whether the namespace can be loaded with stated dependencies
whether the namespace can be unloaded cleanly
PDF version of manual without hyperrefs or index
loading without being on the library search path

Malformed Title field: should not end in a period.
Non-standard file/directory found at top level:
  ‘doc’
Packages in Depends field not imported from:
  ‘Rglpk’ ‘corrplot’ ‘lattice’ ‘rgl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
multiplot: no visible global function definition for ‘rainbow’
multiplot: no visible global function definition for ‘plot’
multiplot: no visible global function definition for ‘text’
multiplot: no visible global function definition for ‘lines’
multiplot: no visible global function definition for ‘par’
plot.abf2: no visible global function definition for ‘plot’
plot.abf2: no visible global function definition for ‘abline’
plot.abf2: no visible global function definition for ‘text’
plot.abf2split: no visible global function definition for ‘plot’
Undefined global functions or variables:
  abline lines par plot rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "par", "plot", "text")
to your NAMESPACE file.
Package suggested but not available for checking: ‘INLA’
Malformed Description field: should contain one or more complete sentences.
fillCSVData: no visible global function definition for ‘read.table’
fillData: no visible global function definition for ‘edit’
plotGraphs: no visible global function definition for ‘par’
plotGraphs: no visible global function definition for ‘plot’
plotGraphs: no visible global function definition for ‘lines’
plotGraphs: no visible global function definition for ‘legend’
plotGraphs: no visible global function definition for ‘dev.new’
Undefined global functions or variables:
  dev.new edit legend lines par plot read.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "lines", "par", "plot")
  importFrom("utils", "edit", "read.table")
to your NAMESPACE file.
Package has no Sweave vignette sources and no VignetteBuilder field.
print.funlinWLS: no visible global function definition for ‘pchisq’
print.linML: no visible global function definition for ‘pchisq’
print.loglinML: no visible global function definition for ‘pchisq’
print.satMarML: no visible global function definition for ‘pchisq’
print.satMcarWLS: no visible global function definition for ‘pchisq’
summary.funlinWLS: no visible global function definition for ‘pchisq’
summary.linML: no visible global function definition for ‘pchisq’
summary.loglinML: no visible global function definition for ‘pchisq’
summary.satMarML: no visible global function definition for ‘pchisq’
summary.satMcarWLS: no visible global function definition for ‘pchisq’
summary.waldTest: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
Package in Depends field not imported from: ‘MASS’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
acm: no visible global function definition for ‘read.table’
clusters: no visible global function definition for ‘write.matrix’
clusters: no visible global function definition for ‘dev.new’
clusters: no visible global function definition for ‘par’
clusters: no visible global function definition for ‘hist’
clusters: no visible global function definition for ‘legend’
clusters: no visible global function definition for ‘pdf’
clusters: no visible global function definition for ‘dev.off’
erra: no visible global function definition for ‘read.table’
erra: no visible global function definition for ‘pbeta’
Undefined global functions or variables:
  dev.new dev.off hist legend par pbeta pdf read.table write.matrix
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("graphics", "hist", "legend", "par")
  importFrom("stats", "pbeta")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘acopula-Ex.R’
'library' or 'require' call to ‘mvtnorm’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  print.eCopulaArchimax print.eCopulaGeneric print.gCopula
  print.isCopula
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Aggregate: no visible global function definition for ‘aggregate’
Aggregate: no visible binding for global variable ‘tail’
Aggregate: no visible binding for global variable ‘var’
cocktailEnsemble: no visible global function definition for ‘glm’
cocktailEnsemble: no visible global function definition for ‘binomial’
cocktailEnsemble: no visible global function definition for ‘step’
cocktailEnsemble: no visible binding for global variable ‘na.omit’
imputeMissings : <anonymous>: no visible global function definition for
  ‘median’
predict.cocktailEnsemble: no visible global function definition for
  ‘predict’
Undefined global functions or variables:
  aggregate binomial glm median na.omit predict step tail var
Consider adding
  importFrom("stats", "aggregate", "binomial", "glm", "median",
             "na.omit", "predict", "step", "var")
  importFrom("utils", "tail")
to your NAMESPACE file.
