev.off’
plot.LRT: no visible global function definition for ‘jpeg’
plot.Logistic : internalLog: no visible global function definition for
  ‘points’
plot.Logistic : internalLog: no visible global function definition for
  ‘text’
plot.Logistic : internalLog: no visible global function definition for
  ‘abline’
plot.Logistic : internalLog: no visible global function definition for
  ‘lines’
plot.Logistic : internalLog: no visible global function definition for
  ‘legend’
plot.Logistic: no visible global function definition for ‘pdf’
plot.Logistic: no visible global function definition for ‘dev.off’
plot.Logistic: no visible global function definition for ‘jpeg’
plot.Lord : internalLord: no visible global function definition for
  ‘points’
plot.Lord : internalLord: no visible global function definition for
  ‘text’
plot.Lord : internalLord: no visible global function definition for
  ‘abline’
plot.Lord : internalLord: no visible global function definition for
  ‘lines’
plot.Lord : internalLord: no visible global function definition for
  ‘legend’
plot.Lord: no visible global function definition for ‘pdf’
plot.Lord: no visible global function definition for ‘dev.off’
plot.Lord: no visible global function definition for ‘jpeg’
plot.MH : internalMH: no visible global function definition for ‘plot’
plot.MH : internalMH: no visible global function definition for
  ‘points’
plot.MH : internalMH: no visible global function definition for ‘text’
plot.MH : internalMH: no visible global function definition for
  ‘abline’
plot.MH: no visible global function definition for ‘pdf’
plot.MH: no visible global function definition for ‘dev.off’
plot.MH: no visible global function definition for ‘jpeg’
plot.PDIF : internalSTD: no visible global function definition for
  ‘plot’
plot.PDIF : internalSTD: no visible global function definition for
  ‘points’
plot.PDIF : internalSTD: no visible global function definition for
  ‘text’
plot.PDIF : internalSTD: no visible global function definition for
  ‘abline’
plot.PDIF: no visible global function definition for ‘pdf’
plot.PDIF: no visible global function definition for ‘dev.off’
plot.PDIF: no visible global function definition for ‘jpeg’
plot.Raj : internalRaju: no visible global function definition for
  ‘plot’
plot.Raj : internalRaju: no visible global function definition for
  ‘points’
plot.Raj : internalRaju: no visible global function definition for
  ‘text’
plot.Raj : internalRaju: no visible global function definition for
  ‘abline’
plot.Raj: no visible global function definition for ‘pdf’
plot.Raj: no visible global function definition for ‘dev.off’
plot.Raj: no visible global function definition for ‘jpeg’
plot.TID : internalTID: no visible global function definition for
  ‘points’
plot.TID : internalTID: no visible global function definition for
  ‘text’
plot.TID : internalTID: no visible global function definition for
  ‘abline’
plot.TID: no visible global function definition for ‘pdf’
plot.TID: no visible global function definition for ‘dev.off’
plot.TID: no visible global function definition for ‘jpeg’
plot.genLogistic : internalGenLog: no visible global function
  definition for ‘points’
plot.genLogistic : internalGenLog: no visible global function
  definition for ‘text’
plot.genLogistic : internalGenLog: no visible global function
  definition for ‘abline’
plot.genLogistic : internalGenLog: no visible global function
  definition for ‘lines’
plot.genLogistic : internalGenLog: no visible global function
  definition for ‘legend’
plot.genLogistic: no visible global function definition for ‘pdf’
plot.genLogistic: no visible global function definition for ‘dev.off’
plot.genLogistic: no visible global function definition for ‘jpeg’
print.BD: no visible global function definition for ‘symnum’
print.BD: no visible global function definition for ‘qchisq’
print.GMH: no visible global function definition for ‘pchisq’
print.GMH: no visible global function definition for ‘symnum’
print.GenLord: no visible global function definition for ‘pchisq’
print.GenLord: no visible global function definition for ‘symnum’
print.LRT: no visible global function definition for ‘pchisq’
print.LRT: no visible global function definition for ‘symnum’
print.Logistic: no visible global function definition for ‘pchisq’
print.Logistic: no visible global function definition for ‘symnum’
print.Lord: no visible global function definition for ‘pchisq’
print.Lord: no visible global function definition for ‘symnum’
print.MH: no visible global function definition for ‘pchisq’
print.MH: no visible global function definition for ‘pnorm’
print.MH: no visible global function definition for ‘symnum’
print.PDIF: no visible global function definition for ‘symnum’
print.Raj: no visible global function definition for ‘pnorm’
print.Raj: no visible global function definition for ‘symnum’
print.TID: no visible global function definition for ‘symnum’
print.genLogistic: no visible global function definition for ‘pchisq’
print.genLogistic: no visible global function definition for ‘symnum’
print.subLogistic: no visible global function definition for ‘symnum’
print.subLogistic: no visible global function definition for ‘qchisq’
subtestLogistic: no visible global function definition for ‘pchisq’
trItemDiff: no visible global function definition for ‘qnorm’
trItemDiff: no visible global function definition for ‘cov’
Undefined global functions or variables:
  abline binomial capture.output coefficients cov dev.off deviance glm
  jpeg legend lines mantelhaen.test pchisq pdf plot pnorm points qchisq
  qnorm sd symnum text vcov
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "pdf")
  importFrom("graphics", "abline", "legend", "lines", "plot", "points",
             "text")
  importFrom("stats", "binomial", "coefficients", "cov", "deviance",
             "glm", "mantelhaen.test", "pchisq", "pnorm", "qchisq",
             "qnorm", "sd", "symnum", "vcov")
  importFrom("utils", "capture.output")
to your NAMESPACE.

DONE
Status: 1 NOTE

dlnm (2.1.3)

Maintainer: Antonio Gasparrini

checking R code for possible problems ... NOTE
crossbasis: no visible global function definition for ‘modifyList’
fci: no visible global function definition for ‘modifyList’
lines.crosspred: no visible global function definition for ‘modifyList’
lines.crossreduce: no visible global function definition for
  ‘modifyList’
plot.crosspred: no visible global function definition for ‘modifyList’
plot.crossreduce: no visible global function definition for
  ‘modifyList’
points.crosspred: no visible global function definition for
  ‘modifyList’
points.crossreduce: no visible global function definition for
  ‘modifyList’
Undefined global functions or variables:
  modifyList
Consider adding
  importFrom("utils", "modifyList")
to your NAMESPACE.

DONE
Status: 1 NOTE

doBy (4.5-14)

Maintainer: Sren Hjsgaard

OK

effects (3.0-5)

Maintainer: John Fox

OK

Epi (2.0)

Maintainer: Bendix Carstensen

OK

expp (1.1)

Maintainer: Mihai Valcu

checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.

checking dependencies in R code ... NOTE
'library' or 'require' call to ‘spatstat’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.

checking R code for possible problems ... NOTE
eppSimDat: no visible global function definition for ‘rnorm’
eppSimDat: no visible global function definition for ‘rpois’
DirichletPolygons,SpatialPointsBreeding-missing: no visible global
  function definition for ‘ripras’
barplot,epp: no visible global function definition for ‘axis’
barplot,epp: no visible global function definition for ‘par’
plot,SpatialPointsBreeding-eppMatrix: no visible global function
  definition for ‘points’
plot,SpatialPointsBreeding-eppMatrix: no visible global function
  definition for ‘text’
plot,SpatialPointsBreeding-eppMatrix: no visible global function
  definition for ‘arrows’
plot,SpatialPointsBreeding-missing: no visible global function
  definition for ‘points’
plot,SpatialPointsBreeding-missing: no visible global function
  definition for ‘text’
Undefined global functions or variables:
  arrows axis par points ripras rnorm rpois text
Consider adding
  importFrom("graphics", "arrows", "axis", "par", "points", "text")
  importFrom("stats", "rnorm", "rpois")
to your NAMESPACE.

DONE
Status: 3 NOTEs

eyetrackingR (0.1.4)

Maintainer: Jacob Dink
Bug reports: https://github.com/jwdink/eyetrackingR/issues

checking examples ... ERROR
Running examples in ‘eyetrackingR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: analyze_time_bins
> ### Title: analyze_time_bins()
> ### Aliases: analyze_time_bins analyze_time_bins.time_sequence_data
> 
> ### ** Examples
> 
> data(word_recognition)
> data <- make_eyetrackingr_data(word_recognition, 
+                                participant_column = "ParticipantName",
+                                trial_column = "Trial",
+                                time_column = "TimeFromTrialOnset",
+                                trackloss_column = "TrackLoss",
+                                aoi_columns = c('Animate','Inanimate'),
+                                treat_non_aoi_looks_as_missing = TRUE
+ )
> response_time <- make_time_sequence_data(data, time_bin_size = 250, 
+                                          predictor_columns = c("MCDI_Total"),
+                                          aois = "Animate", summarize_by = "ParticipantName")
> tb_analysis <- analyze_time_bins(response_time, predictor_column = "MCDI_Total", 
+                                  test = "lm", threshold = 2)
Computing lm for each time bin...
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘coda’
Calls: analyze_time_bins ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted

checking tests ... ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(eyetrackingR)
  > 
  > test_check("eyetrackingR")
  Avg. window length in new data will be 5500
  Performing Trackloss Analysis...
  Will exclude trials whose trackloss proportion is greater than : 0.25
    ...removed  33  trials.
  Computing t.test for each time bin...
  Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
    there is no package called 'coda'
  Calls: test_check ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  Execution halted

DONE
Status: 2 ERRORs

ez (4.3)

Maintainer: Michael A. Lawrence

OK

fishmethods (1.9-0)

Maintainer: Gary A. Nelson

OK

flexmix (2.3-13)

Maintainer: Bettina Gruen

checking dependencies in R code ... NOTE
Missing or unexported object: ‘lme4::sigma’

checking R code for possible problems ... NOTE
ExLinear: no visible global function definition for ‘rnorm’
ExLinear: no visible global function definition for ‘rpois’
ExNPreg: no visible global function definition for ‘runif’
ExNPreg: no visible global function definition for ‘binomial’
ExNPreg: no visible global function definition for ‘rnorm’
ExNPreg: no visible global function definition for ‘rpois’
ExNPreg: no visible global function definition for ‘rbinom’
FLXMCfactanal : <anonymous>: no visible global function definition for
  ‘cov.wt’
FLXMCfactanal : <anonymous>: no visible global function definition for
  ‘factanal’
FLXMCmvcombi : <anonymous>: no visible global function definition for
  ‘cov.wt’
FLXMCmvnorm : <anonymous>: no visible global function definition for
  ‘cov.wt’
FLXMCnorm1 : <anonymous>: no visible global function definition for
  ‘cov.wt’
FLXMRglm : glmrefit: no visible global function definition for
  ‘glm.fit’
FLXMRglm : glmrefit: no visible binding for global variable ‘glm.fit’
FLXMRglm : <anonymous>: no visible global function definition for
  ‘lm.wfit’
FLXMRglm : <anonymous>: no visible global function definition for
  ‘coef’
FLXMRglm : <anonymous>: no visible global function definition for
  ‘glm.fit’
FLXMRglm : <anonymous>: no visible global function definition for
  ‘binomial’
FLXMRglm : <anonymous>: no visible global function definition for
  ‘poisson’
FLXMRglm : <anonymous>: no visible global function definition for
  ‘Gamma’
FLXMRglmfix : <anonymous>: no visible global function definition for
  ‘lm.wfit’
FLXMRglmfix : <anonymous>: no visible global function definition for
  ‘coef’
FLXMRglmfix : <anonymous>: no visible global function definition for
  ‘glm.fit’
FLXMRglmfix : <anonymous>: no visible global function definition for
  ‘binomial’
FLXMRglmfix : <anonymous>: no visible global function definition for
  ‘poisson’
FLXMRglmfix : <anonymous>: no visible global function definition for
  ‘Gamma’
FLXMRglmnet : <anonymous>: no visible global function definition for
  ‘lm.wfit’
FLXMRglmnet : <anonymous>: no visible global function definition for
  ‘glm.fit’
FLXMRglmnet : <anonymous>: no visible global function definition for
  ‘binomial’
FLXMRglmnet : <anonymous>: no visible global function definition for
  ‘poisson’
FLXMRlmer : <anonymous>: no visible global function definition for
  ‘coef’
FLXMRlmm : lmm.wfit: no visible global function definition for ‘resid’
FLXMRlmm : lmm.wfit: no visible global function definition for ‘coef’
FLXMRlmm : <anonymous>: no visible binding for global variable
  ‘weighted.mean’
FLXMRlmm : <anonymous> : <anonymous>: no visible global function
  definition for ‘coef’
FLXMRlmm : <anonymous>: no visible global function definition for
  ‘coef’
FLXMRlmmc : lmc.wfit: no visible global function definition for
  ‘lm.wfit’
FLXMRlmmc : lmc.wfit: no visible global function definition for ‘resid’
FLXMRlmmc : <anonymous> : <anonymous> : <anonymous>: no visible global
  function definition for ‘var’
FLXMRlmmc : <anonymous> : <anonymous>: no visible global function
  definition for ‘coef’
FLXMRlmmc : <anonymous> : <anonymous>: no visible global function
  definition for ‘var’
FLXMRlmmc : <anonymous>: no visible global function definition for
  ‘coef’
FLXMRlmmc : lmmc.wfit: no visible global function definition for
  ‘lm.wfit’
FLXMRlmmc : <anonymous>: no visible binding for global variable
  ‘weighted.mean’
FLXdist: no visible global function definition for ‘update.formula’
FLXglm : glmrefit: no visible global function definition for ‘glm.fit’
FLXglm : glmrefit: no visible binding for global variable ‘glm.fit’
FLXglm : <anonymous>: no visible global function definition for
  ‘lm.wfit’
FLXglm : <anonymous>: no visible global function definition for ‘coef’
FLXglm : <anonymous>: no visible global function definition for
  ‘glm.fit’
FLXglm : <anonymous>: no visible global function definition for
  ‘binomial’
FLXglm : <anonymous>: no visible global function definition for
  ‘poisson’
FLXglm : <anonymous>: no visible global function definition for ‘Gamma’
FLXglmFix : <anonymous>: no visible global function definition for
  ‘lm.wfit’
FLXglmFix : <anonymous>: no visible global function definition for
  ‘coef’
FLXglmFix : <anonymous>: no visible global function definition for
  ‘glm.fit’
FLXglmFix : <anonymous>: no visible global function definition for
  ‘binomial’
FLXglmFix : <anonymous>: no visible global function definition for
  ‘poisson’
FLXglmFix : <anonymous>: no visible global function definition for
  ‘Gamma’
FLXmclust : <anonymous>: no visible global function definition for
  ‘cov.wt’
confidence.panel.boot : <anonymous>: no visible global function
  definition for ‘quantile’
confidence.panel.boot: no visible global function definition for ‘rgb’
formattedTicksAndLabels: no visible binding for global variable
  ‘axisTicks’
getCoefs : <anonymous>: no visible global function definition for
  ‘qnorm’
hist.constructor: no visible global function definition for ‘hist’
modelMatrix: no visible global function definition for ‘model.frame’
modelMatrix: no visible global function definition for ‘model.response’
modelMatrix: no visible global function definition for ‘.getXlevels’
modelMatrix: no visible global function definition for ‘terms’
modelMatrix: no visible global function definition for ‘model.matrix’
modelMatrix: no visible global function definition for ‘update’
moments_truncated: no visible global function definition for ‘pnorm’
moments_truncated: no visible global function definition for ‘dnorm’
panel.rootogram: no visible global function definition for ‘quantile’
plotEll: no visible global function definition for ‘model.frame’
plotEll: no visible global function definition for ‘model.response’
plotEll: no visible global function definition for ‘lines’
plotEll: no visible global function definition for ‘text’
prepanel.rootogram: no visible global function definition for
  ‘quantile’
rmvbinary : <anonymous>: no visible global function definition for
  ‘rbinom’
rmvbinom : <anonymous>: no visible global function definition for
  ‘rbinom’
unipolarCols: no visible global function definition for ‘hcl’
update.Residual: no visible global function definition for ‘resid’
weighted.glm.fit: no visible global function definition for ‘glm.fit’
weighted.glm.fit: no visible binding for global variable ‘glm.fit’
FLXfillConcomitant,FLXPmultinom: no visible global function definition
  for ‘coef’
FLXgetModelmatrix,FLXM: no visible global function definition for
  ‘update’
FLXgetModelmatrix,FLXM: no visible global function definition for
  ‘terms’
FLXgetModelmatrix,FLXM: no visible global function definition for
  ‘model.frame’
FLXgetModelmatrix,FLXM: no visible global function definition for
  ‘model.response’
FLXgetModelmatrix,FLXM: no visible global function definition for
  ‘delete.response’
FLXgetModelmatrix,FLXM: no visible global function definition for
  ‘model.matrix’
FLXgetModelmatrix,FLXM: no visible global function definition for
  ‘.getXlevels’
FLXgetModelmatrix,FLXMRcondlogit: no visible global function definition
  for ‘update’
FLXgetModelmatrix,FLXMRcondlogit: no visible global function definition
  for ‘terms’
FLXgetModelmatrix,FLXMRcondlogit: no visible global function definition
  for ‘model.frame’
FLXgetModelmatrix,FLXMRcondlogit: no visible global function definition
  for ‘model.matrix’
FLXgetModelmatrix,FLXMRcondlogit: no visible global function definition
  for ‘model.response’
FLXgetModelmatrix,FLXMRcondlogit: no visible global function definition
  for ‘delete.response’
FLXgetModelmatrix,FLXMRfix: no visible global function definition for
  ‘update.formula’
FLXgetModelmatrix,FLXMRlmc: no visible global function definition for
  ‘update’
FLXgetModelmatrix,FLXMRlmc: no visible global function definition for
  ‘terms’
FLXgetModelmatrix,FLXMRlmc: no visible global function definition for
  ‘model.frame’
FLXgetModelmatrix,FLXMRlmc: no visible global function definition for
  ‘delete.response’
FLXgetModelmatrix,FLXMRlmc: no visible global function definition for
  ‘model.matrix’
FLXgetModelmatrix,FLXMRlmer: no visible global function definition for
  ‘update’
FLXgetModelmatrix,FLXMRlmm: no visible global function definition for
  ‘update’
FLXgetModelmatrix,FLXMRlmm: no visible global function definition for
  ‘terms’
FLXgetModelmatrix,FLXMRlmm: no visible global function definition for
  ‘model.frame’
FLXgetModelmatrix,FLXMRlmm: no visible global function definition for
  ‘delete.response’
FLXgetModelmatrix,FLXMRlmm: no visible global function definition for
  ‘model.matrix’
FLXgetModelmatrix,FLXMRlmmc: no visible global function definition for
  ‘terms’
FLXgetModelmatrix,FLXMRlmmc: no visible global function definition for
  ‘model.frame’
FLXgetModelmatrix,FLXMRlmmc: no visible global function definition for
  ‘delete.response’
FLXgetModelmatrix,FLXMRlmmc: no visible global function definition for
  ‘model.matrix’
FLXgetModelmatrix,FLXMRmgcv: no visible global function definition for
  ‘update’
FLXgetModelmatrix,FLXMRmgcv: no visible global function definition for
  ‘terms’
FLXgetModelmatrix,FLXMRmgcv: no visible global function definition for
  ‘model.frame’
FLXgetModelmatrix,FLXMRmgcv: no visible global function definition for
  ‘model.response’
FLXgetModelmatrix,FLXMRmgcv: no visible global function definition for
  ‘delete.response’
FLXgetModelmatrix,FLXMRmgcv: no visible global function definition for
  ‘.getXlevels’
FLXgetModelmatrix,FLXMRrobglm: no visible global function definition
  for ‘terms’
FLXgetModelmatrix,FLXMRziglm: no visible global function definition for
  ‘terms’
FLXgetModelmatrix,FLXP: no visible global function definition for
  ‘terms’
FLXgetModelmatrix,FLXP: no visible global function definition for
  ‘model.frame’
FLXgetModelmatrix,FLXP: no visible global function definition for
  ‘delete.response’
FLXgetModelmatrix,FLXP: no visible global function definition for
  ‘model.matrix’
FLXmstep,FLXMRrobglm: no visible global function definition for
  ‘cov.wt’
VarianceCovariance,flexmix: no visible global function definition for
  ‘optim’
flexmix,formula-ANY-ANY-ANY-list: no visible global function definition
  for ‘model.frame’
getModel,stepFlexmix : <anonymous>: no visible global function
  definition for ‘AIC’
getModel,stepFlexmix : <anonymous>: no visible global function
  definition for ‘BIC’
plot,FLXboot-missing: no visible global function definition for ‘qnorm’
plot,FLXboot-missing: no visible global function definition for
  ‘rmvnorm’
plot,FLXboot-missing: no visible binding for global variable ‘quantile’
plot,FLXboot-missing: no visible global function definition for
  ‘as.formula’
plot,FLXboot-missing: no visible global function definition for
  ‘na.omit’
plot,flexmix-missing: no visible binding for global variable ‘cluster’
plot,stepFlexmix-missing: no visible global function definition for
  ‘matplot’
plot,stepFlexmix-missing: no visible global function definition for
  ‘points’
predict,FLXMRmgcv : predict_gam: no visible global function definition
  for ‘delete.response’
predict,FLXMRmgcv : predict_gam: no visible global function definition
  for ‘model.frame’
predict,FLXMRmgcv : predict_gam: no visible global function definition
  for ‘.checkMFClasses’
predict,FLXMRmgcv : predict_gam: no visible global function definition
  for ‘model.matrix’
rFLXM,FLXMRglm-FLXcomponent: no visible global function definition for
  ‘rnorm’
rFLXM,FLXMRglm-FLXcomponent: no visible global function definition for
  ‘rbinom’
rFLXM,FLXMRglm-FLXcomponent: no visible global function definition for
  ‘rpois’
rFLXM,FLXMRglm-FLXcomponent: no visible global function definition for
  ‘rgamma’
refit_optim,FLXM : <anonymous>: no visible global function definition
  for ‘pnorm’
refit_optim,FLXP : <anonymous>: no visible global function definition
  for ‘pnorm’
show,Coefmat: no visible global function definition for ‘printCoefmat’
show,stepFlexmix: no visible global function definition for ‘AIC’
show,stepFlexmix: no visible global function definition for ‘BIC’
simulate,FLXdist: no visible global function definition for ‘runif’
summary,FLXRmstep : <anonymous>: no visible global function definition
  for ‘printCoefmat’
summary,FLXRmstep : <anonymous>: no visible global function definition
  for ‘coef’
summary,FLXRmstep: no visible global function definition for ‘coef’
summary,FLXRmstep : <anonymous>: no visible global function definition
  for ‘pnorm’
summary,flexmix: no visible global function definition for ‘AIC’
summary,flexmix: no visible global function definition for ‘BIC’
Undefined global functions or variables:
  .checkMFClasses .getXlevels AIC BIC Gamma as.formula axisTicks
  binomial cluster coef cov.wt delete.response dnorm factanal glm.fit
  hcl hist lines lm.wfit matplot model.frame model.matrix
  model.response na.omit optim pnorm points poisson printCoefmat qnorm
  quantile rbinom resid rgamma rgb rmvnorm rnorm rpois runif terms text
  update update.formula var weighted.mean
Consider adding
  importFrom("grDevices", "axisTicks", "hcl", "rgb")
  importFrom("graphics", "hist", "lines", "matplot", "points", "text")
  importFrom("stats", ".checkMFClasses", ".getXlevels", "AIC", "BIC",
             "Gamma", "as.formula", "binomial", "coef", "cov.wt",
             "delete.response", "dnorm", "factanal", "glm.fit",
             "lm.wfit", "model.frame", "model.matrix", "model.response",
             "na.omit", "optim", "pnorm", "poisson", "printCoefmat",
             "qnorm", "quantile", "rbinom", "resid", "rgamma", "rnorm",
             "rpois", "runif", "terms", "update", "update.formula",
             "var", "weighted.mean")
to your NAMESPACE.

DONE
Status: 2 NOTEs

fullfact (1.0)

Maintainer: Aimee Lee Houde
Bug reports: Aimee Lee Houde

OK

gamm4 (0.2-3)

Maintainer: Simon Wood

checking R code for possible problems ... NOTE
gamm4: no visible global function definition for ‘gaussian’
gamm4: no visible global function definition for ‘packageVersion’
gamm4: no visible global function definition for ‘as.formula’
gamm4: no visible global function definition for ‘delete.response’
gamm4: no visible global function definition for ‘reformulate’
gamm4: no visible global function definition for ‘residuals’
gamm4: no visible global function definition for ‘deviance’
gamm4.oldwork: no visible global function definition for ‘deviance’
Undefined global functions or variables:
  as.formula delete.response deviance gaussian packageVersion
  reformulate residuals
Consider adding
  importFrom("stats", "as.formula", "delete.response", "deviance",
             "gaussian", "reformulate", "residuals")
  importFrom("utils", "packageVersion")
to your NAMESPACE.

DONE
Status: 1 NOTE

glmulti (1.0.7)

Maintainer: Vincent Calcagno

checking dependencies in R code ... 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.

checking R code for possible problems ... NOTE
Found an obsolete/platform-specific call in the following function:
  ‘plot.glmulti’
Found the platform-specific device:
  ‘windows’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
coef.glmulti: no visible global function definition for ‘coef’
coef.glmulti : <anonymous>: no visible global function definition for
  ‘qt’
coef.glmulti: no visible global function definition for ‘qnorm’
coef.glmulti: no visible global function definition for ‘qt’
plot.glmulti: no visible global function definition for ‘plot’
plot.glmulti: no visible global function definition for ‘abline’
plot.glmulti: no visible global function definition for ‘par’
plot.glmulti : <anonymous>: no visible global function definition for
  ‘delete.response’
plot.glmulti : <anonymous>: no visible global function definition for
  ‘terms’
plot.glmulti: no visible global function definition for ‘barplot’
predict.glmulti: no visible global function definition for ‘predict’
predict.glmulti : <anonymous>: no visible global function definition
  for ‘qt’
predict.glmulti: no visible global function definition for ‘qnorm’
predict.glmulti: no visible global function definition for ‘qt’
aic,ANY: no visible global function definition for ‘logLik’
aicc,ANY: no visible global function definition for ‘logLik’
aicc,ANY: no visible global function definition for ‘nobs’
bic,ANY: no visible global function definition for ‘logLik’
bic,ANY: no visible global function definition for ‘nobs’
consensus,list : <anonymous>: no visible global function definition for
  ‘as.formula’
getfit,coxph: no visible global function definition for ‘logLik’
glmulti,character-character-ANY-ANY: no visible global function
  definition for ‘model.frame’
glmulti,character-character-ANY-ANY: no visible global function
  definition for ‘as.formula’
glmulti,character-character-ANY-ANY: no visible global function
  definition for ‘logLik’
glmulti,character-character-ANY-ANY: no visible global function
  definition for ‘flush.console’
glmulti,character-character-ANY-ANY : <anonymous>: no visible global
  function definition for ‘as.formula’
glmulti,character-character-ANY-ANY: no visible global function
  definition for ‘plot’
glmulti,character-character-ANY-ANY: no visible global function
  definition for ‘abline’
glmulti,character-character-ANY-ANY: no visible binding for global
  variable ‘as.formula’
glmulti,character-character-ANY-ANY: no visible global function
  definition for ‘regsubsets’
glmulti,character-character-ANY-ANY: no visible global function
  definition for ‘resid’
glmulti,character-character-ANY-ANY: no visible global function
  definition for ‘lm’
glmulti,character-missing-ANY-missing: no visible global function
  definition for ‘as.formula’
glmulti,formula-missing-ANY-missing: no visible global function
  definition for ‘terms’
glmulti,formula-missing-ANY-missing: no visible global function
  definition for ‘as.formula’
glmulti,glm-missing-ANY-missing: no visible global function definition
  for ‘formula’
glmulti,list-ANY-ANY-ANY: no visible global function definition for
  ‘flush.console’
glmulti,list-ANY-ANY-ANY : modeval: no visible global function
  definition for ‘terms’
glmulti,list-ANY-ANY-ANY : modeval: no visible global function
  definition for ‘formula’
glmulti,list-ANY-ANY-ANY : modeval: no visible global function
  definition for ‘logLik’
glmulti,list-ANY-ANY-ANY: no visible binding for global variable
  ‘as.formula’
glmulti,lm-missing-ANY-missing: no visible global function definition
  for ‘formula’
qaic,ANY: no visible global function definition for ‘logLik’
qaicc,ANY: no visible global function definition for ‘logLik’
qaicc,ANY: no visible global function definition for ‘nobs’
write,glmulti: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  abline as.formula barplot coef delete.response flush.console formula
  lm logLik model.frame nobs par plot predict qnorm qt regsubsets resid
  terms write.table
Consider adding
  importFrom("graphics", "abline", "barplot", "par", "plot")
  importFrom("stats", "as.formula", "coef", "delete.response", "formula",
             "lm", "logLik", "model.frame", "nobs", "predict", "qnorm",
             "qt", "resid", "terms")
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE.

checking Rd line widths ... NOTE
Rd file 'glmulti.Rd':
  \usage lines wider than 90 characters:
     glmulti(y, xr, data, exclude = c(), name = "glmulti.analysis", intercept = TRUE, marginality = FALSE, bunch=30, chunk = 1, chunks = 1,
                     level = 2, minsize = 0, maxsize = -1, minK = 0, maxK = -1, method = "h", crit = "aic", confsetsize = 100, popsize = 100 ... [TRUNCATED]
  \examples lines wider than 100 characters:
     # It explains the general approach and shows how to use glmulti with mixed models from the lme4 package.
     # this procedure allows support of arbitrarily any fitting function, or the use of sophisticated constraints on the model structure

Rd file 'write.Rd':
  \usage lines wider than 90 characters:
     write(x, file = "data", ncolumns = if (is.character(x)) 1 else 5, append = FALSE, sep = " ")

These lines will be truncated in the PDF manual.

DONE
Status: 3 NOTEs

gmodels (2.16.2)

Maintainer: Gregory R. Warnes

OK

GWAF (2.2)

Maintainer: Ming-Huei Chen

checking R code for possible problems ... NOTE
GWplot: no visible global function definition for ‘bitmap’
GWplot: no visible global function definition for ‘par’
GWplot: no visible global function definition for ‘write.table’
GWplot: no visible binding for global variable ‘median’
GWplot: no visible global function definition for ‘plot’
GWplot: no visible global function definition for ‘axis’
GWplot: no visible global function definition for ‘points’
GWplot: no visible global function definition for ‘abline’
GWplot: no visible global function definition for ‘dev.off’
auto: no visible global function definition for ‘read.table’
geepack.lgst: no visible global function definition for ‘na.omit’
geepack.lgst : cor.snp: no visible global function definition for ‘sd’
geepack.lgst : cor.snp: no visible global function definition for ‘cor’
geepack.lgst: no visible global function definition for ‘fisher.test’
geepack.lgst: no visible global function definition for ‘chisq.test’
geepack.lgst: no visible global function definition for ‘as.formula’
geepack.lgst: no visible global function definition for ‘glm’
geepack.lgst: no visible binding for global variable ‘na.omit’
geepack.lgst: no visible global function definition for ‘pchisq’
geepack.lgst.batch : read.in.data: no visible global function
  definition for ‘read.table’
geepack.lgst.batch: no visible global function definition for ‘na.omit’
geepack.lgst.batch: no visible global function definition for ‘var’
geepack.lgst.batch: no visible binding for global variable ‘var’
geepack.lgst.batch: no visible global function definition for ‘cor’
geepack.lgst.batch: no visible global function definition for
  ‘write.table’
geepack.lgst.batch.imputed : read.in.data: no visible global function
  definition for ‘read.table’
geepack.lgst.batch.imputed: no visible global function definition for
  ‘na.omit’
geepack.lgst.batch.imputed: no visible global function definition for
  ‘var’
geepack.lgst.batch.imputed: no visible binding for global variable
  ‘var’
geepack.lgst.batch.imputed: no visible global function definition for
  ‘cor’
geepack.lgst.batch.imputed: no visible global function definition for
  ‘write.table’
geepack.lgst.imputed: no visible global function definition for
  ‘na.omit’
geepack.lgst.imputed : cor.snp: no visible global function definition
  for ‘sd’
geepack.lgst.imputed : cor.snp: no visible global function definition
  for ‘cor’
geepack.lgst.imputed: no visible global function definition for
  ‘chisq.test’
geepack.lgst.imputed: no visible global function definition for
  ‘as.formula’
geepack.lgst.imputed: no visible global function definition for ‘glm’
geepack.lgst.imputed: no visible binding for global variable ‘na.omit’
geepack.lgst.imputed: no visible global function definition for
  ‘pchisq’
geepack.lgst.int: no visible global function definition for ‘na.omit’
geepack.lgst.int : cor.snp: no visible global function definition for
  ‘sd’
geepack.lgst.int : cor.snp: no visible global function definition for
  ‘cor’
geepack.lgst.int: no visible global function definition for ‘cor’
geepack.lgst.int: no visible global function definition for
  ‘chisq.test’
geepack.lgst.int: no visible global function definition for ‘glm’
geepack.lgst.int: no visible global function definition for ‘pchisq’
geepack.lgst.int.batch : read.in.data: no visible global function
  definition for ‘read.table’
geepack.lgst.int.batch: no visible global function definition for
  ‘na.omit’
geepack.lgst.int.batch: no visible global function definition for ‘var’
geepack.lgst.int.batch: no visible binding for global variable ‘var’
geepack.lgst.int.batch: no visible global function definition for ‘cor’
geepack.lgst.int.batch: no visible global function definition for
  ‘write.table’
geepack.lgst.int.batch.imputed : read.in.data: no visible global
  function definition for ‘read.table’
geepack.lgst.int.batch.imputed: no visible global function definition
  for ‘na.omit’
geepack.lgst.int.batch.imputed: no visible global function definition
  for ‘var’
geepack.lgst.int.batch.imputed: no visible binding for global variable
  ‘var’
geepack.lgst.int.batch.imputed: no visible global function definition
  for ‘cor’
geepack.lgst.int.batch.imputed: no visible global function definition
  for ‘write.table’
geepack.lgst.int.imputed: no visible global function definition for
  ‘var’
geepack.lgst.int.imputed: no visible binding for global variable ‘var’
geepack.lgst.int.imputed: no visible global function definition for
  ‘na.omit’
geepack.lgst.int.imputed : cor.snp: no visible global function
  definition for ‘sd’
geepack.lgst.int.imputed : cor.snp: no visible global function
  definition for ‘cor’
geepack.lgst.int.imputed: no visible global function definition for
  ‘cor’
geepack.lgst.int.imputed: no visible global function definition for
  ‘glm’
geepack.lgst.int.imputed: no visible global function definition for
  ‘pchisq’
geepack.quant.batch : cor.snp: no visible global function definition
  for ‘sd’
geepack.quant.batch : cor.snp: no visible global function definition
  for ‘cor’
geepack.quant.batch : read.in.data: no visible global function
  definition for ‘read.table’
geepack.quant.batch: no visible global function definition for
  ‘na.omit’
geepack.quant.batch: no visible global function definition for ‘var’
geepack.quant.batch: no visible binding for global variable ‘var’
geepack.quant.batch: no visible global function definition for ‘cor’
geepack.quant.batch: no visible global function definition for ‘pchisq’
geepack.quant.batch: no visible global function definition for
  ‘write.table’
geepack.quant.batch.imputed : cor.snp: no visible global function
  definition for ‘sd’
geepack.quant.batch.imputed : cor.snp: no visible global function
  definition for ‘cor’
geepack.quant.batch.imputed : read.in.data: no visible global function
  definition for ‘read.table’
geepack.quant.batch.imputed: no visible global function definition for
  ‘na.omit’
geepack.quant.batch.imputed: no visible global function definition for
  ‘var’
geepack.quant.batch.imputed: no visible binding for global variable
  ‘var’
geepack.quant.batch.imputed: no visible global function definition for
  ‘cor’
geepack.quant.batch.imputed: no visible global function definition for
  ‘pchisq’
geepack.quant.batch.imputed: no visible global function definition for
  ‘write.table’
geepack.quant.int.batch : cor.snp: no visible global function
  definition for ‘sd’
geepack.quant.int.batch : cor.snp: no visible global function
  definition for ‘cor’
geepack.quant.int.batch : read.in.data: no visible global function
  definition for ‘read.table’
geepack.quant.int.batch: no visible global function definition for
  ‘na.omit’
geepack.quant.int.batch: no visible global function definition for
  ‘pchisq’
geepack.quant.int.batch: no visible global function definition for
  ‘write.table’
geepack.quant.int.batch.imputed : cor.snp: no visible global function
  definition for ‘sd’
geepack.quant.int.batch.imputed : cor.snp: no visible global function
  definition for ‘cor’
geepack.quant.int.batch.imputed : read.in.data: no visible global
  function definition for ‘read.table’
geepack.quant.int.batch.imputed: no visible global function definition
  for ‘na.omit’
geepack.quant.int.batch.imputed: no visible global function definition
  for ‘pchisq’
geepack.quant.int.batch.imputed: no visible global function definition
  for ‘write.table’
glmm.lgst: no visible global function definition for ‘na.omit’
glmm.lgst : cor.snp: no visible global function definition for ‘sd’
glmm.lgst : cor.snp: no visible global function definition for ‘cor’
glmm.lgst: no visible global function definition for ‘fisher.test’
glmm.lgst: no visible global function definition for ‘chisq.test’
glmm.lgst: no visible global function definition for ‘coef’
glmm.lgst: no visible global function definition for ‘pchisq’
glmm.lgst: no visible global function definition for ‘vcov’
glmm.lgst.batch : read.in.data: no visible global function definition
  for ‘read.table’
glmm.lgst.batch: no visible global function definition for ‘na.omit’
glmm.lgst.batch: no visible global function definition for ‘var’
glmm.lgst.batch: no visible binding for global variable ‘var’
glmm.lgst.batch: no visible global function definition for ‘cor’
glmm.lgst.batch: no visible global function definition for
  ‘write.table’
lmeVpack.batch.imputed : cor.snp: no visible global function definition
  for ‘sd’
lmeVpack.batch.imputed : cor.snp: no visible global function definition
  for ‘cor’
lmeVpack.batch.imputed : read.in.data: no visible global function
  definition for ‘read.table’
lmeVpack.batch.imputed: no visible global function definition for
  ‘na.omit’
lmeVpack.batch.imputed: no visible global function definition for ‘var’
lmeVpack.batch.imputed: no visible binding for global variable ‘var’
lmeVpack.batch.imputed: no visible global function definition for ‘cor’
lmeVpack.batch.imputed: no visible binding for global variable
  ‘na.omit’
lmeVpack.batch.imputed: no visible global function definition for
  ‘pchisq’
lmeVpack.batch.imputed: no visible global function definition for
  ‘write.table’
lmepack.batch : cor.snp: no visible global function definition for ‘sd’
lmepack.batch : cor.snp: no visible global function definition for
  ‘cor’
lmepack.batch : read.in.data: no visible global function definition for
  ‘read.table’
lmepack.batch: no visible global function definition for ‘na.omit’
lmepack.batch: no visible global function definition for ‘var’
lmepack.batch: no visible binding for global variable ‘var’
lmepack.batch: no visible global function definition for ‘cor’
lmepack.batch: no visible binding for global variable ‘na.omit’
lmepack.batch: no visible global function definition for ‘pchisq’
lmepack.batch: no visible global function definition for ‘write.table’
lmepack.batch.imputed : cor.snp: no visible global function definition
  for ‘sd’
lmepack.batch.imputed : cor.snp: no visible global function definition
  for ‘cor’
lmepack.batch.imputed : read.in.data: no visible global function
  definition for ‘read.table’
lmepack.batch.imputed: no visible global function definition for
  ‘na.omit’
lmepack.batch.imputed: no visible global function definition for ‘var’
lmepack.batch.imputed: no visible binding for global variable ‘var’
lmepack.batch.imputed: no visible global function definition for ‘cor’
lmepack.batch.imputed: no visible binding for global variable ‘na.omit’
lmepack.batch.imputed: no visible global function definition for
  ‘pchisq’
lmepack.batch.imputed: no visible global function definition for
  ‘write.table’
lmepack.int.batch : cor.snp: no visible global function definition for
  ‘sd’
lmepack.int.batch : cor.snp: no visible global function definition for
  ‘cor’
lmepack.int.batch : read.in.data: no visible global function definition
  for ‘read.table’
lmepack.int.batch: no visible global function definition for ‘na.omit’
lmepack.int.batch: no visible binding for global variable ‘na.omit’
lmepack.int.batch: no visible global function definition for ‘pchisq’
lmepack.int.batch: no visible global function definition for
  ‘write.table’
lmepack.int.batch.imputed : cor.snp: no visible global function
  definition for ‘sd’
lmepack.int.batch.imputed : cor.snp: no visible global function
  definition for ‘cor’
lmepack.int.batch.imputed : read.in.data: no visible global function
  definition for ‘read.table’
lmepack.int.batch.imputed: no visible global function definition for
  ‘na.omit’
lmepack.int.batch.imputed: no visible binding for global variable
  ‘na.omit’
lmepack.int.batch.imputed: no visible global function definition for
  ‘pchisq’
lmepack.int.batch.imputed: no visible global function definition for
  ‘write.table’
qq: no visible global function definition for ‘bitmap’
qq: no visible global function definition for ‘na.omit’
qq: no visible global function definition for ‘median’
qq: no visible global function definition for ‘qchisq’
qq: no visible global function definition for ‘par’
qq: no visible global function definition for ‘qqplot’
qq: no visible global function definition for ‘abline’
qq: no visible global function definition for ‘text’
qq: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  abline as.formula axis bitmap chisq.test coef cor dev.off fisher.test
  glm median na.omit par pchisq plot points qchisq qqplot read.table sd
  text var vcov write.table
Consider adding
  importFrom("grDevices", "bitmap", "dev.off")
  importFrom("graphics", "abline", "axis", "par", "plot", "points",
             "text")
  importFrom("stats", "as.formula", "chisq.test", "coef", "cor",
             "fisher.test", "glm", "median", "na.omit", "pchisq",
             "qchisq", "qqplot", "sd", "var", "vcov")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE.

DONE
Status: 1 NOTE

hamlet (0.9.4-2)

Maintainer: Teemu Daniel Laajala

OK

HLMdiag (0.3.1)

Maintainer: Adam Loy
Bug reports: https://github.com/aloy/HLMdiag/issues

OK

hnp (1.1)

Maintainer: Rafael de Andrade Moral

OK

HSAUR2 (1.1-14)

Maintainer: Torsten Hothorn

OK

HSAUR3 (1.0-5)

Maintainer: Torsten Hothorn

OK

HSAUR (1.3-7)

Maintainer: Torsten Hothorn

OK

iccbeta (1.0)

Maintainer: Steven Andrew Culpepper

OK

inferference (0.4.62)

Maintainer: Bradley Saul

checking R code for possible problems ... NOTE
interference: no visible global function definition for ‘binomial’
interference: no visible global function definition for ‘terms’
interference: no visible global function definition for ‘coef’
interference: no visible global function definition for ‘model.matrix’
ipw_interference: no visible binding for global variable ‘integrate’
log_likelihood: no visible binding for global variable ‘integrate’
log_likelihood: no visible global function definition for ‘is’
logit_integrand: no visible global function definition for ‘plogis’
logit_integrand: no visible global function definition for ‘dbinom’
logit_integrand: no visible global function definition for ‘dnorm’
print.interference: no visible global function definition for
  ‘quantile’
score_calc: no visible binding for global variable ‘integrate’
score_calc : <anonymous>: no visible global function definition for
  ‘is’
score_matrix: no visible binding for global variable ‘integrate’
wght_calc: no visible binding for global variable ‘integrate’
wght_calc: no visible global function definition for ‘is’
wght_deriv_calc: no visible binding for global variable ‘integrate’
wght_deriv_calc : <anonymous>: no visible global function definition
  for ‘is’
Undefined global functions or variables:
  binomial coef dbinom dnorm integrate is model.matrix plogis quantile
  terms
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "binomial", "coef", "dbinom", "dnorm", "integrate",
             "model.matrix", "plogis", "quantile", "terms")
to your NAMESPACE (and ensure that your DESCRIPTION Imports field
contains 'methods').

DONE
Status: 1 NOTE

influence.ME (0.9-6)

Maintainer: Rense Nieuwenhuis

OK

irtrees (0.1.0)

Maintainer: Ivailo Partchev

checking R code for possible problems ... NOTE
dendrify: no visible binding for global variable ‘item’
dendrify: no visible binding for global variable ‘node’
dendrify: no visible binding for global variable ‘value’
exogenize: no visible binding for global variable ‘item’
Undefined global functions or variables:
  item node value

DONE
Status: 1 NOTE

JAGUAR (3.0.0)

Maintainer: Chaitanya Acharya

OK

KFAS (1.2.0)

Maintainer: Jouni Helske
Bug reports: https://github.com/helske/KFAS/issues

OK

kulife (0.1-14)

Maintainer: Claus Ekstrom

checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.

checking dependencies in R code ... NOTE
'library' or 'require' call to ‘XML’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.

checking R code for possible problems ... NOTE
auc: no visible global function definition for ‘approx’
kulife.colors: no visible global function definition for ‘palette’
rootonorm: no visible global function definition for ‘sd’
rootonorm: no visible global function definition for ‘hist’
rootonorm: no visible global function definition for ‘pnorm’
rootonorm: no visible global function definition for ‘dnorm’
rootonorm: no visible global function definition for ‘plot’
rootonorm: no visible global function definition for ‘rect’
rootonorm: no visible global function definition for ‘lines’
rootonorm: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline approx dnorm hist lines palette plot pnorm rect sd
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "abline", "hist", "lines", "plot", "rect")
  importFrom("stats", "approx", "dnorm", "pnorm", "sd")
to your NAMESPACE.