Rd file 'cocktailEnsemble.Rd':
  \examples lines wider than 100 characters:
     Credit <- data.frame(Credit[order(runif(nrow(Credit ))),])[1:100,c('V2','V3','V8','V11','V14','V15','Response')]

Rd file 'predict.cocktailEnsemble.Rd':
  \examples lines wider than 100 characters:
     Credit <- data.frame(Credit[order(runif(nrow(Credit ))),])[1:100,c('V2','V3','V8','V11','V14','V15','Response')]

These lines will be truncated in the PDF manual.
Missing or unexported object: ‘devtools::clean_source’
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘SemiPar’ ‘nlme’
  Please remove these calls from your code.
asp: no visible global function definition for ‘as.formula’
asp: no visible global function definition for ‘var’
aspm: no visible binding for global variable ‘X.Declan’
aspm: no visible binding for global variable ‘Z.Jaida’
aspm: no visible binding for global variable ‘group.vec.Handan’
aspm: no visible global function definition for ‘as.formula’
aspm: no visible global function definition for ‘glm’
aspm: no visible global function definition for ‘binomial’
aspm: no visible global function definition for ‘poisson’
Undefined global functions or variables:
  X.Declan Z.Jaida as.formula binomial glm group.vec.Handan poisson var
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "poisson", "var")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘AdaptFit/R/aspm.R’:
  assign("group.vec.Handan", group.vec, pos = 1)
  assign("X.Declan", X, pos = 1)
  assign("Z.Jaida", Z, pos = 1)

Found the following calls to attach():
File ‘AdaptFit/R/asp.R’:
  attach(theta.frame)
  attach(theta.frame)
See section ‘Good practice’ in ‘?attach’.
Rd file 'asp.Rd':
  \usage lines wider than 90 characters:
                     spar.method="REML",omit.missing=NULL,niter=20,niter.var=50,tol=1e-06,returnFit=FALSE,weights=NULL,correlation=NULL,cont ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Package required but not available: ‘phyloseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Depends: includes the non-default packages:
  'Matrix', 'coda', 'mvtnorm', 'MCMCpack', 'spatstat', 'parallel'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  ‘MCMCpack’ ‘Matrix’ ‘coda’ ‘mvtnorm’ ‘parallel’ ‘spatstat’
  Please remove these calls from your code.
Package in Depends field not imported from: ‘lattice’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'getpar.Rd':
  \examples lines wider than 100 characters:
     ## Plot the conditional error function of the Lehmacher-Wassmer (1999) type that runs through (p1,p2)=(0.3,0.7)

Rd file 'parconv.Rd':
  \examples lines wider than 100 characters:
     ## Obtain the parameter c for Fisher's combination test, using the local level 0.05 for the test after the second stage

Rd file 'pathCEF.Rd':
  \examples lines wider than 100 characters:
     ## Compare the tests by Bauer and Koehne (1994), Lehmacher and Wassmer (1999) and Vandemeulebroecke (2006)

Rd file 'tsT.Rd':
  \examples lines wider than 100 characters:
     ## An example of non-uniqueness: the maximal alpha1 is returned; any smaller value would also be valid

These lines will be truncated in the PDF manual.
critical.values: no visible global function definition for ‘rnorm’
critical.values: no visible global function definition for ‘quantile’
mandel.test: no visible global function definition for ‘qf’
mtukey.test : p.test: no visible global function definition for ‘qf’
mtukey.test: no visible binding for global variable ‘quantile’
mtukey.test: no visible global function definition for ‘rnorm’
tukey.test: no visible global function definition for ‘qf’
Undefined global functions or variables:
  qf quantile rnorm
Consider adding
  importFrom("stats", "qf", "quantile", "rnorm")
to your NAMESPACE file.