DONE
Status: 3 NOTEs

kyotil (2015.11-13)

Maintainer: Youyi Fong

OK

languageR (1.4.1)

Maintainer: R. H. Baayen

checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.

checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘MASS’ ‘lattice’ ‘lme4’ ‘rms’ ‘zipfR’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.

checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  head.growth tail.growth
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.

checking R code for possible problems ... NOTE
acf.fnc: no visible global function definition for ‘acf’
acf.fnc: no visible global function definition for ‘xyplot’
acf.fnc : <anonymous>: no visible global function definition for
  ‘panel.abline’
acf.fnc : <anonymous>: no visible global function definition for
  ‘panel.number’
acf.fnc : <anonymous>: no visible global function definition for
  ‘panel.xyplot’
acf.fnc: no visible global function definition for ‘strip.custom’
collin.fnc : std.fnc: no visible global function definition for ‘var’
compare.richness.fnc: no visible global function definition for ‘N’
compare.richness.fnc: no visible global function definition for ‘lnre’
compare.richness.fnc: no visible global function definition for ‘VV’
compare.richness.fnc: no visible global function definition for ‘VVm’
compare.richness.fnc: no visible global function definition for ‘V’
compare.richness.fnc: no visible global function definition for ‘Vm’
compare.richness.fnc: no visible global function definition for ‘pnorm’
corsup.fnc: no visible global function definition for ‘text’
growth.fnc: no visible binding for global variable ‘alice’
growth.fnc: no visible global function definition for ‘coef’
growth.fnc: no visible global function definition for ‘lm’
growth2vgc.fnc: no visible global function definition for ‘vgc’
herdan.fnc: no visible global function definition for ‘coef’
herdan.fnc: no visible global function definition for ‘lm’
item.fnc: no visible global function definition for ‘lm’
items.quasif.fnc: no visible global function definition for ‘lm’
lmerPlotInt.fnc: no visible global function definition for ‘isLMM’
lmerPlotInt.fnc: no visible global function definition for ‘isGLMM’
lmerPlotInt.fnc: no visible global function definition for ‘fixef’
lmerPlotInt.fnc: no visible global function definition for ‘quantile’
lmerPlotInt.fnc: no visible global function definition for ‘rnorm’
lmerPlotInt.fnc: no visible global function definition for ‘par’
lmerPlotInt.fnc: no visible global function definition for ‘persp’
lmerPlotInt.fnc: no visible global function definition for ‘formula’
lmerPlotInt.fnc: no visible global function definition for ‘contour’
lmerPlotInt.fnc: no visible global function definition for ‘matplot’
lmerPlotInt.fnc: no visible global function definition for ‘text’
lmerPlotInt.fnc: no visible global function definition for ‘mtext’
lmerPlotInt.fnc: no visible global function definition for ‘image’
lmerPlotInt.fnc: no visible global function definition for
  ‘heat.colors’
make.reg.fnc: no visible global function definition for ‘rnorm’
makeDefaultMatrix.fnc: no visible global function definition for
  ‘fixef’
makeDefaultMatrix.fnc: no visible global function definition for
  ‘median’
makeSplineData.fnc: no visible global function definition for ‘rnorm’
mvrnormplot.fnc: no visible global function definition for ‘mvrnorm’
mvrnormplot.fnc: no visible global function definition for ‘plot’
mvrnormplot.fnc: no visible global function definition for ‘abline’
mvrnormplot.fnc: no visible global function definition for ‘lm’
mvrnormplot.fnc: no visible global function definition for ‘mtext’
mvrnormplot.fnc: no visible global function definition for ‘cor’
pairscor.fnc : panel.hist: no visible global function definition for
  ‘par’
pairscor.fnc : panel.hist: no visible global function definition for
  ‘rect’
pairscor.fnc : pairscor.lower: no visible global function definition
  for ‘par’
pairscor.fnc : pairscor.lower: no visible global function definition
  for ‘cor.test’
pairscor.fnc : pairscor.lower: no visible global function definition
  for ‘text’
pairscor.fnc : pairscor.lower: no visible global function definition
  for ‘lines’
pairscor.fnc : panel.smooth2: no visible global function definition for
  ‘par’
pairscor.fnc : panel.smooth2: no visible global function definition for
  ‘points’
pairscor.fnc : panel.smooth2: no visible global function definition for
  ‘lines’
pairscor.fnc: no visible global function definition for ‘pairs’
plot.corres: no visible global function definition for ‘plot’
plot.corres: no visible global function definition for ‘lines’
plot.corres: no visible global function definition for ‘mtext’
plot.corres: no visible global function definition for ‘text’
plot.corres: no visible binding for global variable ‘quantile’
plot.growth: no visible global function definition for ‘par’
plot.growth: no visible global function definition for ‘plot’
plotAll.fnc: no visible global function definition for ‘plot’
plotAll.fnc: no visible global function definition for ‘lines’
plotAll.fnc: no visible global function definition for ‘text’
plotAll.fnc: no visible global function definition for ‘mtext’
plotAll.fnc: no visible global function definition for ‘points’
plotLMER.fnc: no visible binding for global variable ‘plogis’
plotLMER.fnc: no visible global function definition for ‘ranef’
plotlogistic.fit.fnc: no visible global function definition for ‘terms’
plotlogistic.fit.fnc: no visible global function definition for
  ‘fitted’
plotlogistic.fit.fnc: no visible global function definition for
  ‘formula’
plotlogistic.fit.fnc: no visible global function definition for
  ‘predict’
plotlogistic.fit.fnc: no visible global function definition for ‘cut2’
plotlogistic.fit.fnc: no visible global function definition for
  ‘equal.count’
plotlogistic.fit.fnc: no visible global function definition for ‘plot’
plotlogistic.fit.fnc: no visible global function definition for
  ‘abline’
plotlogistic.fit.fnc: no visible global function definition for
  ‘symbols’
plotlogistic.fit.fnc: no visible global function definition for
  ‘points’
plotlogistic.fit.fnc: no visible global function definition for ‘mtext’
plotlogistic.fit.fnc: no visible global function definition for ‘cor’
preparePredictor.fnc: no visible global function definition for ‘fixef’
preparePredictor.fnc: no visible global function definition for ‘ranef’
quasiF.fnc: no visible global function definition for ‘pf’
quasiFsim.fnc: no visible global function definition for ‘lm’
quasiFsim.fnc: no visible global function definition for ‘anova’
shadenormal.fnc: no visible global function definition for ‘plot’
shadenormal.fnc: no visible global function definition for ‘dnorm’
shadenormal.fnc: no visible global function definition for ‘abline’
shadenormal.fnc: no visible global function definition for ‘qnorm’
shadenormal.fnc: no visible global function definition for ‘polygon’
simulateLatinsquare.fnc: no visible global function definition for
  ‘lmer’
simulateLatinsquare.fnc: no visible global function definition for
  ‘rnorm’
simulateLatinsquare.fnc: no visible global function definition for ‘sd’
simulateLatinsquare.fnc: no visible global function definition for
  ‘ranef’
simulateLatinsquare.fnc: no visible global function definition for
  ‘relevel’
simulateLatinsquare.fnc: no visible global function definition for
  ‘fixef’
simulateLatinsquare.fnc: no visible global function definition for
  ‘resid’
simulateQuasif.fnc: no visible global function definition for ‘lmer’
simulateQuasif.fnc: no visible global function definition for ‘mvrnorm’
simulateQuasif.fnc: no visible global function definition for ‘cov’
simulateQuasif.fnc: no visible global function definition for ‘ranef’
simulateQuasif.fnc: no visible global function definition for ‘rnorm’
simulateQuasif.fnc: no visible global function definition for ‘sd’
simulateQuasif.fnc: no visible global function definition for ‘fixef’
simulateQuasif.fnc: no visible global function definition for ‘relevel’
simulateQuasif.fnc: no visible global function definition for ‘resid’
simulateRegression.fnc: no visible global function definition for
  ‘lmer’
simulateRegression.fnc: no visible global function definition for
  ‘VarCorr’
simulateRegression.fnc: no visible global function definition for
  ‘lmList’
simulateRegression.fnc: no visible global function definition for
  ‘coef’
simulateRegression.fnc: no visible binding for global variable ‘t.test’
subjects.latinsquare.fnc: no visible global function definition for
  ‘lm’
subjects.latinsquare.fnc: no visible global function definition for
  ‘anova’
subjects.latinsquare.fnc: no visible global function definition for
  ‘pf’
subjects.quasif.fnc: no visible global function definition for ‘lm’
subjects.quasif.fnc: no visible global function definition for ‘anova’
subjects.quasif.fnc: no visible global function definition for ‘pf’
text2spc.fnc: no visible global function definition for ‘spc’
xylowess.fnc: no visible global function definition for ‘xyplot’
xylowess.fnc : <anonymous>: no visible global function definition for
  ‘panel.grid’
xylowess.fnc : <anonymous>: no visible global function definition for
  ‘panel.xyplot’
xylowess.fnc : <anonymous>: no visible global function definition for
  ‘panel.loess’
Undefined global functions or variables:
  N V VV VVm VarCorr Vm abline acf alice anova coef contour cor
  cor.test cov cut2 dnorm equal.count fitted fixef formula heat.colors
  image isGLMM isLMM lines lm lmList lmer lnre matplot median mtext
  mvrnorm pairs panel.abline panel.grid panel.loess panel.number
  panel.xyplot par persp pf plogis plot pnorm points polygon predict
  qnorm quantile ranef rect relevel resid rnorm sd spc strip.custom
  symbols t.test terms text var vgc xyplot
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "abline", "contour", "image", "lines",
             "matplot", "mtext", "pairs", "par", "persp", "plot",
             "points", "polygon", "rect", "symbols", "text")
  importFrom("stats", "acf", "anova", "coef", "cor", "cor.test", "cov",
             "dnorm", "fitted", "formula", "lm", "median", "pf",
             "plogis", "pnorm", "predict", "qnorm", "quantile",
             "relevel", "resid", "rnorm", "sd", "t.test", "terms", "var")
to your NAMESPACE.

DONE
Status: 4 NOTEs

lava (1.4.1)

Maintainer: Klaus K. Holst

checking R code for possible problems ... NOTE
Col: no visible global function definition for ‘col2rgb’
Col: no visible global function definition for ‘colors’
Col: no visible global function definition for ‘par’
Col: no visible global function definition for ‘plot.new’
Col: no visible global function definition for ‘title’
Col: no visible global function definition for ‘rect’
Col: no visible global function definition for ‘text’
Col: no visible global function definition for ‘locator’
Col : <anonymous>: no visible binding for global variable ‘rgb’
Col : <anonymous>: no visible global function definition for ‘col2rgb’
Graph.lvm: no visible global function definition for ‘plot’
click.default: no visible global function definition for ‘xy.coords’
click.default: no visible global function definition for ‘identify’
click.default: no visible global function definition for ‘points’
click.default: no visible global function definition for ‘text’
colorbar: no visible global function definition for ‘rainbow’
colorbar: no visible global function definition for ‘rect’
colorbar: no visible global function definition for ‘text’
confband: no visible global function definition for ‘segments’
confband: no visible global function definition for ‘points’
devcoords: no visible global function definition for ‘par’
edgelabels.graphNEL: no visible global function definition for ‘as’
finalize.lvm: no visible global function definition for ‘as’
finalize.lvm: no visible global function definition for ‘new’
forestplot: no visible global function definition for ‘par’
forestplot: no visible global function definition for ‘layout’
forestplot: no visible global function definition for ‘plot’
forestplot: no visible global function definition for ‘box’
forestplot: no visible global function definition for ‘axis’
forestplot: no visible global function definition for ‘abline’
forestplot: no visible global function definition for ‘mtext’
forestplot: no visible global function definition for ‘plot.new’
forestplot: no visible global function definition for ‘plot.window’
fplot: no visible global function definition for ‘topo.colors’
graph2lvm: no visible global function definition for ‘as’
idplot: no visible global function definition for ‘plot’
images: no visible global function definition for ‘layout’
images: no visible global function definition for ‘par’
images: no visible global function definition for ‘plot.new’
images: no visible global function definition for ‘plot.window’
images: no visible global function definition for ‘text’
img: no visible global function definition for ‘gray.colors’
img: no visible global function definition for ‘image’
img: no visible global function definition for ‘axis’
img: no visible global function definition for ‘title’
lmerplot: no visible global function definition for ‘par’
lmerplot: no visible global function definition for ‘gray.colors’
lmerplot: no visible global function definition for ‘image’
lmerplot: no visible global function definition for ‘plot’
lmerplot: no visible global function definition for ‘points’
lmerplot: no visible global function definition for ‘lines’
matrices.lvm: no visible global function definition for ‘as’
moments.lvm: no visible global function definition for ‘as’
mypal: no visible global function definition for ‘palette’
plot.estimate: no visible global function definition for ‘plot’
plot.estimate: no visible global function definition for ‘lines’
plot.lvm: no visible global function definition for ‘plot’
plot.lvmfit: no visible global function definition for ‘plot’
plot.multigroup: no visible global function definition for ‘plot’
plot.multigroupfit: no visible global function definition for ‘plot’
plotConf: no visible global function definition for ‘box’
plotConf: no visible global function definition for ‘axis’
plotConf: no visible global function definition for ‘lines’
plotConf: no visible global function definition for ‘polygon’
plotConf: no visible global function definition for ‘points’
plotConf0: no visible binding for global variable ‘plot’
plotConf0: no visible global function definition for ‘box’
plotConf0: no visible global function definition for ‘axis’
plotConf0: no visible global function definition for ‘lines’
plotConf0: no visible global function definition for ‘polygon’
plotConf0: no visible global function definition for ‘points’
reindex: no visible global function definition for ‘as’
spaghetti: no visible global function definition for ‘matplot’
spaghetti: no visible global function definition for ‘lines’
subgraph: no visible global function definition for ‘new’
surface: no visible global function definition for ‘topo.colors’
surface: no visible global function definition for ‘colorRampPalette’
surface: no visible global function definition for ‘heat.colors’
surface: no visible binding for global variable ‘par’
surface: no visible global function definition for ‘par’
surface: no visible binding for global variable ‘contour.default’
Undefined global functions or variables:
  abline as axis box col2rgb colorRampPalette colors contour.default
  gray.colors heat.colors identify image layout lines locator matplot
  mtext new palette par plot plot.new plot.window points polygon
  rainbow rect rgb segments text title topo.colors xy.coords
Consider adding
  importFrom("grDevices", "col2rgb", "colorRampPalette", "colors",
             "gray.colors", "heat.colors", "palette", "rainbow", "rgb",
             "topo.colors", "xy.coords")
  importFrom("graphics", "abline", "axis", "box", "contour.default",
             "identify", "image", "layout", "lines", "locator",
             "matplot", "mtext", "par", "plot", "plot.new",
             "plot.window", "points", "polygon", "rect", "segments",
             "text", "title")
  importFrom("methods", "as", "new")
to your NAMESPACE (and ensure that your DESCRIPTION Imports field
contains 'methods').

DONE
Status: 1 NOTE

likelihoodAsy (0.40)

Maintainer: Ruggero Bellio

checking R code for possible problems ... NOTE
.mpl: no visible global function definition for ‘nlminb’
.mpl: no visible global function definition for ‘txtProgressBar’
.mpl: no visible global function definition for ‘setTxtProgressBar’
plot.rstarci: no visible global function definition for ‘par’
plot.rstarci: no visible global function definition for ‘plot’
plot.rstarci: no visible global function definition for ‘grid’
plot.rstarci: no visible global function definition for ‘lines’
plot.rstarci: no visible global function definition for ‘spline’
plot.rstarci: no visible global function definition for ‘points’
plot.rstarci: no visible global function definition for ‘qnorm’
plot.rstarci: no visible global function definition for ‘axis’
plot.rstarci: no visible global function definition for ‘mtext’
plot.rstarci: no visible global function definition for ‘legend’
rstar: no visible global function definition for ‘nlminb’
rstar: no visible global function definition for ‘txtProgressBar’
rstar: no visible global function definition for ‘setTxtProgressBar’
rstar.ci: no visible global function definition for ‘nlminb’
rstar.ci: no visible global function definition for ‘qnorm’
rstar.ci: no visible global function definition for ‘smooth.spline’
rstar.ci: no visible global function definition for ‘predict’
summary.rstar: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  axis grid legend lines mtext nlminb par plot pnorm points predict
  qnorm setTxtProgressBar smooth.spline spline txtProgressBar
Consider adding
  importFrom("graphics", "axis", "grid", "legend", "lines", "mtext",
             "par", "plot", "points")
  importFrom("stats", "nlminb", "pnorm", "predict", "qnorm",
             "smooth.spline", "spline")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE.

DONE
Status: 1 NOTE

LMERConvenienceFunctions (2.10)

Maintainer: "Antoine Tremblay, Dalhousie University"

checking R code for possible problems ... NOTE
adjust.se: no visible global function definition for ‘qt’
bfFixefLMER_F.fnc: no visible global function definition for ‘anova’
bfFixefLMER_F.fnc: no visible global function definition for ‘na.omit’
bfFixefLMER_t.fnc: no visible global function definition for ‘anova’
bfFixefLMER_t.fnc: no visible global function definition for ‘rnorm’
bfFixefLMER_t.fnc: no visible global function definition for ‘is’
ffRanefLMER.fnc: no visible global function definition for ‘rnorm’
ffRanefLMER.fnc: no visible global function definition for ‘anova’
mcp.fnc: no visible global function definition for ‘par’
mcp.fnc: no visible global function definition for ‘resid’
mcp.fnc: no visible global function definition for ‘plot’
mcp.fnc: no visible global function definition for ‘density’
mcp.fnc: no visible global function definition for ‘qqnorm’
mcp.fnc: no visible global function definition for ‘qqline’
mcp.fnc: no visible global function definition for ‘abline’
mcposthoc.fnc : my.update: no visible global function definition for
  ‘relevel’
mcposthoc.fnc: no visible global function definition for ‘pt’
mcposthoc.fnc : my.mc.update: no visible global function definition for
  ‘relevel’
pamer.fnc: no visible global function definition for ‘anova’
pamer.fnc: no visible global function definition for ‘pf’
perSubjectTrim.fnc: no visible binding for global variable ‘sd’
perSubjectTrim.fnc: no visible global function definition for ‘na.omit’
plotDensity3d.fnc: no visible global function definition for ‘density’
plotDensity3d.fnc: no visible global function definition for
  ‘heat.colors’
plotDensity3d.fnc: no visible global function definition for
  ‘topo.colors’
plotDensity3d.fnc: no visible global function definition for
  ‘cm.colors’
plotDensity3d.fnc: no visible global function definition for
  ‘terrain.colors’
plotDensity3d.fnc: no visible global function definition for ‘gray’
plotDensity3d.fnc: no visible global function definition for ‘contour’
plotDensity3d.fnc: no visible global function definition for ‘box’
plotDensity3d.fnc: no visible global function definition for
  ‘colorRampPalette’
plotDensity3d.fnc: no visible global function definition for ‘persp’
plotLMER.fnc : makeDefaultMatrix.fnc: no visible global function
  definition for ‘median’
plotLMER.fnc : plotAll.fnc: no visible global function definition for
  ‘plot’
plotLMER.fnc : plotAll.fnc: no visible global function definition for
  ‘lines’
plotLMER.fnc : plotAll.fnc: no visible global function definition for
  ‘text’
plotLMER.fnc : plotAll.fnc: no visible global function definition for
  ‘mtext’
plotLMER.fnc : plotAll.fnc: no visible global function definition for
  ‘points’
plotLMER.fnc: no visible global function definition for ‘is’
plotLMER.fnc: no visible binding for global variable ‘plogis’
plotLMER3d.fnc : makeDefaultMatrix.fnc: no visible global function
  definition for ‘median’
plotLMER3d.fnc : plotLMERTweaked: no visible global function definition
  for ‘is’
plotLMER3d.fnc : plotLMERTweaked: no visible binding for global
  variable ‘plogis’
plotLMER3d.fnc: no visible global function definition for ‘quantile’
plotLMER3d.fnc: no visible global function definition for ‘heat.colors’
plotLMER3d.fnc: no visible global function definition for ‘topo.colors’
plotLMER3d.fnc: no visible global function definition for ‘cm.colors’
plotLMER3d.fnc: no visible global function definition for
  ‘terrain.colors’
plotLMER3d.fnc: no visible global function definition for ‘gray’
plotLMER3d.fnc: no visible global function definition for ‘jpeg’
plotLMER3d.fnc: no visible global function definition for ‘dev.off’
plotLMER3d.fnc: no visible global function definition for ‘contour’
plotLMER3d.fnc: no visible global function definition for ‘points’
plotLMER3d.fnc: no visible global function definition for ‘box’
plotLMER3d.fnc: no visible global function definition for
  ‘colorRampPalette’
plotLMER3d.fnc: no visible global function definition for ‘persp’
plotLMER3d.fnc: no visible global function definition for ‘trans3d’
plotRaw3d.fnc: no visible global function definition for ‘heat.colors’
plotRaw3d.fnc: no visible global function definition for ‘topo.colors’
plotRaw3d.fnc: no visible global function definition for ‘cm.colors’
plotRaw3d.fnc: no visible global function definition for
  ‘terrain.colors’
plotRaw3d.fnc: no visible global function definition for ‘gray’
plotRaw3d.fnc: no visible global function definition for ‘contour’
plotRaw3d.fnc: no visible global function definition for ‘dev.new’
plotRaw3d.fnc: no visible global function definition for
  ‘colorRampPalette’
plotRaw3d.fnc: no visible global function definition for ‘dev.off’
plotRaw3d.fnc: no visible global function definition for ‘persp’
relLik: no visible global function definition for ‘AIC’
relLik: no visible global function definition for ‘BIC’
romr.fnc: no visible global function definition for ‘resid’
summary.mcposthoc: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  AIC BIC abline anova box cm.colors colorRampPalette contour density
  dev.new dev.off gray heat.colors is jpeg lines median mtext na.omit
  par persp pf plogis plot points pt qqline qqnorm qt quantile relevel
  resid rnorm sd terrain.colors text topo.colors trans3d
Consider adding
  importFrom("grDevices", "cm.colors", "colorRampPalette", "dev.new",
             "dev.off", "gray", "heat.colors", "jpeg", "terrain.colors",
             "topo.colors", "trans3d")
  importFrom("graphics", "abline", "box", "contour", "lines", "mtext",
             "par", "persp", "plot", "points", "text")
  importFrom("methods", "is")
  importFrom("stats", "AIC", "BIC", "anova", "density", "median",
             "na.omit", "pf", "plogis", "pt", "qqline", "qqnorm", "qt",
             "quantile", "relevel", "resid", "rnorm", "sd")
to your NAMESPACE (and ensure that your DESCRIPTION Imports field
contains 'methods').

DONE
Status: 1 NOTE

lmerTest (2.0-29)

Maintainer: Alexandra Kuznetsova

checking tests ... ERROR
Running the tests in ‘tests/envir.R’ failed.
Last 13 lines of output:
  liking ~ pig.type + pig.type:landro + pig.type:lskatol + (1 | 
      pig) + (1 | consumer) + gender
  <environment: 0x7343170>
  [1] "formula"
  fixed-effect model matrix is rank deficient so dropping 2 columns / coefficients
  > ls2 <- lapply(mlist, anova, type=1)
  anova from lme4 is returned
  some computational error has occurred in lmerTest
  anova from lme4 is returned
  some computational error has occurred in lmerTest
  > stopifnot("Pr(>F)" %in% colnames(ls2[[1]]))
  Error: "Pr(>F)" %in% colnames(ls2[[1]]) is not TRUE
  Execution halted

DONE
Status: 1 ERROR

lmSupport (2.9.2)

Maintainer: John Curtin

checking R code for possible problems ... NOTE
dfReadDat: no visible global function definition for ‘read.table’
dfWriteDat: no visible global function definition for ‘write.table’
figConfidenceBand: no visible global function definition for ‘col2rgb’
figConfidenceBand: no visible global function definition for ‘polygon’
figStripChart: no visible global function definition for ‘par’
figStripChart: no visible global function definition for ‘stripchart’
modelAssumptions: no visible global function definition for ‘dev.new’
modelAssumptions: no visible global function definition for ‘par’
modelAssumptions: no visible global function definition for ‘plot’
modelAssumptions: no visible global function definition for ‘density’
modelAssumptions: no visible global function definition for ‘rstudent’
modelAssumptions: no visible global function definition for ‘lines’
modelAssumptions: no visible global function definition for ‘dnorm’
modelAssumptions: no visible global function definition for ‘sd’
modelAssumptions: no visible global function definition for ‘abline’
modelBoxCox: no visible global function definition for ‘pchisq’
modelCaseAnalysis: no visible global function definition for ‘par’
modelCaseAnalysis: no visible global function definition for ‘plot’
modelCaseAnalysis: no visible global function definition for ‘hist’
modelCaseAnalysis: no visible global function definition for ‘points’
modelCaseAnalysis: no visible global function definition for ‘abline’
modelCaseAnalysis: no visible global function definition for ‘sd’
modelCaseAnalysis: no visible global function definition for ‘IQR’
modelCaseAnalysis: no visible global function definition for ‘median’
modelCaseAnalysis: no visible global function definition for ‘identify’
modelCaseAnalysis: no visible global function definition for
  ‘hatvalues’
modelCaseAnalysis: no visible global function definition for ‘rstudent’
modelCaseAnalysis: no visible global function definition for ‘coef’
modelCaseAnalysis: no visible global function definition for ‘qt’
modelCaseAnalysis: no visible global function definition for
  ‘cooks.distance’
modelCaseAnalysis: no visible global function definition for ‘qf’
modelCaseAnalysis: no visible global function definition for ‘dfbetas’
modelCaseAnalysis: no visible global function definition for ‘covratio’
modelCompare: no visible global function definition for ‘residuals’
modelCompare: no visible global function definition for ‘coef’
modelCompare: no visible global function definition for ‘terms’
modelCompare: no visible global function definition for ‘pf’
modelCorrectSE: no visible global function definition for ‘pt’
modelEffectSizes: no visible global function definition for ‘residuals’
modelErrors: no visible global function definition for ‘residuals’
modelPredictions: no visible global function definition for
  ‘fitted.values’
modelPredictions: no visible global function definition for ‘pt’
modelPredictions: no visible global function definition for ‘predict’
modelR2: no visible global function definition for ‘pf’
modelSummary: no visible global function definition for ‘printCoefmat’
modelSummary: no visible global function definition for ‘nobs’
modelSummary: no visible global function definition for ‘AIC’
modelSummary: no visible global function definition for ‘BIC’
modelSummary: no visible global function definition for ‘logLik’
modelSummary: no visible global function definition for ‘deviance’
varContrasts: no visible global function definition for
  ‘contr.treatment’
varContrasts: no visible global function definition for ‘contr.sum’
varContrasts: no visible global function definition for ‘contr.helmert’
varPlot: no visible global function definition for ‘par’
varPlot: no visible global function definition for ‘hist’
varPlot: no visible global function definition for ‘rug’
varPlot: no visible global function definition for ‘density’
varPlot: no visible global function definition for ‘lines’
varPlot: no visible global function definition for ‘identify’
varRegressors: no visible global function definition for ‘model.matrix’
varRegressors: no visible global function definition for ‘as.formula’
Undefined global functions or variables:
  AIC BIC IQR abline as.formula coef col2rgb contr.helmert contr.sum
  contr.treatment cooks.distance covratio density dev.new deviance
  dfbetas dnorm fitted.values hatvalues hist identify lines logLik
  median model.matrix nobs par pchisq pf plot points polygon predict
  printCoefmat pt qf qt read.table residuals rstudent rug sd stripchart
  terms write.table
Consider adding
  importFrom("grDevices", "col2rgb", "dev.new")
  importFrom("graphics", "abline", "hist", "identify", "lines", "par",
             "plot", "points", "polygon", "rug", "stripchart")
  importFrom("stats", "AIC", "BIC", "IQR", "as.formula", "coef",
             "contr.helmert", "contr.sum", "contr.treatment",
             "cooks.distance", "covratio", "density", "deviance",
             "dfbetas", "dnorm", "fitted.values", "hatvalues", "logLik",
             "median", "model.matrix", "nobs", "pchisq", "pf", "predict",
             "printCoefmat", "pt", "qf", "qt", "residuals", "rstudent",
             "sd", "terms")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE.

DONE
Status: 1 NOTE

longpower (1.0-11)

Maintainer: Michael C. Donohue

checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  print.power.longtest
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.

checking R code for possible problems ... NOTE
diggle.linear.power: no visible global function definition for
  ‘uniroot’
edland.linear.power: no visible global function definition for
  ‘uniroot’
liu.liang.linear.power: no visible global function definition for
  ‘uniroot’
lmmpower.gee: no visible global function definition for ‘qnorm’
lmmpower.lme: no visible global function definition for ‘qnorm’
power.mmrm: no visible global function definition for ‘uniroot’
power.mmrm.ar1: no visible global function definition for ‘uniroot’
lmmpower,merMod: no visible global function definition for ‘coef’
lmmpower,merMod: no visible global function definition for ‘fixef’
lmmpower,merMod: no visible global function definition for ‘qnorm’
lmmpower,merMod: no visible global function definition for ‘getME’
Undefined global functions or variables:
  coef fixef getME qnorm uniroot
Consider adding
  importFrom("stats", "coef", "qnorm", "uniroot")
to your NAMESPACE.

DONE
Status: 2 NOTEs

lsmeans (2.22)

Maintainer: Russell Lenth

checking package dependencies ... NOTE
Package suggested but not available for checking: ‘lme4.0’

DONE
Status: 1 NOTE

lucid (1.3)

Maintainer: Kevin Wright
Bug reports: https://github.com/kwstat/lucid/issues

OK

marked (1.1.10)

Maintainer: Jeff Laake

OK

mbest (0.4)

Maintainer: Patrick O. Perry

checking S3 generic/method consistency ... WARNING
VarCorr:
  function(x, sigma, ...)
VarCorr.mhglm:
  function(x, sigma, rdig)

VarCorr:
  function(x, sigma, ...)
VarCorr.mhglm:
  function(x, sigma, rdig)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.

checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘logistf’

DONE
Status: 1 WARNING, 1 NOTE

mediation (4.4.5)

Maintainer: Teppei Yamamoto

OK

MEMSS (0.9-2)

Maintainer: Steve Walker

OK

merTools (0.1.0)

Maintainer: Jared E. Knowles

OK

MESS (0.3-2)

Maintainer: Claus Ekstrom

checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  QIC.geeglm QIC.geekin QIC.ordgee common.shared.pedigree
  common.shared.pedigreeList desctable.character desctable.data.frame
  desctable.default desctable.factor desctable.integer
  desctable.numeric drop1.geeglm print.geekin residualplot.default
  residualplot.lm wallyplot.default wallyplot.lm
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.

checking R code for possible problems ... NOTE
QIC.geeglm : computeqic: no visible global function definition for
  ‘family’
QIC.geeglm : computeqic: no visible global function definition for
  ‘coef’
QIC.ordgee : computeqic: no visible global function definition for
  ‘family’
QIC.ordgee : computeqic: no visible global function definition for
  ‘coef’
adaptive.weights : <anonymous>: no visible global function definition
  for ‘lm.fit’
adaptive.weights: no visible global function definition for ‘lm.fit’
auc: no visible global function definition for ‘approx’
auc: no visible global function definition for ‘integrate’
auc: no visible global function definition for ‘splinefun’
common.shared.pedigreeList: no visible global function definition for
  ‘as’
desctable.factor: no visible global function definition for
  ‘chisq.test’
desctable.numeric: no visible global function definition for ‘sd’
desctable.numeric: no visible binding for global variable ‘sd’
desctable.numeric: no visible global function definition for
  ‘oneway.test’
drop1.geeglm: no visible global function definition for ‘model.matrix’
drop1.geeglm: no visible global function definition for ‘drop.scope’
drop1.geeglm: no visible global function definition for ‘terms’
drop1.geeglm: no visible global function definition for
  ‘update.formula’
drop1.geeglm: no visible global function definition for ‘coef’
drop1.geeglm: no visible global function definition for ‘pchisq’
drop1.geeglm: no visible global function definition for ‘formula’
drop1.geese: no visible global function definition for ‘model.matrix’
drop1.geese: no visible global function definition for ‘formula’
drop1.geese: no visible global function definition for ‘terms’
drop1.geese: no visible global function definition for ‘drop.scope’
drop1.geese: no visible global function definition for ‘update.formula’
drop1.geese: no visible global function definition for ‘coef’
drop1.geese: no visible global function definition for ‘pchisq’
feature.test: no visible global function definition for ‘sd’
feature.test: no visible global function definition for ‘coef’
feature.test: no visible global function definition for ‘predict’
feature.test: no visible global function definition for ‘lm’
feature.test: no visible global function definition for ‘pf’
feature.test : <anonymous>: no visible global function definition for
  ‘coef’
feature.test : <anonymous>: no visible global function definition for
  ‘predict’
feature.test : <anonymous>: no visible global function definition for
  ‘lm’
feature.test : <anonymous>: no visible global function definition for
  ‘pf’
fitted.geese: no visible global function definition for ‘model.matrix’
fitted.geese: no visible global function definition for ‘formula’
fitted.geese: no visible global function definition for ‘model.offset’
fitted.geese: no visible global function definition for ‘family’
geekin: no visible binding for global variable ‘gaussian’
geekin: no visible global function definition for ‘model.frame’
gkgamma: no visible global function definition for ‘pnorm’
gkgamma: no visible global function definition for ‘qnorm’
plot3x3: no visible binding for global variable ‘plot’
plot3x3: no visible global function definition for ‘par’
plot3x3: no visible global function definition for ‘box’
power.binom.test : pfun: no visible global function definition for
  ‘pbinom’
power.binom.test : pfun: no visible global function definition for
  ‘qbinom’
power.binom.test : pfun: no visible global function definition for
  ‘dbinom’
power.binom.test: no visible global function definition for ‘uniroot’
power.mcnemar.test : f : <anonymous>: no visible global function
  definition for ‘pbinom’
power.mcnemar.test: no visible global function definition for ‘uniroot’
print.geekin: no visible global function definition for ‘naprint’
residualplot.default: no visible global function definition for ‘plot’
residualplot.default : <anonymous>: no visible binding for global
  variable ‘rgb’
residualplot.default : <anonymous>: no visible global function
  definition for ‘col2rgb’
residualplot.default: no visible global function definition for ‘lines’
residualplot.default: no visible global function definition for
  ‘smooth.spline’
residualplot.default: no visible global function definition for ‘sd’
residualplot.default: no visible global function definition for
  ‘polygon’
residualplot.lm: no visible global function definition for ‘rstudent’
residualplot.lm: no visible global function definition for ‘predict’
rootonorm: no visible global function definition for ‘sd’
rootonorm: no visible global function definition for ‘hist’
rootonorm: no visible global function definition for ‘pnorm’
rootonorm: no visible global function definition for ‘dnorm’
rootonorm: no visible global function definition for ‘plot’
rootonorm: no visible global function definition for ‘rect’
rootonorm: no visible global function definition for ‘lines’
rootonorm: no visible global function definition for ‘abline’
scorefct: no visible global function definition for ‘coef’
scorefct: no visible global function definition for ‘model.matrix’
segregate.genes : <anonymous>: no visible global function definition
  for ‘rbinom’
wallyplot: no visible binding for global variable ‘rnorm’
wallyplot.default: no visible binding for global variable ‘rnorm’
wallyplot.default: no visible global function definition for
  ‘complete.cases’
wallyplot.lm: no visible binding for global variable ‘rnorm’
wallyplot.lm: no visible global function definition for ‘rstandard’
wallyplot.lm: no visible global function definition for ‘predict’
Undefined global functions or variables:
  abline approx as box chisq.test coef col2rgb complete.cases dbinom
  dnorm drop.scope family formula gaussian hist integrate lines lm
  lm.fit model.frame model.matrix model.offset naprint oneway.test par
  pbinom pchisq pf plot pnorm polygon predict qbinom qnorm rbinom rect
  rgb rnorm rstandard rstudent sd smooth.spline splinefun terms uniroot
  update.formula
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
  importFrom("graphics", "abline", "box", "hist", "lines", "par", "plot",
             "polygon", "rect")
  importFrom("methods", "as")
  importFrom("stats", "approx", "chisq.test", "coef", "complete.cases",
             "dbinom", "dnorm", "drop.scope", "family", "formula",
             "gaussian", "integrate", "lm", "lm.fit", "model.frame",
             "model.matrix", "model.offset", "naprint", "oneway.test",
             "pbinom", "pchisq", "pf", "pnorm", "predict", "qbinom",
             "qnorm", "rbinom", "rnorm", "rstandard", "rstudent", "sd",
             "smooth.spline", "splinefun", "terms", "uniroot",
             "update.formula")
to your NAMESPACE (and ensure that your DESCRIPTION Imports field
contains 'methods').

DONE
Status: 2 NOTEs

metafor (1.9-8)

Maintainer: Wolfgang Viechtbauer

OK

metaplus (0.7-6)

Maintainer: Ken Beath

OK

Metatron (0.1-1)

Maintainer: Huiling Huang

checking R code for possible problems ... NOTE
fit.bivar: no visible binding for global variable ‘binomial’
summary.fit.bivar: no visible global function definition for ‘qt’
summary.fit.bivar: no visible global function definition for ‘pt’
Undefined global functions or variables:
  binomial pt qt
Consider adding
  importFrom("stats", "binomial", "pt", "qt")
to your NAMESPACE.

DONE
Status: 1 NOTE

MethComp (1.22.2)

Maintainer: Bendix Carstensen

checking package dependencies ... NOTE
Package suggested but not available for checking: ‘BRugs’

checking dependencies in R code ... NOTE
'library' or 'require' call to ‘nlme’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘BRugs’ ‘R2WinBUGS’ ‘coda’ ‘rjags’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘nlme’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘nlme:::VarCorr’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘VC.est.fixed’ ‘VC.est.random’

checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.VarComp
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.

checking R code for possible problems ... NOTE
AB.plot: no visible global function definition for ‘complete.cases’
AB.plot: no visible global function definition for ‘ave’
AB.plot: no visible global function definition for ‘segments’
AltReg: no visible global function definition for ‘complete.cases’
AltReg: no visible global function definition for ‘fitted’
AltReg: no visible global function definition for ‘lm’
AltReg: no visible global function definition for ‘lme’
AltReg: no visible global function definition for ‘flush.console’
BA.est: no visible global function definition for ‘lmeControl’
BA.est: no visible global function definition for ‘qt’
BA.plot: no visible global function definition for ‘grey’
BA.plot: no visible global function definition for ‘str’
BlandAltman: no visible global function definition for ‘qt’
BlandAltman: no visible global function definition for ‘sd’
BlandAltman: no visible global function definition for ‘pt’
BlandAltman : cnr: no visible global function definition for ‘par’
BlandAltman: no visible global function definition for ‘lm’
BlandAltman: no visible global function definition for ‘coef’
BlandAltman: no visible global function definition for ‘plot.default’
BlandAltman: no visible global function definition for ‘abline’
BlandAltman: no visible global function definition for ‘text’
BlandAltman: no visible global function definition for ‘points’
BlandAltman: no visible global function definition for ‘axis’
BlandAltman: no visible global function definition for ‘box’
BlandAltman: no visible global function definition for ‘par’
Deming: no visible global function definition for ‘complete.cases’
Deming: no visible global function definition for ‘var’
Deming: no visible global function definition for ‘cov’
Deming: no visible binding for global variable ‘quantile’
MCmcmc: no visible global function definition for ‘flush.console’
MCmcmc: no visible global function definition for ‘jags.model’
MCmcmc: no visible global function definition for ‘bugs’
MCmcmc: no visible global function definition for ‘read.bugs’
Meth.sim: no visible global function definition for ‘runif’
Meth.sim: no visible global function definition for ‘rnorm’
Meth.sim: no visible global function definition for ‘rbinom’
PBreg: no visible global function definition for ‘complete.cases’
PBreg: no visible global function definition for ‘combn’
PBreg: no visible global function definition for ‘qnorm’
PBreg: no visible global function definition for ‘median’
TDI: no visible global function definition for ‘sd’
TDI: no visible global function definition for ‘qnorm’
TDI : FF: no visible global function definition for ‘pnorm’
TDI: no visible global function definition for ‘uniroot’
TDI: no visible global function definition for ‘quantile’
VC.est: no visible global function definition for ‘lmeControl’
VC.est.fixed: no visible global function definition for ‘lmeControl’
VC.est.fixed: no visible global function definition for ‘lme’
VC.est.fixed: no visible global function definition for ‘pdIdent’
VC.est.fixed: no visible global function definition for ‘varIdent’
VC.est.fixed: no visible global function definition for ‘pdDiag’
VC.est.fixed: no visible global function definition for ‘pdSymm’
VC.est.fixed: no visible global function definition for ‘residuals’
VC.est.random: no visible global function definition for ‘lmeControl’
VC.est.random: no visible global function definition for ‘lme’
VC.est.random: no visible global function definition for ‘pdBlocked’
VC.est.random: no visible global function definition for ‘pdIdent’
VC.est.random: no visible global function definition for ‘varIdent’
VC.est.random: no visible global function definition for ‘ranef’
VC.est.random: no visible global function definition for ‘pdDiag’
VC.est.random: no visible global function definition for ‘tail’
VC.est.random: no visible global function definition for ‘residuals’
bothlines: no visible global function definition for ‘abline’
bothlines: no visible global function definition for ‘lm’
bothlines: no visible global function definition for ‘coef’
connect2mean: no visible global function definition for ‘ave’
connect2mean: no visible global function definition for ‘segments’
corr.measures: no visible global function definition for
  ‘complete.cases’
corr.measures: no visible global function definition for ‘var’
corr.measures: no visible global function definition for ‘cov’
corr.measures: no visible global function definition for ‘cor’
do.DA.reg: no visible global function definition for ‘complete.cases’
do.DA.reg: no visible global function definition for ‘lm’
find.mean: no visible global function definition for ‘varnames’
find.vars: no visible global function definition for ‘varnames’
lines.MethComp: no visible global function definition for ‘par’
lines.MethComp: no visible global function definition for ‘qt’
lines.MethComp: no visible global function definition for ‘matlines’
lines.MethComp: no visible global function definition for ‘axis’
lines.MethComp: no visible global function definition for ‘box’
mean.Meth: no visible global function definition for ‘aggregate’
middle: no visible global function definition for ‘quantile’
pairs.MCmcmc: no visible global function definition for ‘rainbow’
pairs.MCmcmc: no visible global function definition for ‘pairs’
pairs.MCmcmc: no visible global function definition for ‘varnames’
perm.repl: no visible global function definition for ‘runif’
plot.MCmcmc: no visible global function definition for ‘gray’
plot.MCmcmc : conv.pair: no visible global function definition for
  ‘abline’
plot.MCmcmc : conv.pair: no visible global function definition for
  ‘strwidth’
plot.MCmcmc : conv.pair: no visible global function definition for
  ‘strheight’
plot.MCmcmc : conv.pair: no visible global function definition for
  ‘rect’
plot.MCmcmc : conv.pair: no visible global function definition for
  ‘par’
plot.MCmcmc : conv.pair: no visible global function definition for
  ‘text’
plot.MCmcmc : conv.pair: no visible global function definition for
  ‘box’
plot.MCmcmc: no visible global function definition for ‘par’
plot.MCmcmc: no visible global function definition for ‘plot’
plot.MCmcmc: no visible global function definition for ‘axis’
plot.MCmcmc: no visible global function definition for ‘mtext’
plot.Meth : pnl: no visible global function definition for ‘abline’
plot.Meth : pnl: no visible global function definition for ‘points’
plot.Meth : pnu: no visible global function definition for ‘sd’
plot.Meth : pnu: no visible global function definition for ‘abline’
plot.Meth : pnu: no visible global function definition for ‘points’
plot.Meth: no visible global function definition for ‘par’
plot.Meth: no visible global function definition for ‘plot’
plot.Meth: no visible global function definition for ‘text’
plot.Meth: no visible global function definition for ‘box’
plot.Meth: no visible global function definition for ‘axis’
plot.MethComp: no visible global function definition for ‘grey’
plot.MethComp: no visible global function definition for ‘plot’
plot.MethComp: no visible global function definition for ‘abline’
plot.MethComp: no visible global function definition for ‘box’
plot.MethComp: no visible global function definition for ‘strwidth’
plot.MethComp: no visible global function definition for ‘strheight’
plot.MethComp: no visible global function definition for ‘par’
plot.MethComp: no visible global function definition for ‘rect’
plot.MethComp: no visible global function definition for ‘text’
plot.PBreg: no visible global function definition for ‘predict’
plot.PBreg: no visible global function definition for ‘plot’
plot.PBreg: no visible global function definition for ‘polygon’
plot.PBreg: no visible global function definition for ‘abline’
plot.PBreg: no visible global function definition for ‘points’
plot.PBreg: no visible global function definition for ‘text’
plot.PBreg: no visible global function definition for ‘IQR’
plot.PBreg: no visible global function definition for ‘hist’
plot.PBreg: no visible global function definition for ‘density’
plot.PBreg: no visible global function definition for ‘lines’
plot.VarComp: no visible global function definition for ‘gray’
plot.VarComp: no visible global function definition for ‘density’
plot.VarComp: no visible global function definition for ‘quantile’
plot.VarComp: no visible global function definition for ‘plot’
plot.VarComp: no visible global function definition for ‘abline’
plot.VarComp: no visible global function definition for ‘lines’
plot.VarComp: no visible global function definition for ‘axis’
plot.VarComp: no visible global function definition for ‘par’
plot.VarComp: no visible global function definition for ‘text’
plot.VarComp: no visible global function definition for ‘mtext’
points.MethComp: no visible global function definition for ‘points’
post.MCmcmc: no visible global function definition for ‘rainbow’
post.mean: no visible global function definition for ‘gray’
post.sd: no visible global function definition for ‘gray’
predict.PBreg: no visible global function definition for ‘qnorm’
predict.PBreg: no visible global function definition for ‘median’
predict.PBreg: no visible global function definition for ‘quantile’
print.MCmcmc: no visible global function definition for ‘ftable’
print.MethComp: no visible global function definition for ‘ftable’
sort.Meth: no visible global function definition for ‘ave’
subset.MCmcmc : char.2.num: no visible global function definition for
  ‘varnames’
summary.MCmcmc: no visible binding for global variable ‘quantile’
summary.Meth: no visible global function definition for ‘addmargins’
to.long: no visible global function definition for ‘reshape’
to.wide: no visible global function definition for ‘reshape’
trace.mean: no visible global function definition for ‘gray’
trace.sd: no visible global function definition for ‘gray’
Undefined global functions or variables:
  IQR abline addmargins aggregate ave axis box bugs coef combn
  complete.cases cor cov density fitted flush.console ftable gray grey
  hist jags.model lines lm lme lmeControl matlines median mtext pairs
  par pdBlocked pdDiag pdIdent pdSymm plot plot.default pnorm points
  polygon predict pt qnorm qt quantile rainbow ranef rbinom read.bugs
  rect reshape residuals rnorm runif sd segments str strheight strwidth
  tail text uniroot var varIdent varnames
Consider adding
  importFrom("grDevices", "gray", "grey", "rainbow")
  importFrom("graphics", "abline", "axis", "box", "hist", "lines",
             "matlines", "mtext", "pairs", "par", "plot", "plot.default",
             "points", "polygon", "rect", "segments", "strheight",
             "strwidth", "text")
  importFrom("stats", "IQR", "addmargins", "aggregate", "ave", "coef",
             "complete.cases", "cor", "cov", "density", "fitted",
             "ftable", "lm", "median", "pnorm", "predict", "pt", "qnorm",
             "qt", "quantile", "rbinom", "reshape", "residuals", "rnorm",
             "runif", "sd", "uniroot", "var")
  importFrom("utils", "combn", "flush.console", "str", "tail")
to your NAMESPACE.