closure_total_fair: no visible global function definition for ‘is’
closure_transitive: no visible global function definition for ‘is’
de_transitive: no visible global function definition for ‘is’
get_equivalence_classes: no visible global function definition for ‘is’
get_incomparable_pairs: no visible global function definition for ‘is’
get_independent_sets: no visible global function definition for ‘is’
is_reflexive: no visible global function definition for ‘is’
is_total: no visible global function definition for ‘is’
is_transitive: no visible global function definition for ‘is’
pareto2_estimate_mle: no visible global function definition for
  ‘uniroot’
pareto2_test_f: no visible global function definition for ‘qf’
pareto2_test_f: no visible global function definition for ‘pf’
plot.citfun: no visible global function definition for ‘plot’
plot.citfun: no visible global function definition for ‘par’
plot.citfun: no visible global function definition for ‘segments’
plot.citfun: no visible global function definition for ‘points’
plot_producer: no visible global function definition for ‘plot’
plot_producer: no visible global function definition for ‘par’
plot_producer: no visible global function definition for ‘segments’
plot_producer: no visible global function definition for ‘points’
rpareto2: no visible global function definition for ‘runif’
Undefined global functions or variables:
  is par pf plot points qf runif segments uniroot
Consider adding
  importFrom("graphics", "par", "plot", "points", "segments")
  importFrom("methods", "is")
  importFrom("stats", "pf", "qf", "runif", "uniroot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package unavailable to check Rd xrefs: ‘Starr’
Namespace with empty importFrom: ‘survival’
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘survival’
A package should be listed in only one of these fields.
backfit.cox.interaction: no visible global function definition for
  ‘coxph’
backfit.lm.interaction: no visible global function definition for ‘lm’
backfit.logistic.interaction: no visible global function definition for
  ‘glm’
backfit.logistic.main: no visible global function definition for ‘glm’
cox.interaction: no visible global function definition for ‘coxph’
cv.cox.interaction: no visible global function definition for ‘coxph’
cv.cox.main: no visible global function definition for ‘coxph’
cv.lm.interaction: no visible global function definition for ‘lm’
cv.lm.main: no visible global function definition for ‘lm’
cv.logistic.interaction: no visible global function definition for
  ‘glm’
cv.logistic.main: no visible global function definition for ‘glm’
lm.interaction: no visible global function definition for ‘lm’
logistic.interaction: no visible global function definition for ‘glm’
logistic.main: no visible global function definition for ‘glm’
Undefined global functions or variables:
  coxph glm lm
Consider adding
  importFrom("stats", "glm", "lm")
to your NAMESPACE file.
dke.fun.default: no visible global function definition for ‘hist’
kef: no visible global function definition for ‘dbinom’
kef: no visible global function definition for ‘dgamma’
kef: no visible global function definition for ‘dlnorm’
plot.dke.fun: no visible global function definition for ‘hist’
plot.dke.fun: no visible global function definition for ‘lines’
plot.hcvc.fun1d: no visible global function definition for
  ‘plot.default’
plot.hcvd.fun1d: no visible global function definition for
  ‘plot.default’
plot.kern.fun1d: no visible global function definition for
  ‘plot.default’
plot.kpmfe.fun1d: no visible global function definition for
  ‘plot.default’
plot.reg.fun1d: no visible global function definition for
  ‘plot.default’
simp_int: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx dbinom dgamma dlnorm hist lines plot.default
Consider adding
  importFrom("graphics", "hist", "lines", "plot.default")
  importFrom("stats", "approx", "dbinom", "dgamma", "dlnorm")
to your NAMESPACE file.