DONE
Status: 4 NOTEs

miceadds (1.6-0)

Maintainer: Alexander Robitzsch

OK

mice (2.25)

Maintainer: Stef van Buuren

OK

mitml (0.2-4)

Maintainer: Simon Grund

OK

mixAK (4.2)

Maintainer: Arnošt Komárek

checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘bayesSurv’

DONE
Status: 1 NOTE

mixlm (1.1.1)

Maintainer: Kristian Hovde Liland

OK

MixMAP (1.3.4)

Maintainer: Gregory J. Matthews

OK

mlma (1.0-0)

Maintainer: Qingzhao Yu

OK

mlmRev (1.0-6)

Maintainer: Steve Walker

OK

mlVAR (0.1.0)

Maintainer: Sacha Epskamp

checking R code for possible problems ... NOTE
mlVAR: no visible global function definition for ‘ave’
mlVAR: no visible global function definition for ‘txtProgressBar’
mlVAR: no visible global function definition for ‘as.formula’
mlVAR: no visible global function definition for ‘setTxtProgressBar’
mlVAR: no visible global function definition for ‘pnorm’
simulateVAR: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  as.formula ave pnorm rnorm setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "as.formula", "ave", "pnorm", "rnorm")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE.

DONE
Status: 1 NOTE

multcomp (1.4-2)

Maintainer: Torsten Hothorn

OK

MultiRR (1.1)

Maintainer: Yimen G. Araya-Ajoy

OK

MuMIn (1.15.6)

Maintainer: Kamil Bartoń

checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  ‘logistf’ ‘splm’ ‘geeM’

checking Rd cross-references ... NOTE
Packages unavailable to check Rd xrefs: ‘geeM’, ‘bestglm’, ‘splm’, ‘logistf’, ‘RMark’

DONE
Status: 2 NOTEs

mztwinreg (1.0-1)

Maintainer: Aldo Cordova-Palomera

checking R code for possible problems ... NOTE
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.

DONE
Status: 1 NOTE

NanoStringNorm (1.1.21)

Maintainer: Paul Boutros

checking package dependencies ... ERROR
Package required but not available: ‘vsn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

DONE
Status: 1 ERROR

nonrandom (1.42)

Maintainer: Susanne Stampf

checking dependencies in R code ... NOTE
'library' or 'require' call to ‘colorspace’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.

checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.pscore plot.stdf
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.

checking R code for possible problems ... NOTE
balance.classical: no visible global function definition for
  ‘chisq.test’
balance.classical: no visible global function definition for ‘na.omit’
balance.classical: no visible global function definition for ‘t.test’
balance.stand.diff: no visible global function definition for
  ‘mahalanobis’
balance.stand.diff: no visible global function definition for ‘na.omit’
balance.stand.diff: no visible global function definition for ‘sd’
dist.plot.bar.plot: no visible global function definition for ‘dev.new’
dist.plot.bar.plot: no visible global function definition for ‘par’
dist.plot.bar.plot: no visible global function definition for
  ‘rainbow_hcl’
dist.plot.bar.plot: no visible global function definition for
  ‘heat.colors’
dist.plot.bar.plot: no visible global function definition for ‘barplot’
dist.plot.bar.plot: no visible global function definition for ‘mtext’
dist.plot.bar.plot: no visible global function definition for ‘legend’
dist.plot.bar.plot: no visible global function definition for
  ‘split.screen’
dist.plot.bar.plot: no visible global function definition for ‘screen’
dist.plot.bar.plot: no visible global function definition for
  ‘close.screen’
dist.plot.hist : func.breaks: no visible global function definition for
  ‘hist’
dist.plot.hist : func.counts: no visible global function definition for
  ‘hist’
dist.plot.hist.plot: no visible global function definition for
  ‘dev.new’
dist.plot.hist.plot: no visible global function definition for ‘par’
dist.plot.hist.plot: no visible global function definition for
  ‘rainbow_hcl’
dist.plot.hist.plot: no visible global function definition for
  ‘heat.colors’
dist.plot.hist.plot: no visible global function definition for
  ‘barplot’
dist.plot.hist.plot: no visible global function definition for ‘axis’
dist.plot.hist.plot: no visible global function definition for ‘legend’
dist.plot.hist.plot: no visible global function definition for ‘mtext’
find.factors: no visible global function definition for ‘formula’
plot.pscore: no visible global function definition for ‘density’
plot.pscore: no visible global function definition for ‘plot’
plot.pscore: no visible global function definition for ‘legend’
plot.stdf: no visible global function definition for ‘rainbow_hcl’
plot.stdf: no visible global function definition for ‘grey.colors’
plot.stdf: no visible global function definition for ‘par’
plot.stdf: no visible global function definition for ‘plot’
plot.stdf: no visible global function definition for ‘points’
plot.stdf: no visible global function definition for ‘axis’
plot.stdf: no visible global function definition for ‘box’
plot.stdf : <anonymous>: no visible global function definition for
  ‘lines’
plot.stdf: no visible global function definition for ‘abline’
plot.stdf: no visible global function definition for ‘legend’
print.est.data.frame: no visible global function definition for ‘qnorm’
print.est.matched.data.frame: no visible global function definition for
  ‘qnorm’
print.est.matched.pscore: no visible global function definition for
  ‘qnorm’
print.est.stratified.data.frame: no visible global function definition
  for ‘qnorm’
print.est.stratified.pscore: no visible global function definition for
  ‘qnorm’
ps.estimate.bin: no visible global function definition for ‘glm’
ps.estimate.bin: no visible global function definition for ‘vcov’
ps.estimate.bin: no visible global function definition for
  ‘model.frame’
ps.estimate.bin: no visible global function definition for ‘formula’
ps.estimate.data.frame: no visible global function definition for
  ‘formula’
ps.estimate.data.frame: no visible global function definition for
  ‘model.frame’
ps.estimate.data.frame: no visible global function definition for
  ‘model.matrix’
ps.estimate.gauss: no visible global function definition for ‘glm’
ps.estimate.gauss: no visible global function definition for ‘sd’
ps.estimate.gauss: no visible global function definition for ‘var’
ps.estimate.gauss: no visible global function definition for ‘vcov’
ps.estimate.gauss: no visible global function definition for
  ‘model.frame’
ps.estimate.gauss: no visible global function definition for ‘formula’
ps.estimate.matched.data.frame: no visible global function definition
  for ‘formula’
ps.estimate.matched.data.frame: no visible global function definition
  for ‘model.frame’
ps.estimate.matched.data.frame: no visible global function definition
  for ‘model.matrix’
ps.estimate.matched.pscore: no visible global function definition for
  ‘formula’
ps.estimate.matched.pscore: no visible global function definition for
  ‘model.frame’
ps.estimate.matched.pscore: no visible global function definition for
  ‘model.matrix’
ps.estimate.regr: no visible global function definition for ‘glm’
ps.estimate.regr: no visible global function definition for ‘vcov’
ps.estimate.regr: no visible global function definition for ‘cov’
ps.estimate.stratified.data.frame: no visible global function
  definition for ‘formula’
ps.estimate.stratified.data.frame: no visible global function
  definition for ‘model.frame’
ps.estimate.stratified.data.frame: no visible global function
  definition for ‘model.matrix’
ps.estimate.stratified.pscore: no visible global function definition
  for ‘formula’
ps.estimate.stratified.pscore: no visible global function definition
  for ‘model.frame’
ps.estimate.stratified.pscore: no visible global function definition
  for ‘model.matrix’
ps.matchcaliper: no visible global function definition for ‘sd’
pscore: no visible binding for global variable ‘binomial’
pscore: no visible binding for global variable ‘na.exclude’
pscore: no visible global function definition for ‘model.frame’
pscore: no visible global function definition for ‘glm’
pscore: no visible global function definition for ‘predict’
relative.effect: no visible global function definition for
  ‘model.frame’
relative.effect: no visible global function definition for ‘glm’
summary.est.data.frame: no visible global function definition for
  ‘qnorm’
summary.est.matched.data.frame: no visible global function definition
  for ‘qnorm’
summary.est.matched.pscore: no visible global function definition for
  ‘qnorm’
summary.est.stratified.data.frame: no visible global function
  definition for ‘qnorm’
summary.est.stratified.pscore: no visible global function definition
  for ‘qnorm’
Undefined global functions or variables:
  abline axis barplot binomial box chisq.test close.screen cov density
  dev.new formula glm grey.colors heat.colors hist legend lines
  mahalanobis model.frame model.matrix mtext na.exclude na.omit par
  plot points predict qnorm rainbow_hcl screen sd split.screen t.test
  var vcov
Consider adding
  importFrom("grDevices", "dev.new", "grey.colors", "heat.colors")
  importFrom("graphics", "abline", "axis", "barplot", "box",
             "close.screen", "hist", "legend", "lines", "mtext", "par",
             "plot", "points", "screen", "split.screen")
  importFrom("stats", "binomial", "chisq.test", "cov", "density",
             "formula", "glm", "mahalanobis", "model.frame",
             "model.matrix", "na.exclude", "na.omit", "predict", "qnorm",
             "sd", "t.test", "var", "vcov")
to your NAMESPACE.

DONE
Status: 3 NOTEs

omics (0.1-3)

Maintainer: Gianluca Campanella

OK

ordinal (2015.6-28)

Maintainer: Rune Haubo Bojesen Christensen

OK

pamm (0.9)

Maintainer: Julien Martin
Bug reports: https://github.com/JulienGAMartin/pamm_R/issues

OK

pan (1.3)

Maintainer: Jing hua Zhao

OK

PBImisc (0.999)

Maintainer: Przemyslaw Biecek

checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.

checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘MASS’ ‘Matrix’ ‘lme4’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.

checking R code for possible problems ... NOTE
boxplotInTime: no visible global function definition for ‘rgb’
boxplotInTime: no visible global function definition for ‘plot’
boxplotInTime: no visible global function definition for ‘Axis’
boxplotInTime: no visible global function definition for ‘segments’
boxplotInTime: no visible global function definition for ‘boxplot’
boxplotpp: no visible global function definition for ‘plot’
boxplotpp: no visible global function definition for ‘Axis’
boxplotpp: no visible global function definition for ‘segments’
boxplotpp: no visible global function definition for ‘boxplot’
boxplotpp: no visible global function definition for ‘points’
groupDisp: no visible global function definition for ‘lmer’
groupDisp : <anonymous>: no visible global function definition for
  ‘lmer’
groupDisp : <anonymous>: no visible global function definition for
  ‘fixef’
groupDisp : <anonymous>: no visible global function definition for
  ‘VarCorr’
groupDisp: no visible global function definition for ‘logLik’
histpp: no visible global function definition for ‘hist’
histpp: no visible global function definition for ‘rug’
obsDisp: no visible global function definition for ‘lmer’
obsDisp : <anonymous>: no visible global function definition for ‘lmer’
obsDisp : <anonymous>: no visible global function definition for
  ‘fixef’
obsDisp : <anonymous>: no visible global function definition for
  ‘VarCorr’
obsDisp: no visible global function definition for ‘logLik’
plotPairwiseTests: no visible global function definition for ‘par’
plotPairwiseTests: no visible global function definition for ‘plot’
plotPairwiseTests: no visible global function definition for ‘axis’
plotPairwiseTests: no visible global function definition for ‘abline’
plotPairwiseTests: no visible global function definition for ‘na.omit’
plotPairwiseTests: no visible global function definition for ‘lines’
plotPairwiseTests: no visible global function definition for ‘points’
recalculateLogLik: no visible global function definition for ‘VarCorr’
recalculateLogLik: no visible global function definition for ‘getME’
recalculateLogLik: no visible global function definition for ‘Matrix’
recalculateLogLik: no visible global function definition for ‘Diagonal’
Undefined global functions or variables:
  Axis Diagonal Matrix VarCorr abline axis boxplot fixef getME hist
  lines lmer logLik na.omit par plot points rgb rug segments
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "Axis", "abline", "axis", "boxplot", "hist",
             "lines", "par", "plot", "points", "rug", "segments")
  importFrom("stats", "logLik", "na.omit")
to your NAMESPACE.

DONE
Status: 3 NOTEs

pbkrtest (0.4-6)

Maintainer: Sren Hjsgaard

OK

pedigreemm (0.3-3)

Maintainer: Ana Ines Vazquez

OK

pez (1.1-1)

Maintainer: William D. Pearse

OK

phia (0.2-1)

Maintainer: Helios De Rosario-Martinez

OK

phmm (0.7-5)

Maintainer: Michael Donohue

checking R code for possible problems ... NOTE
phmm: no visible binding for global variable ‘na.fail’
phmm: no visible global function definition for ‘model.extract’
phmm: no visible global function definition for ‘terms’
phmm: no visible global function definition for ‘model.matrix’
phmm: no visible global function definition for ‘as.formula’
plot.phmm: no visible global function definition for ‘formula’
print.phmm: no visible global function definition for ‘coef’
print.summary.phmm: no visible global function definition for ‘coef’
Undefined global functions or variables:
  as.formula coef formula model.extract model.matrix na.fail terms
Consider adding
  importFrom("stats", "as.formula", "coef", "formula", "model.extract",
             "model.matrix", "na.fail", "terms")
to your NAMESPACE.

checking compiled code ... NOTE
File ‘phmm/libs/phmm.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘arms.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.

DONE
Status: 2 NOTEs

piecewiseSEM (1.0.0)

Maintainer: Jon Lefcheck

checking examples ... ERROR
Running examples in ‘piecewiseSEM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: partial.resid
> ### Title: Calculates partial residuals for two variables
> ### Aliases: partial.resid
> 
> ### ** Examples
> 
> # Create example data
> set.seed(1)
> 
> example.data = data.frame(
+   y = rnorm(100, 0, 1),
+   x1 = rnorm(100, 10, 50),
+   random = letters[1:5]
+ )
> 
> example.data$x2 = example.data$y + runif(100, 0, 5)
> 
> example.data$x3 = example.data$x2 + runif(100, 0, 5)
> 
> # Run regular linear model using lm()
> lm.model = lm(y ~ x1 + x2 + x3, example.data)
> 
> partial.resid(y ~ x3, lm.model, example.data)
              y          x3
1   -0.76367214  0.17429669
2   -0.80928484 -0.37940771
3    0.13310265 -0.12688260
4    0.39517230  1.44608687
5    0.38401484 -0.23892171
6   -0.80506058 -2.85888329
7   -2.11721532  1.12562573
8    0.49155369  0.76127916
9   -0.08885036 -1.65984001
10  -0.08922272  0.61335860
11   0.86523518  0.08532083
12   0.30321870 -1.20433279
13   0.46884589  0.89451603
14  -0.05224294  0.35936580
15   0.67656368  1.49793861
16   0.53400225  0.63615320
17  -0.23436780 -0.96851546
18  -1.09986037 -1.67045298
19   0.58362725 -0.69492253
20   0.02975701  1.93299431
21   0.34075153  1.56254020
22  -1.72305387  1.07655164
23  -0.88593566  2.10700975
24  -1.30820930  0.62128114
25  -0.26065279  2.14901137
26   0.37916701  0.05639281
27   0.37940407 -2.24525863
28   0.38821708 -1.02909016
29  -0.21274754 -1.08996332
30  -0.57957686 -1.82514865
31  -0.82048651 -2.34276562
32  -0.68410984 -0.84118458
33   0.43981937 -0.71052260
34   0.74532243 -1.79721600
35   0.60690338  0.32421789
36  -0.04785286  0.20624201
37   0.32887975 -0.21367573
38   0.04217119  2.07625742
39   0.38787513  0.75837895
40   0.18399773 -1.05420219
41  -0.31995776 -1.37089825
42  -0.52559186 -1.89402398
43   0.43876221  2.07565539
44  -0.06961166 -1.02577914
45   0.28315729  0.48615410
46  -0.41993117 -0.43705345
47   1.07861445  1.32262205
48  -0.35845231  1.39881380
49  -0.45505363  0.27924585
50   0.33608738 -2.53913894
51  -0.52051942  2.22977651
52   1.51428835  1.45167711
53   1.16000625 -0.85077030
54  -0.41316333 -2.32232283
55  -1.49549903 -2.45411616
56   0.17053685  1.52780960
57  -0.91118998  1.93262871
58   0.44731045  1.44428248
59   2.15964933  0.49546624
60  -0.07891229 -1.95297318
61   1.11410935 -0.93310600
62   0.05227721  0.90387757
63  -0.33959883  2.12208534
64  -0.42202175  0.32920928
65  -1.70049064 -1.35832399
66   1.40078090  0.76089421
67   0.06629782 -1.24249169
68   0.47934533 -0.72915750
69   1.30415615  1.82919343
70   0.40750006 -2.19103255
71  -1.18176449 -0.71932324
72   0.12302247 -1.60546787
73  -0.63816082 -2.05460041
74  -0.52553782  1.79368947
75   0.47573440  0.05639418
76  -0.84327676  0.45653162
77   0.07910065 -0.85982871
78   0.01902109  1.41340616
79   0.14511545  1.28325799
80  -0.71747824  0.83723343
81  -0.87138203 -0.82577667
82   0.30147833  2.11711512
83   0.36101628  0.28999909
84  -1.82842899 -2.35822153
85   0.27203183  0.16366630
86   0.16591980 -0.59464318
87   1.16405083 -2.42354385
88   0.31445019  0.31889811
89  -0.29743446  2.00968922
90   0.99501709  1.23369139
91   0.56389670  1.13623209
92   0.13017693  0.38184590
93   0.27411788 -1.79343399
94   1.03044338  1.31165704
95   0.90579071  0.57569735
96   1.19517747  1.55108879
97   0.35858182  0.68486596
98  -0.88926838 -0.30901458
99  -0.55525046 -0.01358866
100 -1.41424639 -0.85935272
> 
> # Works with interactions too
> lm.model2 = lm(y ~ x1 * x2 + x3, example.data)
> 
> partial.resid(y ~ x1 * x2, lm.model2, example.data, return.data.frame = FALSE)
> 
> # Run generalized least squared regression
> library(nlme)
> 
> gls.model = gls(y ~ x1 + x2 + x3, example.data)
> 
> partial.resid(y ~ x3, gls.model, example.data, return.data.frame = FALSE)
> 
> # Run mixed effects model using lme()
> lme.model = lme(y ~ x1 + x2 + x3, random = ~ 1 | random, example.data)
> 
> partial.resid(y ~ x3, lme.model, example.data, return.data.frame = FALSE)
> 
> # Run mixed effects model using lmer()
> library(lme4) 
Loading required package: Matrix

Attaching package: ‘lme4’

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

    lmList

> 
> lmer.model = lmer(y ~ x1 + x2 + x3 + (1 | random), example.data)
> 
> partial.resid(y ~ x3, lmer.model, example.data, return.data.frame = FALSE)
> 
> # Remove some values of x3 from data.frame
> example.data[c(12, 23, 45), "x3"] = NA
> 
> # Run regular linear model using lm()
> lm.model = lm(y ~ x1 + x2 + x3, example.data)
> 
> sum(!is.na(partial.resid(y ~ x3, lm.model, example.data)$x3)) # Should be 97
[1] 97
> 
> ### SEM EXAMPLE ###
> 
> # Load model package
> library(nlme)
> 
> # Load data from Shipley (2013)
> data(shipley2013) 
> 
> shipley2013.modlist = list(
+   
+   lme(x2~x1, random = ~x1 | species, data = shipley2013),
+   
+   lme(x3~x2, random = ~x2 | species, data = shipley2013),
+   
+   lme(x4~x2, random = ~x2 | species, data = shipley2013),
+   
+   lme(x5~x3+x4, random = ~x3+x4 | species, data = shipley2013)
+   
+ )
> 
> # Get partial residuals of x3 on x5 conditional on x4
> resids.df = partial.resid(x5 ~ x3, shipley2013.modlist, shipley2013, 
+   list(lmeControl(opt = "optim")))
Error in model.control[[which(sapply(model.control, length) == 15)]] : 
  attempt to select less than one element in get1index
Calls: partial.resid -> get.model.control
Execution halted

DONE
Status: 1 ERROR

predictmeans (0.99)

Maintainer: Dongwen Luo

checking R code for possible problems ... NOTE
CookD: no visible global function definition for ‘update’
CookD: no visible global function definition for ‘model.frame’
CookD : <anonymous>: no visible global function definition for ‘update’
CookD: no visible global function definition for ‘dev.new’
CookD: no visible global function definition for ‘text’
CookD: no visible global function definition for ‘points’
Kmatrix: no visible global function definition for ‘slot’
Kmatrix: no visible global function definition for ‘model.matrix’
Kmatrix: no visible global function definition for ‘terms’
Kmatrix: no visible global function definition for ‘delete.response’
Kmatrix: no visible global function definition for ‘formula’
Kmatrix: no visible global function definition for ‘as.formula’
Kmatrix: no visible global function definition for ‘model.frame’
Kmatrix: no visible binding for global variable ‘na.omit’
Kmatrix: no visible binding for global variable ‘na.pass’
PMplot: no visible global function definition for ‘dev.new’
PMplot: no visible global function definition for ‘na.omit’
PMplot: no visible global function definition for ‘par’
PMplot: no visible global function definition for ‘image’
PMplot: no visible global function definition for ‘axis’
PMplot: no visible global function definition for ‘abline’
PMplot: no visible global function definition for ‘box’
PMplot: no visible global function definition for ‘legend’
contrastmeans: no visible global function definition for ‘edit’
contrastmeans: no visible global function definition for ‘terms’
contrastmeans: no visible global function definition for ‘update’
contrastmeans: no visible global function definition for ‘as.formula’
contrastmeans: no visible global function definition for ‘pt’
contrastmeans: no visible global function definition for ‘p.adjust’
covariatemeans: no visible global function definition for ‘terms’
covariatemeans: no visible global function definition for ‘update’
covariatemeans: no visible global function definition for ‘as.formula’
covariatemeans: no visible global function definition for ‘slot’
covariatemeans: no visible global function definition for ‘qt’
covariatemeans: no visible global function definition for ‘model.frame’
covariatemeans: no visible global function definition for ‘dev.new’
model.frame.gls: no visible global function definition for
  ‘model.frame’
model.frame.gls: no visible global function definition for ‘formula’
model.matrix.gls: no visible global function definition for
  ‘model.matrix’
model.matrix.gls: no visible global function definition for ‘terms’
model.matrix.lme: no visible global function definition for
  ‘model.matrix’
model.matrix.lme: no visible global function definition for ‘terms’
model.matrix.lme: no visible global function definition for
  ‘model.frame’
mymodelparm.aovlist: no visible binding for global variable ‘coef’
mymodelparm.aovlist: no visible binding for global variable ‘vcov’
mymodelparm.default: no visible binding for global variable ‘coef’
mymodelparm.default: no visible binding for global variable ‘vcov’
mymodelparm.default: no visible global function definition for
  ‘na.omit’
mymodelparm.glmerMod: no visible binding for global variable ‘vcov’
mymodelparm.lme: no visible binding for global variable ‘vcov’
mymodelparm.lmerMod: no visible binding for global variable ‘vcov’
permmodels: no visible global function definition for ‘terms’
permmodels: no visible global function definition for ‘formula’
permmodels : <anonymous>: no visible global function definition for
  ‘model.frame’
permmodels : <anonymous>: no visible global function definition for
  ‘update’
permmodels : <anonymous>: no visible global function definition for
  ‘anova’
permmodels : tTable: no visible global function definition for ‘coef’
permmodels: no visible global function definition for ‘anova’
predictmeans: no visible global function definition for ‘slot’
predictmeans: no visible global function definition for ‘model.frame’
predictmeans: no visible global function definition for ‘xtabs’
predictmeans: no visible global function definition for ‘ftable’
predictmeans: no visible global function definition for ‘na.omit’
predictmeans: no visible global function definition for ‘terms’
predictmeans: no visible global function definition for ‘update’
predictmeans: no visible global function definition for ‘as.formula’
predictmeans: no visible global function definition for ‘qt’
predictmeans: no visible global function definition for ‘ptukey’
predictmeans: no visible global function definition for ‘pt’
predictmeans: no visible global function definition for ‘p.adjust’
predictmeans: no visible global function definition for ‘dev.new’
residplot: no visible global function definition for ‘dev.new’
residplot: no visible global function definition for ‘par’
residplot: no visible global function definition for ‘plot’
residplot : glm.diag: no visible global function definition for
  ‘family’
residplot : glm.diag: no visible global function definition for
  ‘fitted’
residplot : glm.diag: no visible global function definition for
  ‘residuals’
residplot : glm.diag: no visible global function definition for
  ‘lm.influence’
residplot: no visible global function definition for ‘predict’
residplot: no visible global function definition for ‘qnorm’
residplot: no visible global function definition for ‘ppoints’
residplot: no visible global function definition for ‘abline’
residplot: no visible global function definition for ‘identify’
rsplot.gls: no visible global function definition for ‘model.frame’
rsplot.gls: no visible global function definition for ‘terms’
rsplot.gls: no visible global function definition for ‘fitted’
rsplot.gls: no visible global function definition for ‘resid’
rsplot.gls: no visible global function definition for ‘na.omit’
rsplot.gls: no visible global function definition for ‘par’
rsplot.gls: no visible global function definition for ‘plot’
rsplot.gls: no visible global function definition for ‘abline’
rsplot.gls: no visible global function definition for ‘qqnorm’
rsplot.gls: no visible global function definition for ‘qqline’
rsplot.gls: no visible global function definition for ‘loess.smooth’
rsplot.gls: no visible global function definition for ‘lines’
rsplot.gls: no visible global function definition for ‘identify’
rsplot.lme: no visible global function definition for ‘model.frame’
rsplot.lme: no visible global function definition for ‘terms’
rsplot.lme: no visible global function definition for ‘fitted’
rsplot.lme: no visible global function definition for ‘resid’
rsplot.lme: no visible global function definition for ‘na.omit’
rsplot.lme: no visible global function definition for ‘par’
rsplot.lme: no visible global function definition for ‘qqnorm’
rsplot.lme: no visible global function definition for ‘qqline’
rsplot.lme: no visible global function definition for ‘model.matrix’
rsplot.lme: no visible global function definition for ‘plot’
rsplot.lme: no visible global function definition for ‘abline’
rsplot.lme: no visible global function definition for ‘loess.smooth’
rsplot.lme: no visible global function definition for ‘lines’
rsplot.lme: no visible global function definition for ‘identify’
rsplot.lme: no visible global function definition for ‘text’
rsplot.lme: no visible global function definition for ‘title’
rsplot.lme: no visible global function definition for ‘points’
terms.gls: no visible global function definition for ‘terms’
terms.gls: no visible global function definition for ‘model.frame’
Undefined global functions or variables:
  abline anova as.formula axis box coef delete.response dev.new edit
  family fitted formula ftable identify image legend lines lm.influence
  loess.smooth model.frame model.matrix na.omit na.pass p.adjust par
  plot points ppoints predict pt ptukey qnorm qqline qqnorm qt resid
  residuals slot terms text title update vcov xtabs
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axis", "box", "identify", "image",
             "legend", "lines", "par", "plot", "points", "text", "title")
  importFrom("methods", "slot")
  importFrom("stats", "anova", "as.formula", "coef", "delete.response",
             "family", "fitted", "formula", "ftable", "lm.influence",
             "loess.smooth", "model.frame", "model.matrix", "na.omit",
             "na.pass", "p.adjust", "ppoints", "predict", "pt", "ptukey",
             "qnorm", "qqline", "qqnorm", "qt", "resid", "residuals",
             "terms", "update", "vcov", "xtabs")
  importFrom("utils", "edit")
to your NAMESPACE (and ensure that your DESCRIPTION Imports field
contains 'methods').

DONE
Status: 1 NOTE

prLogistic (1.2)

Maintainer: Raydonal Ospina

checking R code for possible problems ... NOTE
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.

DONE
Status: 1 NOTE

purge (0.2.0)

Maintainer: Marc Maier

OK

R2admb (0.7.13)

Maintainer: Ben Bolker

checking R code for possible problems ... NOTE
AIC.admb: no visible global function definition for ‘deviance’
AIC.admb: no visible global function definition for ‘coef’
check_section : make_names: no visible global function definition for
  ‘na.omit’
compile_admb: no visible global function definition for ‘head’
confint.admb: no visible global function definition for ‘coef’
confint.admb: no visible global function definition for ‘qnorm’
confint.admb: no visible binding for global variable ‘quantile’
dat_write: no visible global function definition for ‘write.table’
logLik.admb: no visible global function definition for ‘coef’
pin_write: no visible global function definition for ‘write.table’
print.admb: no visible global function definition for ‘coef’
print.summary.admb: no visible global function definition for
  ‘printCoefmat’
read_admb: no visible global function definition for ‘read.table’
read_pars0: no visible global function definition for ‘count.fields’
reptoRlist: no visible global function definition for ‘read.table’
rt: no visible global function definition for ‘read.table’
summary.admb: no visible global function definition for ‘coef’
summary.admb: no visible global function definition for ‘vcov’
summary.admb: no visible global function definition for ‘pnorm’
write_dat: no visible global function definition for ‘write.table’
write_pin: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  coef count.fields deviance head na.omit pnorm printCoefmat qnorm
  quantile read.table vcov write.table
Consider adding
  importFrom("stats", "coef", "deviance", "na.omit", "pnorm",
             "printCoefmat", "qnorm", "quantile", "vcov")
  importFrom("utils", "count.fields", "head", "read.table",
             "write.table")
to your NAMESPACE.

Found the following calls to attach():
File ‘R2admb/R/check_section.R’:
  attach(R_list, name = "R_list", warn.conflicts = FALSE)
See section ‘Good practice’ in ‘?attach’.

DONE
Status: 1 NOTE

R2STATS (0.68-38)

Maintainer: Yvonnick Noel

OK

RcmdrPlugin.NMBU (1.8.5)

Maintainer: Kristian Hovde Liland

OK

refund (0.1-14)

Maintainer: Lei Huang

OK

RLRsim (3.1-2)

Maintainer: Fabian Scheipl
Bug reports: https://github.com/fabian-s/RLRsim/issues

checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘SemiPar’

DONE
Status: 1 NOTE

robustlmm (1.8)

Maintainer: Manuel Koller

OK

rockchalk (1.8.92)

Maintainer: Paul E. Johnson

checking R code for possible problems ... NOTE
addLines: no visible global function definition for ‘lines’
cutByQuantile: no visible global function definition for ‘quantile’
cutBySD: no visible global function definition for ‘sd’
formatVC : <anonymous>: no visible global function definition for ‘as’
genCorrelatedData: no visible global function definition for ‘rnorm’
genCorrelatedData2: no visible global function definition for ‘rnorm’
getDeltaRsquare: no visible global function definition for ‘drop1’
getPartialCor: no visible global function definition for ‘model.matrix’
getPartialCor: no visible global function definition for ‘terms’
getPartialCor: no visible global function definition for
  ‘model.response’
getPartialCor: no visible global function definition for ‘model.frame’
getPartialCor: no visible global function definition for ‘cor’
lmAuxiliary: no visible global function definition for ‘model.matrix’
lmAuxiliary: no visible global function definition for ‘terms’
lmAuxiliary: no visible global function definition for ‘formula’
mcDiagnose: no visible global function definition for ‘coef’
mcDiagnose: no visible global function definition for ‘model.matrix’
mcDiagnose: no visible global function definition for ‘cor’
mcGraph1: no visible global function definition for ‘points’
mcGraph2: no visible global function definition for ‘points’
mcGraph2: no visible global function definition for ‘arrows’
mcGraph3: no visible global function definition for ‘points’
mcGraph3: no visible global function definition for ‘lm’
mcGraph3 : <anonymous>: no visible global function definition for
  ‘predict’
mcGraph3: no visible global function definition for ‘lines’
mcGraph3: no visible global function definition for ‘fitted’
mcGraph3: no visible global function definition for ‘arrows’
meanCenter.default : std: no visible global function definition for
  ‘sd’
meanCenter.default : formulaReplace: no visible global function
  definition for ‘setNames’
model.data.default: no visible binding for global variable ‘na.omit’
model.data.default: no visible global function definition for ‘formula’
model.data.default: no visible global function definition for
  ‘model.frame’
model.data.default: no visible global function definition for
  ‘as.formula’
mvrnorm: no visible global function definition for ‘rnorm’
newdata.default: no visible global function definition for ‘terms’
outreg : checkReg : <anonymous>: no visible global function definition
  for ‘methods’
outreg : harvest: no visible global function definition for ‘pf’
outreg : getBSE: no visible global function definition for ‘coef’
outreg : getBSE: no visible global function definition for
  ‘df.residual’
outreg : getBSE: no visible global function definition for ‘nobs’
outreg : getBSE: no visible global function definition for
  ‘model.matrix’
outreg : getBSE: no visible global function definition for ‘pt’
outreg: no visible global function definition for ‘pchisq’
outreg: no visible global function definition for ‘AIC’
outreg: no visible global function definition for ‘browseURL’
outreg0 : checkReg : <anonymous>: no visible global function definition
  for ‘methods’
outreg0 : harvest: no visible global function definition for ‘pf’
outreg0: no visible global function definition for ‘coef’
outreg0: no visible global function definition for ‘vcov’
outreg0 : sigtest: no visible global function definition for ‘pt’
outreg0: no visible global function definition for ‘pchisq’
outreg0: no visible global function definition for ‘AIC’
pctable.character: no visible global function definition for ‘formula’
pctable.default: no visible global function definition for ‘modifyList’
pctable.default: no visible global function definition for ‘addmargins’
pctable.formula: no visible global function definition for ‘terms’
pctable.formula: no visible binding for global variable ‘na.pass’
pctable.formula: no visible global function definition for ‘modifyList’
perspEmpty: no visible global function definition for ‘modifyList’
plot.testSlopes: no visible global function definition for
  ‘model.response’
plot.testSlopes: no visible global function definition for
  ‘model.frame’
plot.testSlopes: no visible global function definition for ‘qt’
plot.testSlopes: no visible global function definition for ‘terms’
plot.testSlopes: no visible global function definition for ‘coef’
plot.testSlopes: no visible global function definition for ‘vcov’
plot.testSlopes: no visible global function definition for ‘pt’
plot.testSlopes: no visible global function definition for ‘plot’
plot.testSlopes: no visible global function definition for ‘abline’
plot.testSlopes: no visible global function definition for ‘lines’
plot.testSlopes: no visible global function definition for ‘arrows’
plot.testSlopes: no visible global function definition for ‘polygon’
plot.testSlopes: no visible global function definition for ‘mtext’
plot.testSlopes: no visible global function definition for ‘legend’
plot.testSlopes: no visible global function definition for ‘text’
plotCurves: no visible global function definition for ‘formula’
plotCurves: no visible global function definition for ‘model.frame’
plotCurves: no visible global function definition for ‘model.response’
plotCurves: no visible global function definition for ‘nobs’
plotCurves: no visible global function definition for ‘modifyList’
plotFancy: no visible global function definition for ‘modifyList’
plotFancy: no visible global function definition for ‘legend’
plotPlane: no visible global function definition for ‘formula’
plotPlane.default: no visible global function definition for ‘formula’
plotPlane.default: no visible global function definition for
  ‘model.frame’
plotPlane.default: no visible global function definition for
  ‘model.response’
plotPlane.default : myPredict: no visible global function definition
  for ‘predict’
plotPlane.default: no visible global function definition for
  ‘modifyList’
plotPlane.default: no visible global function definition for ‘predict’
plotPlane.default: no visible global function definition for ‘fitted’
plotPlane.default: no visible global function definition for ‘arrows’
plotPlane.default: no visible global function definition for ‘points’
plotPlane.default: no visible global function definition for ‘lines’
plotPlane.default : drawLine: no visible global function definition for
  ‘lines’
plotSlopes.lm: no visible global function definition for ‘model.matrix’
plotSlopes.lm: no visible global function definition for
  ‘model.response’
plotSlopes.lm: no visible global function definition for ‘model.frame’
plotSlopes.lm: no visible global function definition for ‘nobs’
plotSlopes.lm: no visible global function definition for ‘modifyList’
predict.mcreg: no visible global function definition for ‘formula’
predict.mcreg: no visible global function definition for ‘model.frame’
predict.rcreg: no visible global function definition for ‘model.frame’
predict.rcreg: no visible global function definition for ‘terms’
predict.rcreg: no visible global function definition for ‘predict.lm’
predictCI: no visible binding for global variable ‘na.pass’
predictCI: no visible global function definition for ‘modifyList’
predictCI: no visible global function definition for ‘predict’
predictCI: no visible global function definition for ‘predict.lm’
predictCI: no visible global function definition for ‘qnorm’
predictCI: no visible global function definition for ‘qt’
predictCI: no visible global function definition for ‘family’
predictCI: no visible global function definition for ‘napredict’
predictOMatic : <anonymous>: no visible global function definition for
  ‘modifyList’
predictOMatic: no visible global function definition for ‘modifyList’
residualCenter.default : createRCinteraction: no visible global
  function definition for ‘as.formula’
residualCenter.default : createRCinteraction: no visible global
  function definition for ‘terms’
residualCenter.default : createRCinteraction: no visible global
  function definition for ‘lm’
residualCenter.default : createRCinteraction: no visible global
  function definition for ‘resid’
residualCenter.default: no visible global function definition for
  ‘model.matrix’
residualCenter.default: no visible global function definition for
  ‘terms’
residualCenter.default: no visible global function definition for
  ‘as.formula’
residualCenter.default: no visible global function definition for
  ‘model.frame’
standardize.lm : formulaReplace: no visible global function definition
  for ‘setNames’
standardize.lm: no visible global function definition for ‘terms’
standardize.lm: no visible global function definition for ‘model.frame’
standardize.lm: no visible global function definition for
  ‘model.matrix’
standardize.lm: no visible global function definition for ‘formula’
summarize: no visible global function definition for ‘modifyList’
summarizeNumerics: no visible binding for global variable ‘sd’
summarizeNumerics: no visible binding for global variable ‘var’
summary.mcreg: no visible global function definition for ‘model.matrix’
summary.mcreg: no visible global function definition for ‘model.frame’
summary.mcreg: no visible global function definition for ‘terms’
summary.mcreg: no visible binding for global variable ‘sd’
summary.stdreg: no visible global function definition for
  ‘model.matrix’
summary.stdreg: no visible global function definition for ‘model.frame’
summary.stdreg: no visible global function definition for ‘terms’
summary.stdreg: no visible binding for global variable ‘sd’
testSlopes: no visible global function definition for ‘terms’
testSlopes: no visible global function definition for ‘coef’
testSlopes: no visible global function definition for ‘vcov’
testSlopes: no visible global function definition for ‘pt’
testSlopes: no visible global function definition for ‘model.frame’
testSlopes: no visible global function definition for ‘model.matrix’
testSlopes: no visible global function definition for ‘qt’
Undefined global functions or variables:
  AIC abline addmargins arrows as as.formula browseURL coef cor
  df.residual drop1 family fitted formula legend lines lm methods
  model.frame model.matrix model.response modifyList mtext na.omit
  na.pass napredict nobs pchisq pf plot points polygon predict
  predict.lm pt qnorm qt quantile resid rnorm sd setNames terms text
  var vcov
Consider adding
  importFrom("graphics", "abline", "arrows", "legend", "lines", "mtext",
             "plot", "points", "polygon", "text")
  importFrom("methods", "as")
  importFrom("stats", "AIC", "addmargins", "as.formula", "coef", "cor",
             "df.residual", "drop1", "family", "fitted", "formula", "lm",
             "model.frame", "model.matrix", "model.response", "na.omit",
             "na.pass", "napredict", "nobs", "pchisq", "pf", "predict",
             "predict.lm", "pt", "qnorm", "qt", "quantile", "resid",
             "rnorm", "sd", "setNames", "terms", "var", "vcov")
  importFrom("utils", "browseURL", "methods", "modifyList")
to your NAMESPACE (and ensure that your DESCRIPTION Imports field
contains 'methods').

checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘pequod’

checking examples ... ERROR
Running examples in ‘rockchalk-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: outreg
> ### Title: Creates a publication quality result table for regression
> ###   models. Works with models fitted with lm, glm, as well as lme4.
> ### Aliases: outreg
> ### Keywords: regression
> 
> ### ** Examples
> 
> set.seed(2134234)
> dat <- data.frame(x1 = rnorm(100), x2 = rnorm(100))
> dat$y1 <- 30 + 5 * rnorm(100) + 3 * dat$x1 + 4 * dat$x2
> dat$y2 <- rnorm(100) + 5 * dat$x2
> m1 <- lm(y1 ~ x1, data = dat)
> m2 <- lm(y1 ~ x2, data = dat)
> m3 <- lm(y1 ~ x1 + x2, data = dat)
> gm1 <- glm(y1 ~ x1, family = Gamma, data = dat)
> outreg(m1, title = "My One Tightly Printed Regression", float = TRUE )
\begin{table}
\caption{My One Tightly Printed Regression}\label{regrlabl}
 \begin{tabular}{*{2}{l}}
\hline
                  & M1   \tabularnewline
                   &Estimate \tabularnewline
                 &(S.E.) \tabularnewline
 \hline
 \hline
   (Intercept)     &30.245*** \tabularnewline
                 &(0.618)  \tabularnewline
   x1              &1.546* \tabularnewline
                 &(0.692)  \tabularnewline
 \hline
 N                 &100       \tabularnewline
 RMSE             &6.121   \tabularnewline
 $R^2$             &0.048   \tabularnewline
 \hline
\hline
 
 \multicolumn{2}{c}{${*  p}\le 0.05$${*\!\!*  p}\le 0.01$${*\!\!*\!\!*  p}\le 0.001$}\tabularnewline
 \end{tabular}
 \end{table}
> 
> outreg(list("Fingers" = m1), tight = FALSE,
+     title = "My Only Spread Out Regressions", float = TRUE,
+     alpha = c(0.05, 0.01, 0.001))
\begin{table}
\caption{My Only Spread Out Regressions}\label{regrlabl}
 \begin{tabular}{*{3}{l}}
\hline
                  & \multicolumn{2}{c}{Fingers}   \tabularnewline
                   &Estimate  &(S.E.)  \tabularnewline
 \hline
 \hline
   (Intercept)     &30.245***   &   (0.618) \tabularnewline
   x1              &1.546*   &   (0.692) \tabularnewline
 \hline
 N                 &100       &        \tabularnewline
 RMSE             &6.121         & \tabularnewline
 $R^2$             &0.048         & \tabularnewline
 \hline
\hline
 