'library' or 'require' call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
akmeans: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  kmeans
Consider adding
  importFrom("stats", "kmeans")
to your NAMESPACE file.
adpbar: no visible global function definition for ‘optim’
alabama: no visible global function definition for ‘optim’
auglag: no visible global function definition for ‘modifyList’
auglag1: no visible global function definition for ‘optim’
auglag1: no visible global function definition for ‘nlminb’
auglag2: no visible global function definition for ‘optim’
auglag2: no visible global function definition for ‘nlminb’
auglag3: no visible global function definition for ‘optim’
auglag3: no visible global function definition for ‘nlminb’
augpen: no visible global function definition for ‘optim’
constrOptim.nl: no visible global function definition for ‘modifyList’
Undefined global functions or variables:
  modifyList nlminb optim
Consider adding
  importFrom("stats", "nlminb", "optim")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
eval.blockdesign: no visible global function definition for
  ‘model.matrix’
eval.design: no visible global function definition for ‘model.matrix’
expand.formula: no visible global function definition for ‘as.formula’
model.matrix.formula: no visible global function definition for
  ‘model.matrix.default’
model.matrix.terms: no visible global function definition for
  ‘model.matrix.default’
optBlock : set.factors: no visible global function definition for ‘C’
optBlock : remove.nesting: no visible global function definition for
  ‘as.formula’
optBlock: no visible global function definition for ‘formula’
optBlock: no visible global function definition for ‘model.matrix’
optFederov: no visible global function definition for ‘formula’
optFederov: no visible global function definition for ‘model.matrix’
optMonteCarlo : RandomLevels: no visible global function definition for
  ‘runif’
optMonteCarlo : RandomMixture: no visible global function definition
  for ‘rexp’
optMonteCarlo : expand: no visible global function definition for
  ‘model.matrix’
optMonteCarlo: no visible global function definition for ‘as.formula’
Undefined global functions or variables:
  C as.formula formula model.matrix model.matrix.default rexp runif
Consider adding
  importFrom("stats", "C", "as.formula", "formula", "model.matrix",
             "model.matrix.default", "rexp", "runif")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  print.spectral
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
hierarchical: no visible global function definition for ‘terms’
hierarchical: no visible global function definition for ‘loglin’
hierarchical: no visible global function definition for ‘dmultinom’
markov: no visible global function definition for ‘download.file’
metropolis: no visible global function definition for ‘runif’
mpolyListToMat : <anonymous>: no visible global function definition for
  ‘runif’
polyOptim: no visible global function definition for ‘deriv’
print.hierarchical: no visible binding for global variable ‘sd’
spectral : summarize: no visible global function definition for ‘sd’
subsets : <anonymous>: no visible global function definition for
  ‘combn’
Undefined global functions or variables:
  combn deriv dmultinom download.file loglin runif sd terms
Consider adding
  importFrom("stats", "deriv", "dmultinom", "loglin", "runif", "sd",
             "terms")
  importFrom("utils", "combn", "download.file")
to your NAMESPACE file.
gascuel: no visible global function definition for ‘optim’
Undefined global functions or variables:
  optim
Consider adding
  importFrom("stats", "optim")
to your NAMESPACE file.
allanVarSelect: no visible global function definition for ‘read.csv’
fitvbiglm: no visible global function definition for ‘read.csv’
fitvbiglm: no visible global function definition for ‘update’
getbestchunksize: no visible global function definition for ‘read.csv’
getbestchunksize: no visible global function definition for
  ‘object.size’
predictvbiglm: no visible global function definition for ‘read.csv’
predictvbiglm: no visible global function definition for ‘predict’
predictvbiglm: no visible global function definition for
  ‘weighted.mean’
readinbigdata : <anonymous>: no visible global function definition for
  ‘read.csv’
Undefined global functions or variables:
  object.size predict read.csv update weighted.mean
Consider adding
  importFrom("stats", "predict", "update", "weighted.mean")
  importFrom("utils", "object.size", "read.csv")
to your NAMESPACE file.
prepare_Rd: allan-package.Rd:49-51: Dropping empty section \seealso
prepare_Rd: allanVarSelect.Rd:59-60: Dropping empty section \details
prepare_Rd: allanVarSelect.Rd:66-67: Dropping empty section \references
prepare_Rd: allanVarSelect.Rd:78-79: Dropping empty section \seealso
prepare_Rd: fitvbiglm.Rd:38-39: Dropping empty section \details
prepare_Rd: fitvbiglm.Rd:49-50: Dropping empty section \note
prepare_Rd: fitvbiglm.Rd:43-44: Dropping empty section \references
prepare_Rd: fitvbiglm.Rd:53-54: Dropping empty section \seealso
prepare_Rd: getbestchunksize.Rd:35-36: Dropping empty section \details
prepare_Rd: getbestchunksize.Rd:46-47: Dropping empty section \note
prepare_Rd: getbestchunksize.Rd:40-41: Dropping empty section \references
prepare_Rd: getbestchunksize.Rd:50-51: Dropping empty section \seealso
prepare_Rd: predictvbiglm.Rd:44-45: Dropping empty section \details
prepare_Rd: predictvbiglm.Rd:56-57: Dropping empty section \note
prepare_Rd: predictvbiglm.Rd:50-51: Dropping empty section \references
prepare_Rd: predictvbiglm.Rd:60-61: Dropping empty section \seealso
prepare_Rd: readinbigdata.Rd:42-43: Dropping empty section \note
prepare_Rd: readinbigdata.Rd:45-46: Dropping empty section \seealso
Found the following apparent S3 methods exported but not registered:
  print.amAlleleFreq print.amDataset summary.amCluster
  summary.amPairwise summary.amUnique
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
amCSV.amCluster: no visible global function definition for ‘write.csv’
amCSV.amPairwise: no visible global function definition for ‘write.csv’
amCSV.amUnique: no visible global function definition for ‘write.csv’
amCluster: no visible global function definition for ‘hclust’
amCluster: no visible global function definition for ‘as.dist’
amHTML.amCluster: no visible global function definition for ‘browseURL’
amHTML.amPairwise: no visible global function definition for
  ‘browseURL’
amHTML.amUnique: no visible global function definition for ‘browseURL’
amUniqueProfile: no visible global function definition for ‘layout’
amUniqueProfile: no visible global function definition for ‘par’
amUniqueProfile: no visible global function definition for
  ‘plot.default’
amUniqueProfile: no visible global function definition for ‘points’
amUniqueProfile: no visible global function definition for ‘lines’
amUniqueProfile: no visible global function definition for ‘arrows’
amUniqueProfile: no visible global function definition for ‘text’
amUniqueProfile: no visible global function definition for ‘legend’
Undefined global functions or variables:
  arrows as.dist browseURL hclust layout legend lines par plot.default
  points text write.csv
Consider adding
  importFrom("graphics", "arrows", "layout", "legend", "lines", "par",
             "plot.default", "points", "text")
  importFrom("stats", "as.dist", "hclust")
  importFrom("utils", "browseURL", "write.csv")
to your NAMESPACE file.
File ‘allelic/libs/allelic.so’:
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Object: ‘newallelic.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
batch.possSpells.fnc: no visible binding for global variable ‘words’
possSpells.fnc: no visible binding for global variable ‘len.phons’
possSpells.fnc: no visible binding for global variable ‘phon1’
possSpells.fnc: no visible binding for global variable ‘len.total’
possSpells.fnc: no visible binding for global variable ‘poss.spells’
Undefined global functions or variables:
  len.phons len.total phon1 poss.spells words
EXP.step: no visible global function definition for ‘rgamma’
EXP.step: no visible global function definition for ‘rnorm’
MAX.step: no visible global function definition for ‘uniroot’
Norm.GMedian: no visible binding for global variable ‘median’
RNASeq.Data.Gene: no visible binding for global variable ‘quantile’
decom.initial: no visible global function definition for ‘kmeans’
decom.initial: no visible global function definition for ‘quantile’
decom.initial: no visible global function definition for ‘var’
dispersion.nb.QL: no visible binding for global variable ‘quantile’
est.mu.nb.mle: no visible global function definition for ‘runif’
est.v.nb.QL: no visible global function definition for ‘runif’
pdf2grid: no visible global function definition for ‘dnorm’
pdf2grid: no visible global function definition for ‘dgamma’
prior.grid: no visible global function definition for ‘sd’
prior.grid: no visible global function definition for ‘dnorm’
test.AMAP: no visible global function definition for ‘rgamma’
test.AMAP: no visible global function definition for ‘rnorm’
test.AMAP: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  dgamma dnorm kmeans median quantile rgamma rnorm runif sd uniroot var
Consider adding
  importFrom("stats", "dgamma", "dnorm", "kmeans", "median", "quantile",
             "rgamma", "rnorm", "runif", "sd", "uniroot", "var")
to your NAMESPACE file.