 \multicolumn{3}{c}{${*  p}\le 0.05$${*\!\!*  p}\le 0.01$${*\!\!*\!\!*  p}\le 0.001$}\tabularnewline
 \end{tabular}
 \end{table}
> 
> outreg(list("Model A" = m1, "Model B label with Spaces" = m2),
+     varLabels = list(x1 = "Billie"),
+     title = "My Two Linear Regressions", request = c(fstatistic = "F"))
\begin{table}
\caption{My Two Linear Regressions}\label{regrlabl}
 \begin{tabular}{*{3}{l}}
\hline
                  & Model A & Model B label with Spaces   \tabularnewline
                   &Estimate   &Estimate \tabularnewline
                 &(S.E.)   &(S.E.) \tabularnewline
 \hline
 \hline
   (Intercept)     &30.245*** &29.774*** \tabularnewline
                 &(0.618)   &(0.522)  \tabularnewline
   Billie          &1.546*   & .      \tabularnewline
                 &(0.692)   &        \tabularnewline
   x2                & .      &3.413*** \tabularnewline
                 &         &(0.512)  \tabularnewline
 \hline
 N                 &100       &100       \tabularnewline
 RMSE             &6.121   &5.205   \tabularnewline
 $R^2$             &0.048   &0.312   \tabularnewline
 adj $R^2$         &0.039   &0.305   \tabularnewline
 F                &4.98 df(1,98)*   &44.4 df(1,98)***   \tabularnewline
 \hline
\hline
 
 \multicolumn{3}{c}{${*  p}\le 0.05$${*\!\!*  p}\le 0.01$${*\!\!*\!\!*  p}\le 0.001$}\tabularnewline
 \end{tabular}
 \end{table}
> 
> outreg(list("Model A" = m1, "Model B" = m2),
+     modelLabels = c("Overrides ModelA", "Overrides ModelB"),
+     varLabels = list(x1 = "Billie"),
+     title = "Note modelLabels Overrides model names")
\begin{table}
\caption{Note modelLabels Overrides model names}\label{regrlabl}
 \begin{tabular}{*{3}{l}}
\hline
                  & Overrides ModelA & Overrides ModelB   \tabularnewline
                   &Estimate   &Estimate \tabularnewline
                 &(S.E.)   &(S.E.) \tabularnewline
 \hline
 \hline
   (Intercept)     &30.245*** &29.774*** \tabularnewline
                 &(0.618)   &(0.522)  \tabularnewline
   Billie          &1.546*   & .      \tabularnewline
                 &(0.692)   &        \tabularnewline
   x2                & .      &3.413*** \tabularnewline
                 &         &(0.512)  \tabularnewline
 \hline
 N                 &100       &100       \tabularnewline
 RMSE             &6.121   &5.205   \tabularnewline
 $R^2$             &0.048   &0.312   \tabularnewline
 adj $R^2$         &0.039   &0.305   \tabularnewline
 \hline
\hline
 
 \multicolumn{3}{c}{${*  p}\le 0.05$${*\!\!*  p}\le 0.01$${*\!\!*\!\!*  p}\le 0.001$}\tabularnewline
 \end{tabular}
 \end{table}
> 
> ex5 <- outreg(list("Whichever" = m1, "Whatever" = m2),
+     title = "Still have showAIC argument, as in previous versions",
+     showAIC = TRUE, float = TRUE)
\begin{table}
\caption{Still have showAIC argument, as in previous versions}\label{regrlabl}
 \begin{tabular}{*{3}{l}}
\hline
                  & Whichever & Whatever   \tabularnewline
                   &Estimate   &Estimate \tabularnewline
                 &(S.E.)   &(S.E.) \tabularnewline
 \hline
 \hline
   (Intercept)     &30.245*** &29.774*** \tabularnewline
                 &(0.618)   &(0.522)  \tabularnewline
   x1              &1.546*   & .      \tabularnewline
                 &(0.692)   &        \tabularnewline
   x2                & .      &3.413*** \tabularnewline
                 &         &(0.512)  \tabularnewline
 \hline
 N                 &100       &100       \tabularnewline
 RMSE             &6.121   &5.205   \tabularnewline
 $R^2$             &0.048   &0.312   \tabularnewline
 adj $R^2$         &0.039   &0.305   \tabularnewline
 AIC      & 650.109      & 617.694 \tabularnewline
 \hline
\hline
 
 \multicolumn{3}{c}{${*  p}\le 0.05$${*\!\!*  p}\le 0.01$${*\!\!*\!\!*  p}\le 0.001$}\tabularnewline
 \end{tabular}
 \end{table}
> ## make a file:
> ## cat(ex5, file = "some_name_you_choose.tex")
> 
> ## No test: 
> ex5html <- outreg(list("Whichever" = m1, "Whatever" = m2),
+     title = "Still have showAIC argument, as in previous versions",
+     showAIC = TRUE, type = "html")

 You asked for html output, but set browser = FALSE.As a result, we suspect you know what you are doing.Inspect the output object, write it to a file with cat, as in:myreg <- 
outreg(modelList = list(Whichever = m1, Whatever = m2), type = "html", 
    showAIC = TRUE, title = "Still have showAIC argument, as in previous versions")
 
 cat(myreg, file = "reg.html")
 Then open reg.html in a word processor or web browser.
> ## make a file:
> ## cat(ex5html, file = "some_name_you_choose.html")
> ## Open that in LibreOffice or MS Word
> ## End(No test)
> 
> outreg(list("Whatever" = m1, "Whatever" =m2),
+     title = "Another way to get AIC output",
+     runFuns = c("AIC" = "Akaike IC"))
\begin{table}
\caption{Another way to get AIC output}\label{regrlabl}
 \begin{tabular}{*{3}{l}}
\hline
                  & Whatever & Whatever.1   \tabularnewline
                   &Estimate   &Estimate \tabularnewline
                 &(S.E.)   &(S.E.) \tabularnewline
 \hline
 \hline
   (Intercept)     &30.245*** &29.774*** \tabularnewline
                 &(0.618)   &(0.522)  \tabularnewline
   x1              &1.546*   & .      \tabularnewline
                 &(0.692)   &        \tabularnewline
   x2                & .      &3.413*** \tabularnewline
                 &         &(0.512)  \tabularnewline
 \hline
 N                 &100       &100       \tabularnewline
 RMSE             &6.121   &5.205   \tabularnewline
 $R^2$             &0.048   &0.312   \tabularnewline
 adj $R^2$         &0.039   &0.305   \tabularnewline
 Akaike IC        &650.11   &617.69   \tabularnewline
 \hline
\hline
 
 \multicolumn{3}{c}{${*  p}\le 0.05$${*\!\!*  p}\le 0.01$${*\!\!*\!\!*  p}\le 0.001$}\tabularnewline
 \end{tabular}
 \end{table}
> 
> outreg(list("Amod" = m1, "Bmod" = m2, "Gmod" = m3),
+     title = "My Three Linear Regressions", float = FALSE)
\begin{table}
\caption{My Three Linear Regressions}\label{regrlabl}
 \begin{tabular}{*{4}{l}}
\hline
                  & Amod & Bmod & Gmod   \tabularnewline
                   &Estimate   &Estimate   &Estimate \tabularnewline
                 &(S.E.)   &(S.E.)   &(S.E.) \tabularnewline
 \hline
 \hline
   (Intercept)     &30.245*** &29.774*** &30.013*** \tabularnewline
                 &(0.618)   &(0.522)   &(0.490)  \tabularnewline
   x1              &1.546*   & .      &2.217*** \tabularnewline
                 &(0.692)   &         &(0.555)  \tabularnewline
   x2                & .      &3.413*** &3.717*** \tabularnewline
                 &         &(0.512)   &(0.483)  \tabularnewline
 \hline
 N                 &100       &100       &100       \tabularnewline
 RMSE             &6.121   &5.205   &4.849   \tabularnewline
 $R^2$             &0.048   &0.312   &0.409   \tabularnewline
 adj $R^2$         &0.039   &0.305   &0.397   \tabularnewline
 \hline
\hline
 
 \multicolumn{4}{c}{${*  p}\le 0.05$${*\!\!*  p}\le 0.01$${*\!\!*\!\!*  p}\le 0.001$}\tabularnewline
 \end{tabular}
 \end{table}
> 
> ## A new feature in 1.85 is ability to provide vectors of beta estimates
> ## standard errors, and p values if desired.
> ## Suppose you have robust standard errors!
> library(car)
> newSE <- sqrt(diag(car::hccm(m3)))
> ## See 2 versions of m3 in the table?
> outreg(list("Model A" = m1, "Model B" = m2, "Model C" = m3, "Model C w Robust SE" = m3),
+         SElist= list("Model C w Robust SE" = newSE))
\begin{tabular}{*{5}{l}}
\hline
                  & Model A & Model B & Model C & Model C w Robust SE   \tabularnewline
                   &Estimate   &Estimate   &Estimate   &Estimate \tabularnewline
                 &(S.E.)   &(S.E.)   &(S.E.)   &(S.E.) \tabularnewline
 \hline
 \hline
   (Intercept)     &30.245*** &29.774*** &30.013*** &30.013*** \tabularnewline
                 &(0.618)   &(0.522)   &(0.490)   &(0.481)  \tabularnewline
   x1              &1.546*   & .      &2.217*** &2.217*** \tabularnewline
                 &(0.692)   &         &(0.555)   &(0.618)  \tabularnewline
   x2                & .      &3.413*** &3.717*** &3.717*** \tabularnewline
                 &         &(0.512)   &(0.483)   &(0.464)  \tabularnewline
 \hline
 N                 &100       &100       &100       &100       \tabularnewline
 RMSE             &6.121   &5.205   &4.849   &4.849   \tabularnewline
 $R^2$             &0.048   &0.312   &0.409   &0.409   \tabularnewline
 adj $R^2$         &0.039   &0.305   &0.397   &0.397   \tabularnewline
 \hline
\hline
 
 \multicolumn{5}{c}{${*  p}\le 0.05$${*\!\!*  p}\le 0.01$${*\!\!*\!\!*  p}\le 0.001$}\tabularnewline
 \end{tabular}
> 
> ## outreg uses a t or normal approximation to calculate p values, but you can
> ## calculate your own.  Let's dial down those std errors but insist they are
> ## not significantly different from zero
> newSE <- 0.3*newSE
> newPvals <- rep(0.1, length(newSE))
> 
> ## No test: 
> ## Pass in your own SE and P values.
> outreg(list("Model A" = m1, "Model B" = m2, "Model C" = m3),
+        SElist = list("Model C" = newSE),
+        PVlist = list("Model C" = newPvals), alpha = c(0.05, 0.01, 0.001))
\begin{tabular}{*{4}{l}}
\hline
                  & Model A & Model B & Model C   \tabularnewline
                   &Estimate   &Estimate   &Estimate \tabularnewline
                 &(S.E.)   &(S.E.)   &(S.E.) \tabularnewline
 \hline
 \hline
   (Intercept)     &30.245*** &29.774*** &30.013 \tabularnewline
                 &(0.618)   &(0.522)   &(0.144)  \tabularnewline
   x1              &1.546*   & .      &2.217 \tabularnewline
                 &(0.692)   &         &(0.185)  \tabularnewline
   x2                & .      &3.413*** &3.717 \tabularnewline
                 &         &(0.512)   &(0.139)  \tabularnewline
 \hline
 N                 &100       &100       &100       \tabularnewline
 RMSE             &6.121   &5.205   &4.849   \tabularnewline
 $R^2$             &0.048   &0.312   &0.409   \tabularnewline
 adj $R^2$         &0.039   &0.305   &0.397   \tabularnewline
 \hline
\hline
 
 \multicolumn{4}{c}{${*  p}\le 0.05$${*\!\!*  p}\le 0.01$${*\!\!*\!\!*  p}\le 0.001$}\tabularnewline
 \end{tabular}
> ## It took me a while to realize we might as well allow the user to
> ## pass in a vector of Beta estimates as well. Seems obvious now, though.
> outreg(list("Model C" = m3, "Model C Robust SE" = m3, "Model C MLv2" = m3),
+        Blist = list("Model C MLv2" = c("(Intercept)" = 0.222, "x1" = 0.222, "x2" = 0.222)),
+        SElist = list("Model C Robust SE" = newSE, "Model C MLv2" = 1.4*newSE),
+        PVlist = list("Model C" = newPvals),
+        alpha = c(0.05, 0.01, 0.001), type = "html")

 You asked for html output, but set browser = FALSE.As a result, we suspect you know what you are doing.Inspect the output object, write it to a file with cat, as in:myreg <- 
outreg(modelList = list(`Model C` = m3, `Model C Robust SE` = m3, 
    `Model C MLv2` = m3), type = "html", alpha = c(0.05, 0.01, 
    0.001), SElist = list(`Model C Robust SE` = newSE, `Model C MLv2` = 1.4 * 
    newSE), PVlist = list(`Model C` = newPvals), Blist = list(`Model C MLv2` = c(`(Intercept)` = 0.222, 
    x1 = 0.222, x2 = 0.222)))
 
 cat(myreg, file = "reg.html")
 Then open reg.html in a word processor or web browser.
> ## End(No test)
> 
> outreg(list("I Love Long Titles" = m1,
+        "Prefer Brevity" = m2,
+        "Short" = m3), tight = FALSE, float = FALSE)
\begin{tabular}{*{7}{l}}
\hline
                  & \multicolumn{2}{c}{I Love Long Titles} & \multicolumn{2}{c}{Prefer Brevity} & \multicolumn{2}{c}{Short}   \tabularnewline
                   &Estimate  &(S.E.)    &Estimate  &(S.E.)    &Estimate  &(S.E.)  \tabularnewline
 \hline
 \hline
   (Intercept)     &30.245***   &   (0.618) &29.774***   &   (0.522) &30.013***   &   (0.490) \tabularnewline
   x1              &1.546*   &   (0.692)   & .        &         &2.217***   &   (0.555) \tabularnewline
   x2                & .        &         &3.413***   &   (0.512) &3.717***   &   (0.483) \tabularnewline
 \hline
 N                 &100       &        &100       &        &100       &        \tabularnewline
 RMSE             &6.121         & &5.205         & &4.849         & \tabularnewline
 $R^2$             &0.048         & &0.312         & &0.409         & \tabularnewline
 adj $R^2$         &0.039         & &0.305         & &0.397         & \tabularnewline
 \hline
\hline
 
 \multicolumn{7}{c}{${*  p}\le 0.05$${*\!\!*  p}\le 0.01$${*\!\!*\!\!*  p}\le 0.001$}\tabularnewline
 \end{tabular}
> 
> outreg(list("GLM" = gm1), float = TRUE)
\begin{table}
\caption{A Regression}\label{regrlabl}
 \begin{tabular}{*{2}{l}}
\hline
                  & GLM   \tabularnewline
                   &Estimate \tabularnewline
                 &(S.E.) \tabularnewline
 \hline
 \hline
   (Intercept)     &0.033*** \tabularnewline
                 &(0.001)  \tabularnewline
   x1              &-0.002* \tabularnewline
                 &(0.001)  \tabularnewline
 \hline
 N                 &100       \tabularnewline
   Deviance         &4.301   \tabularnewline
 $-2LLR (Model chi^2)$        & 0.208 \tabularnewline
 \hline
\hline
 
 \multicolumn{2}{c}{${*  p}\le 0.05$${*\!\!*  p}\le 0.01$${*\!\!*\!\!*  p}\le 0.001$}\tabularnewline
 \end{tabular}
 \end{table}
> 
> outreg(list("OLS" = m1, "GLM" = gm1), float = TRUE,
+     alpha = c(0.05, 0.01))
\begin{table}
\caption{A Regression}\label{regrlabl}
 \begin{tabular}{*{3}{l}}
\hline
                  & OLS & GLM   \tabularnewline
                   &Estimate   &Estimate \tabularnewline
                 &(S.E.)   &(S.E.) \tabularnewline
 \hline
 \hline
   (Intercept)     &30.245** &0.033** \tabularnewline
                 &(0.618)   &(0.001)  \tabularnewline
   x1              &1.546* &-0.002* \tabularnewline
                 &(0.692)   &(0.001)  \tabularnewline
 \hline
 N                 &100       &100       \tabularnewline
 RMSE             &6.121   &       \tabularnewline
 $R^2$             &0.048   &       \tabularnewline
 Deviance         &       &4.301   \tabularnewline
 $-2LLR (Model chi^2)$         &       & 0.208 \tabularnewline
 \hline
\hline
 
 \multicolumn{3}{c}{${*  p}\le 0.05$${*\!\!*  p}\le 0.01$}\tabularnewline
 \end{tabular}
 \end{table}
> 
> outreg(list(OLS = m1, GLM = gm1), float = TRUE,
+     request = c(fstatistic = "F"), runFuns = c("BIC" = "BIC"))
\begin{table}
\caption{A Regression}\label{regrlabl}
 \begin{tabular}{*{3}{l}}
\hline
                  & OLS & GLM   \tabularnewline
                   &Estimate   &Estimate \tabularnewline
                 &(S.E.)   &(S.E.) \tabularnewline
 \hline
 \hline
   (Intercept)     &30.245*** &0.033*** \tabularnewline
                 &(0.618)   &(0.001)  \tabularnewline
   x1              &1.546* &-0.002* \tabularnewline
                 &(0.692)   &(0.001)  \tabularnewline
 \hline
 N                 &100       &100       \tabularnewline
 RMSE             &6.121   &       \tabularnewline
 $R^2$             &0.048   &       \tabularnewline
 F                &4.98 df(1,98)*   &       \tabularnewline
 Deviance         &       &4.301   \tabularnewline
 $-2LLR (Model chi^2)$         &       & 0.208 \tabularnewline
 BIC              &657.92   &659.82   \tabularnewline
 \hline
\hline
 
 \multicolumn{3}{c}{${*  p}\le 0.05$${*\!\!*  p}\le 0.01$${*\!\!*\!\!*  p}\le 0.001$}\tabularnewline
 \end{tabular}
 \end{table}
> 
> outreg(list(OLS = m1, GLM = gm1), float = TRUE,
+     request = c(fstatistic = "F"), runFuns = c("BIC" = "BIC"),
+     digits = 5, alpha = c(0.01))
\begin{table}
\caption{A Regression}\label{regrlabl}
 \begin{tabular}{*{3}{l}}
\hline
                  & OLS & GLM   \tabularnewline
                   &Estimate   &Estimate \tabularnewline
                 &(S.E.)   &(S.E.) \tabularnewline
 \hline
 \hline
   (Intercept)     &30.24550* &0.03313* \tabularnewline
                 &(0.61763)   &(0.00068)  \tabularnewline
   x1              &1.54553 &-0.00173 \tabularnewline
                 &(0.69242)   &(0.00078)  \tabularnewline
 \hline
 N                 &100       &100       \tabularnewline
 RMSE             &6.12090   &       \tabularnewline
 $R^2$             &0.04838   &       \tabularnewline
 F                &4.9821 df(1,98)   &       \tabularnewline
 Deviance         &       &4.30066   \tabularnewline
 $-2LLR (Model chi^2)$         &       & 0.20827 \tabularnewline
 BIC              &657.92   &659.82   \tabularnewline
 \hline
\hline
 
 \multicolumn{3}{c}{${*  p}\le 0.01$}\tabularnewline
 \end{tabular}
 \end{table}
> 
> outreg(list("OLS 1" = m1, "OLS 2" = m2,  GLM = gm1), float = TRUE,
+     request = c(fstatistic = "F"),
+     runFuns = c("BIC" = "BIC", logLik = "ll"),
+     digits = 5, alpha = c(0.05, 0.01, 0.001))
\begin{table}
\caption{A Regression}\label{regrlabl}
 \begin{tabular}{*{4}{l}}
\hline
                  & OLS 1 & OLS 2 & GLM   \tabularnewline
                   &Estimate   &Estimate   &Estimate \tabularnewline
                 &(S.E.)   &(S.E.)   &(S.E.) \tabularnewline
 \hline
 \hline
   (Intercept)     &30.24550*** &29.77420*** &0.03313*** \tabularnewline
                 &(0.61763)   &(0.52229)   &(0.00068)  \tabularnewline
   x1              &1.54553*   & .      &-0.00173* \tabularnewline
                 &(0.69242)   &         &(0.00078)  \tabularnewline
   x2                & .      &3.41342***   & .      \tabularnewline
                 &         &(0.51222)   &        \tabularnewline
 \hline
 N                 &100       &100       &100       \tabularnewline
 RMSE             &6.12090   &5.20508   &       \tabularnewline
 $R^2$             &0.04838   &0.31184   &       \tabularnewline
 adj $R^2$         &0.03867   &0.30482   &       \tabularnewline
 F                &4.9821 df(1,98)*   &44.409 df(1,98)***   &       \tabularnewline
 Deviance         &       &       &4.30066   \tabularnewline
 $-2LLR (Model chi^2)$         &        &       & 0.20827 \tabularnewline
 BIC              &657.92   &625.51   &659.82   \tabularnewline
 ll               &-322.05 (df=3)   &-305.85 (df=3)   &-323 (df=3)   \tabularnewline
 \hline
\hline
 
 \multicolumn{4}{c}{${*  p}\le 0.05$${*\!\!*  p}\le 0.01$${*\!\!*\!\!*  p}\le 0.001$}\tabularnewline
 \end{tabular}
 \end{table}
> 
> outreg(list("Model A" = gm1, "Model B label with Spaces" = m2),
+     request = c(fstatistic = "F"),
+     runFuns = c("BIC" = "Schwarz IC", "AIC" = "Akaike IC",
+     "nobs" = "N Again?"))
\begin{tabular}{*{3}{l}}
\hline
                  & Model A & Model B label with Spaces   \tabularnewline
                   &Estimate   &Estimate \tabularnewline
                 &(S.E.)   &(S.E.) \tabularnewline
 \hline
 \hline
   (Intercept)     &0.033*** &29.774*** \tabularnewline
                 &(0.001)   &(0.522)  \tabularnewline
   x1              &-0.002*   & .      \tabularnewline
                 &(0.001)   &        \tabularnewline
   x2                & .      &3.413*** \tabularnewline
                 &         &(0.512)  \tabularnewline
 \hline
 N                 &100       &100       \tabularnewline
 RMSE             &       &5.205   \tabularnewline
 $R^2$             &       &0.312   \tabularnewline
 adj $R^2$         &       &0.305   \tabularnewline
 F                &       &44.4 df(1,98)***   \tabularnewline
 Deviance         &4.301   &       \tabularnewline
 $-2LLR (Model chi^2)$        & 0.208        & \tabularnewline
 Schwarz IC       &659.82   &625.51   \tabularnewline
 Akaike IC        &652.00   &617.69   \tabularnewline
 N Again?         &100    &100    \tabularnewline
 \hline
\hline
 
 \multicolumn{3}{c}{${*  p}\le 0.05$${*\!\!*  p}\le 0.01$${*\!\!*\!\!*  p}\le 0.001$}\tabularnewline
 \end{tabular}
> 
> ## Here's a fit example from lme4.
> if (require(lme4)){
+   fm1 <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy)
+   outreg(fm1)
+   ## Fit same with lm for comparison
+   lm1 <- lm(Reaction ~ Days, sleepstudy)
+   ## Get robust standard errors
+   lm1rse <- sqrt(diag(car::hccm(lm1)))
+ ## No test: 
+   outreg(list("Random Effects" = fm1, "OLS" = lm1, "OLS Robust SE" = lm1),
+        SElist = list("OLS Robust SE" = lm1rse), type = "html")
+   
+ ## End(No test)
+   ## From the glmer examples
+   gm2 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd),
+                    data = cbpp, family = binomial)
+   lm2 <- lm(incidence/size ~ period,  data = cbpp)
+   lm2rse <- sqrt(diag(hccm(lm2)))
+   library(MASS)
+   ## Lets see what MASS::rlm objects do? Mostly OK
+   rlm2 <- MASS::rlm(incidence/size ~ period, data = cbpp)
+   ## No test: 
+   outreg(list("GLMER" = gm2, "lm" = lm2, "lm w/robust se" = lm2, "rlm" = rlm2),
+        SElist = list("lm w/robust se" = lm2rse), type = "html")
+   
+ ## End(No test)
+ }
Loading required package: lme4
Loading required package: Matrix
\begin{tabular}{*{2}{l}}
\hline
                  & M1   \tabularnewline
                   &Estimate \tabularnewline
                 &(S.E.) \tabularnewline
 \hline
 \hline
   (Intercept)     &251.405*** \tabularnewline
                 &(6.825)  \tabularnewline
   Days            &10.467*** \tabularnewline
                 &(1.546)  \tabularnewline
 \hline
 N                 &180       \tabularnewline
 RMSE             &25.592   \tabularnewline
  Random Effects ($\sigma$)\tabularnewline
  Residual          & 25.59 \tabularnewline
  Subject          & 24.74 \tabularnewline
  Subject:Days          &  5.92 \tabularnewline
 \hline
\hline
 
 \multicolumn{2}{c}{${*  p}\le 0.05$${*\!\!*  p}\le 0.01$${*\!\!*\!\!*  p}\le 0.001$}\tabularnewline
 \end{tabular}

 You asked for html output, but set browser = FALSE.As a result, we suspect you know what you are doing.Inspect the output object, write it to a file with cat, as in:myreg <- 
outreg(modelList = list(`Random Effects` = fm1, OLS = lm1, `OLS Robust SE` = lm1), 
    type = "html", SElist = list(`OLS Robust SE` = lm1rse))
 
 cat(myreg, file = "reg.html")
 Then open reg.html in a word processor or web browser.

Attaching package: ‘MASS’

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

    mvrnorm

Error in rep(" ", max(2, 6 - nchar(x[mname]))) : invalid 'times' argument
Calls: outreg -> gofPrint -> gofRow -> paste
Execution halted

DONE
Status: 1 ERROR, 2 NOTEs

RRreg (0.6.1)

Maintainer: Daniel W. Heck

OK

rstanarm (2.9.0-1)

Maintainer: Ben Goodrich
Bug reports: https://github.com/stan-dev/rstanarm/issues

checking installed package size ... NOTE
  installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   5.1Mb

checking S3 generic/method consistency ... WARNING
VarCorr:
  function(x, sigma, ...)
VarCorr.stanreg:
  function(x, sigma, rdig)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.

checking tests ... ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Chain 2, Iteration: 201 / 400 [ 50%]  (Sampling)
  Chain 2, Iteration: 400 / 400 [100%]  (Sampling)# 
  #  Elapsed Time: 1.39812 seconds (Warm-up)
  #                0.820442 seconds (Sampling)
  #                2.21857 seconds (Total)
  # 
  testthat results ================================================================
  OK: 900 SKIPPED: 0 FAILED: 1
  1. Failure (at test_posterior_predict.R#205): posterior_predict close to predict.merMod for binomial 
  
  Error: testthat unit tests failed
  In addition: There were 25 warnings (use warnings() to see them)
  Execution halted

DONE
Status: 1 ERROR, 1 WARNING, 1 NOTE

RVAideMemoire (0.9-52)

Maintainer: Maxime Herv

checking Rd cross-references ... NOTE
Packages unavailable to check Rd xrefs: ‘plsRglm’, ‘labdsv’, ‘RGCCA’, ‘mvnormtest’

DONE
Status: 1 NOTE

RVFam (1.1)

Maintainer: Ming-Huei Chen

checking R code for possible problems ... NOTE
coxph.EC : maf.fun: no visible global function definition for ‘na.omit’
coxph.EC : maf.fun.x: no visible global function definition for
  ‘na.omit’
coxph.EC : cor.snp: no visible global function definition for ‘sd’
coxph.EC : cor.snp: no visible global function definition for ‘cor’
coxph.EC: no visible global function definition for ‘pchisq’
coxph.ped : read.in.data: no visible global function definition for
  ‘read.table’
coxph.ped: no visible global function definition for ‘read.csv’
coxph.ped: no visible global function definition for ‘na.omit’
coxph.ped: no visible global function definition for ‘var’
coxph.ped: no visible binding for global variable ‘var’
coxph.ped: no visible global function definition for ‘cor’
coxph.ped: no visible global function definition for ‘write.table’
coxph.ped: no visible global function definition for ‘read.table’
coxph.ped: no visible global function definition for ‘dbeta’
coxph.ped: no visible global function definition for ‘pchisq’
gc.fun: no visible global function definition for ‘read.csv’
gc.fun: no visible global function definition for ‘read.table’
gc.fun: no visible global function definition for ‘qchisq’
gc.fun: no visible global function definition for ‘median’
gc.fun: no visible global function definition for ‘na.omit’
gc.fun: no visible global function definition for ‘pchisq’
gc.fun: no visible global function definition for ‘write.table’
gc.fun: no visible global function definition for ‘dbeta’
glmm.EC : maf.fun: no visible global function definition for ‘na.omit’
glmm.EC : maf.fun.x: no visible global function definition for
  ‘na.omit’
glmm.EC : cor.snp: no visible global function definition for ‘sd’
glmm.EC : cor.snp: no visible global function definition for ‘cor’
glmm.EC: no visible global function definition for ‘logLik’
glmm.EC: no visible global function definition for ‘coef’
glmm.EC: no visible global function definition for ‘pchisq’
glmm.binped : read.in.data: no visible global function definition for
  ‘read.table’
glmm.binped: no visible global function definition for ‘read.csv’
glmm.binped: no visible global function definition for ‘na.omit’
glmm.binped: no visible global function definition for ‘var’
glmm.binped: no visible binding for global variable ‘var’
glmm.binped: no visible global function definition for ‘cor’
glmm.binped: no visible global function definition for ‘write.table’
glmm.binped: no visible global function definition for ‘read.table’
glmm.binped: no visible global function definition for ‘dbeta’
glmm.binped: no visible global function definition for ‘pchisq’
lme.EC : maf.fun: no visible global function definition for ‘na.omit’
lme.EC : maf.fun.x: no visible global function definition for ‘na.omit’
lme.EC : cor.snp: no visible global function definition for ‘sd’
lme.EC : cor.snp: no visible global function definition for ‘cor’
lme.EC: no visible global function definition for ‘pchisq’
lme.ped : read.in.data: no visible global function definition for
  ‘read.table’
lme.ped: no visible global function definition for ‘read.csv’
lme.ped: no visible global function definition for ‘na.omit’
lme.ped: no visible global function definition for ‘var’
lme.ped: no visible binding for global variable ‘var’
lme.ped: no visible global function definition for ‘cor’
lme.ped: no visible global function definition for ‘write.table’
lme.ped: no visible global function definition for ‘read.table’
lme.ped: no visible global function definition for ‘dbeta’
lme.ped: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  coef cor dbeta logLik median na.omit pchisq qchisq read.csv
  read.table sd var write.table
Consider adding
  importFrom("stats", "coef", "cor", "dbeta", "logLik", "median",
             "na.omit", "pchisq", "qchisq", "sd", "var")
  importFrom("utils", "read.csv", "read.table", "write.table")
to your NAMESPACE.

DONE
Status: 1 NOTE

SASmixed (1.0-4)

Maintainer: Steven Walker

OK

simr (1.0.1)

Maintainer: Peter Green
Bug reports: https://github.com/pitakakariki/simr/issues

OK

sjmisc (1.4)

Maintainer: Daniel Lüdecke

OK

sjPlot (1.9)

Maintainer: Daniel Lüdecke
Bug reports: https://github.com/sjPlot/devel/issues

OK

SoyNAM (1.2)

Maintainer: Alencar Xavier

OK

spaMM (1.7.2)

Maintainer: François Rousset

OK

SPOT (1.0.5543)

Maintainer: Martin Zaefferer

checking package dependencies ... NOTE
Packages suggested but not available for checking: ‘penalizedSVM’ ‘tgp’

checking R code for possible problems ... NOTE
dacePrepareFit: no visible binding for global variable ‘sd’
dacePrepareFit: no visible global function definition for ‘sd’
dacePrepareFit: no visible global function definition for ‘tail’
forrBuilder: no visible global function definition for ‘runif’
forrBuilder: no visible global function definition for ‘dist’
forrCoBuilder: no visible global function definition for ‘runif’
forrCoBuilder: no visible global function definition for ‘dist’
spotAlgEs: no visible global function definition for ‘median’
spotAlgEs: no visible global function definition for ‘par’
spotAlgEs: no visible global function definition for ‘plot’
spotAlgEs: no visible global function definition for ‘lines’
spotAlgEsIndividualInitial: no visible global function definition for
  ‘rnorm’
spotAlgEsObjMutation: no visible global function definition for ‘rnorm’
spotAlgEsStratMutation: no visible global function definition for
  ‘runif’
spotAlgEsStratMutation: no visible global function definition for
  ‘rnorm’
spotAlgStartEs: no visible global function definition for ‘read.table’
spotAlgStartEs: no visible global function definition for ‘write.table’
spotAlgStartEsGlg: no visible global function definition for
  ‘read.table’
spotAlgStartEsGlg: no visible global function definition for
  ‘write.table’
spotAlgStartEsVar: no visible global function definition for
  ‘read.table’
spotAlgStartEsVar: no visible global function definition for ‘sd’
spotAlgStartEsVar: no visible global function definition for
  ‘write.table’
spotAlgStartRgp: no visible global function definition for ‘read.table’
spotAlgStartRgp: no visible global function definition for
  ‘write.table’
spotAlgStartSann: no visible global function definition for
  ‘read.table’
spotAlgStartSann: no visible global function definition for ‘runif’
spotAlgStartSann: no visible global function definition for ‘optim’
spotAlgStartSann: no visible global function definition for
  ‘write.table’
spotAlgStartSannVar: no visible global function definition for
  ‘read.table’
spotAlgStartSannVar: no visible global function definition for ‘runif’
spotAlgStartSannVar: no visible global function definition for ‘optim’
spotAlgStartSannVar: no visible global function definition for ‘sd’
spotAlgStartSannVar: no visible global function definition for
  ‘write.table’
spotAlgStartSmsEmoaGlg: no visible global function definition for
  ‘read.table’
spotAlgStartSmsEmoaGlg: no visible global function definition for
  ‘write.table’
spotCalcNoise: no visible global function definition for ‘rnorm’
spotCodeFormulas: no visible global function definition for
  ‘as.formula’
spotEnsembleMultiChoose: no visible global function definition for
  ‘runif’
spotEnsembleSingleBLAbern: no visible global function definition for
  ‘rbeta’
spotEnsembleSingleBLAnorm: no visible global function definition for
  ‘rnorm’
spotEnsembleSingleEpsGreedy: no visible global function definition for
  ‘runif’
spotEnsembleSinglePOKER: no visible global function definition for
  ‘pnorm’
spotEnsembleSingleSoftMax: no visible global function definition for
  ‘runif’
spotEnsembleStatsSd: no visible binding for global variable ‘sd’
spotExiPsi: no visible global function definition for ‘dnorm’
spotExiPsi: no visible global function definition for ‘pnorm’
spotFeedback.sd.interSubModelsFull: no visible binding for global
  variable ‘sd’
spotFuncStartBranin: no visible global function definition for
  ‘read.table’
spotFuncStartBranin: no visible global function definition for
  ‘write.table’
spotFuncStartDisBranin: no visible global function definition for
  ‘read.table’
spotFuncStartDisBranin: no visible global function definition for
  ‘write.table’
spotFuncStartMexicanHat: no visible global function definition for
  ‘read.table’
spotFuncStartMexicanHat: no visible global function definition for
  ‘write.table’
spotFuncStartRastrigin: no visible global function definition for
  ‘read.table’
spotFuncStartRastrigin: no visible global function definition for
  ‘write.table’
spotFuncStartRosenbrock: no visible global function definition for
  ‘read.table’
spotFuncStartRosenbrock: no visible global function definition for
  ‘write.table’
spotFuncStartSixHump: no visible global function definition for
  ‘read.table’
spotFuncStartSixHump: no visible global function definition for
  ‘write.table’
spotFuncStartSphere: no visible global function definition for
  ‘read.table’
spotFuncStartSphere: no visible global function definition for
  ‘write.table’
spotGetRawResData: no visible global function definition for
  ‘read.table’
spotGlgCore: no visible global function definition for ‘runif’
spotGlgCreateRotSearched: no visible global function definition for
  ‘runif’
spotInfillExpImp: no visible global function definition for ‘pnorm’
spotInfillProbImp: no visible global function definition for ‘pnorm’
spotInstAndLoadPackages: no visible global function definition for
  ‘installed.packages’
spotInstAndLoadPackages: no visible global function definition for
  ‘install.packages’
spotInvChisq: no visible global function definition for ‘rchisq’
spotNormDesign: no visible global function definition for ‘runif’
spotNormDesign: no visible global function definition for ‘dist’
spotOptimInterface: no visible global function definition for
  ‘read.table’
spotOptimizationInterface: no visible global function definition for
  ‘runif’
spotOptimizationInterface: no visible global function definition for
  ‘optim’
spotPenalizeMissingValues: no visible global function definition for
  ‘predict’
spotPlotBst: no visible global function definition for ‘par’
spotPlotBst: no visible global function definition for ‘plot’
spotPlotBst: no visible global function definition for ‘mtext’
spotPredictDice: no visible global function definition for ‘predict’
spotPredictEarth: no visible global function definition for ‘predict’
spotPredictEsvm: no visible global function definition for ‘predict’
spotPredictForrester: no visible global function definition for
  ‘predict’
spotPredictGausspr: no visible global function definition for ‘predict’
spotPredictGausspr: no visible global function definition for ‘median’
spotPredictKrig: no visible global function definition for ‘predict’
spotPredictKrig: no visible global function definition for ‘median’
spotPredictKsvm: no visible global function definition for ‘predict’
spotPredictKsvm: no visible global function definition for ‘median’
spotPredictLm: no visible global function definition for ‘as.formula’
spotPredictLm: no visible global function definition for ‘predict’
spotPredictLmFactor: no visible global function definition for ‘lm’
spotPredictLmFactor: no visible global function definition for
  ‘predict’
spotPredictMlegp: no visible global function definition for ‘predict’
spotPredictQrnn: no visible global function definition for ‘median’
spotPredictRandomForest: no visible global function definition for
  ‘predict’
spotPredictRandomForest: no visible binding for global variable ‘sd’
spotPredictTgp: no visible global function definition for ‘predict’
spotPredictTree: no visible global function definition for ‘predict’
spotPrepare: no visible global function definition for ‘graphics.off’
spotPrepareData: no visible binding for global variable ‘var’
spotPrepareData : fnvar: no visible binding for global variable ‘var’
spotReadBstFile: no visible global function definition for ‘read.table’
spotReadRoi: no visible global function definition for ‘read.table’
spotReport3dMulti: no visible binding for global variable ‘C’
spotReportContourMulti : plotFn: no visible global function definition
  for ‘dev.new’
spotReportContourMulti: no visible binding for global variable ‘C’
spotReportDefault: no visible global function definition for ‘pdf’
spotReportDefault: no visible global function definition for ‘par’
spotReportDefault: no visible global function definition for ‘plot’
spotReportDefault: no visible global function definition for ‘text’
spotReportDefault: no visible global function definition for ‘dev.off’
spotReportDefault: no visible global function definition for ‘dev.new’
spotReportEarth: no visible global function definition for ‘dev.new’
spotReportEarth: no visible global function definition for ‘plot’
spotReportMAMP: no visible global function definition for ‘str’
spotReportMAMP: no visible global function definition for ‘dev.new’
spotReportMAMP: no visible global function definition for ‘as.formula’
spotReportMAMP: no visible global function definition for ‘plot’
spotReportMAMP: no visible global function definition for ‘abline’
spotReportMAMP: no visible global function definition for ‘qqnorm’
spotReportMAMP: no visible global function definition for ‘resid’
spotReportMAMP: no visible global function definition for ‘qqline’
spotReportMAMP: no visible global function definition for ‘aggregate’
spotReportMAMP: no visible global function definition for ‘qtukey’
spotReportMetaDefault: no visible global function definition for
  ‘read.table’
spotReportSAMP: no visible global function definition for ‘dev.new’
spotReportSAMP: no visible global function definition for ‘plot’
spotReportSAMP: no visible global function definition for ‘abline’
spotReportSAMP: no visible global function definition for ‘qqnorm’
spotReportSAMP: no visible global function definition for ‘resid’
spotReportSAMP: no visible global function definition for ‘qqline’
spotReportSAMP: no visible global function definition for ‘pf’
spotReportSAMP: no visible global function definition for ‘qt’
spotReportSens: no visible global function definition for ‘sd’
spotReportSens: no visible global function definition for ‘pdf’
spotReportSens: no visible global function definition for ‘matplot’
spotReportSens: no visible global function definition for ‘matpoints’
spotReportSens: no visible global function definition for ‘legend’
spotReportSens: no visible global function definition for ‘dev.off’
spotReportSens: no visible global function definition for ‘dev.new’
spotReportSensY: no visible global function definition for ‘predict’
spotSExI2d: no visible global function definition for ‘pnorm’
spotSelectionScaledSse: no visible global function definition for ‘var’
spotSelectionScaledSse: no visible global function definition for ‘cov’
spotSmsEmoa: no visible global function definition for ‘runif’
spotSmsEmoaKriging: no visible global function definition for ‘runif’
spotStepMetaOpt: no visible global function definition for
  ‘graphics.off’
spotStepMetaOpt: no visible global function definition for ‘read.table’
spotStepMetaOpt: no visible global function definition for
  ‘write.table’
spotSurf3d: no visible global function definition for ‘topo.colors’
spotSurfContour: no visible binding for global variable
  ‘terrain.colors’
spotSurfContour: no visible global function definition for
  ‘filled.contour’
spotSurfContour: no visible global function definition for ‘points’
spotSurfContour: no visible global function definition for ‘axis’
spotVersion: no visible global function definition for
  ‘packageDescription’
spotWriteAroi: no visible global function definition for ‘write.table’
spotWriteBest: no visible global function definition for ‘write.table’
spotWriteDes: no visible global function definition for ‘write.table’
spotWriteRes: no visible global function definition for ‘write.table’
spotWriteRoiFileForRepeats: no visible global function definition for
  ‘read.table’
Undefined global functions or variables:
  C abline aggregate as.formula axis cov dev.new dev.off dist dnorm
  filled.contour graphics.off install.packages installed.packages
  legend lines lm matplot matpoints median mtext optim
  packageDescription par pdf pf plot pnorm points predict qqline qqnorm
  qt qtukey rbeta rchisq read.table resid rnorm runif sd str tail
  terrain.colors text topo.colors var write.table
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "graphics.off", "pdf",
             "terrain.colors", "topo.colors")
  importFrom("graphics", "abline", "axis", "filled.contour", "legend",
             "lines", "matplot", "matpoints", "mtext", "par", "plot",
             "points", "text")
  importFrom("stats", "C", "aggregate", "as.formula", "cov", "dist",
             "dnorm", "lm", "median", "optim", "pf", "pnorm", "predict",
             "qqline", "qqnorm", "qt", "qtukey", "rbeta", "rchisq",
             "resid", "rnorm", "runif", "sd", "var")
  importFrom("utils", "install.packages", "installed.packages",
             "packageDescription", "read.table", "str", "tail",
             "write.table")
to your NAMESPACE.

DONE
Status: 2 NOTEs

Surrogate (0.1-66)

Maintainer: Wim Van der Elst
Bug reports: Wim Van der Elst

OK

TcGSA (0.10.1)

Maintainer: Boris P. Hejblum
Bug reports: https://github.com/borishejblum/TcGSA/issues

checking package dependencies ... ERROR
Package required but not available: ‘multtest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

DONE
Status: 1 ERROR

texreg (1.36)

Maintainer: Philip Leifeld

checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  ‘censReg’ ‘dynlm’ ‘eha’ ‘erer’ ‘fGarch’ ‘gmm’ ‘latentnet’ ‘mnlogit’
  ‘relevent’ ‘RSiena’ ‘sampleSelection’ ‘simex’ ‘systemfit’

DONE
Status: 1 NOTE

tnam (1.6)

Maintainer: Philip Leifeld

OK

TripleR (1.4.1)

Maintainer: Felix Schönbrodt

checking R code for possible problems ... NOTE
RR.bivariate: no visible global function definition for ‘pt’
RR.multi: no visible global function definition for ‘formula’
RR.multi.uni: no visible global function definition for ‘formula’
RR.multi.uni: no visible global function definition for ‘weighted.mean’
RR.multi.uni: no visible global function definition for ‘var’
RR.univariate: no visible global function definition for ‘pt’
RR.univariate: no visible global function definition for
  ‘capture.output’
getEffects: no visible global function definition for ‘formula’
long2matrix: no visible global function definition for ‘as.formula’
noVar: no visible global function definition for ‘var’
parCor: no visible global function definition for ‘sd’
parCor: no visible global function definition for ‘na.omit’
parCor: no visible global function definition for ‘resid’
parCor: no visible global function definition for ‘lm’
parCor: no visible binding for global variable ‘na.exclude’
parCor: no visible global function definition for ‘cor’
parCor: no visible global function definition for ‘pt’
plot.RRmulti: no visible global function definition for ‘rnorm’
plot.RRmulti: no visible global function definition for ‘qt’
plot.RRmulti: no visible global function definition for ‘na.omit’
selfCor: no visible global function definition for ‘cor.test’
weighted.t.test: no visible global function definition for
  ‘weighted.mean’
weighted.t.test: no visible global function definition for ‘pt’
weighted.t.test: no visible global function definition for ‘qt’
Undefined global functions or variables:
  as.formula capture.output cor cor.test formula lm na.exclude na.omit
  pt qt resid rnorm sd var weighted.mean
Consider adding
  importFrom("stats", "as.formula", "cor", "cor.test", "formula", "lm",
             "na.exclude", "na.omit", "pt", "qt", "resid", "rnorm", "sd",
             "var", "weighted.mean")
  importFrom("utils", "capture.output")
to your NAMESPACE.

DONE
Status: 1 NOTE

visreg (2.2-1)

Maintainer: Patrick Breheny

OK