Rd file 'MGN.EM.Rd':
  \usage lines wider than 90 characters:
     MGN.EM(data, nK, p0 = NULL, d0 = 0, nK0 = 0, iter.max = 10, print.steps = FALSE, MGN0 = NULL, model = NULL, nMC = 10000)

Rd file 'test.AMAP.Rd':
  \usage lines wider than 90 characters:
     test.AMAP(data, MGN, del.lim = NULL, FC = NULL, print.steps = FALSE, Integration = "MC",nMC=NULL)
  \examples lines wider than 100 characters:
     data("SimuHapMap")  # a matrix 'counts' storing simulated data with 10000 genes, two treatments, of which each has 5 replicates

These lines will be truncated in the PDF manual.
amltest: no visible global function definition for ‘var’
amltest: no visible global function definition for ‘optim’
amltest: no visible global function definition for ‘lm’
cleanclust: no visible global function definition for ‘cor’
cleanclust: no visible global function definition for ‘hclust’
cleanclust: no visible global function definition for ‘as.dist’
cleanclust: no visible global function definition for ‘cutree’
Undefined global functions or variables:
  as.dist cor cutree hclust lm optim var
Consider adding
  importFrom("stats", "as.dist", "cor", "cutree", "hclust", "lm",
             "optim", "var")
to your NAMESPACE file.
AMOEBA : Classi: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
random.init.MLPneuron: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  track_methods.cpp:22:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  track_methods.cpp:23:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  track_methods.cpp:50:22: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  track_methods.cpp:52:22: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  track_methods.cpp:55:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/amt.Rcheck/00install.out’ for details.
Analyz.loadSteps,Analyz: no visible global function definition for
  ‘read.csv’
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Non-standard files/directories found at top level:
  ‘AnDE.pdf’ ‘DESCRIPTION.dcf’ ‘helpme’
Packages in Depends field not imported from:
  ‘discretization’ ‘foreign’ ‘functional’ ‘stringr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
aode: no visible global function definition for ‘Compose’
mdl: no visible global function definition for ‘cutPoints’
setVar: no visible global function definition for ‘Compose’
Undefined global functions or variables:
  Compose cutPoints
andrews: no visible global function definition for ‘plot.new’
andrews: no visible global function definition for ‘plot.window’
andrews: no visible global function definition for ‘title’
andrews: no visible global function definition for ‘axis’
andrews: no visible global function definition for ‘box’
andrews: no visible global function definition for ‘lines’
andrews: no visible global function definition for ‘rainbow’
andrews: no visible global function definition for ‘hsv’
selectand: no visible global function definition for ‘lines’
Undefined global functions or variables:
  axis box hsv lines plot.new plot.window rainbow title
Consider adding
  importFrom("grDevices", "hsv", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "title")
to your NAMESPACE file.
plot,ANFIS: no visible binding for global variable ‘X’
plotMF,ANFIS : <anonymous>: no visible global function definition for
  ‘lines’
plotMFs,ANFIS: no visible global function definition for ‘par’
Undefined global functions or variables:
  X lines par
Consider adding
  importFrom("graphics", "lines", "par")
to your NAMESPACE file.
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but not in PKG_CFLAGS
  src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but not in PKG_CFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
'library' or 'require' call to ‘tcltk’ which was already attached by Depends.
  Please remove these calls from your code.
annot : annotlist: no visible global function definition for
  ‘read.table’
annot : annotlist: no visible global function definition for
  ‘write.table’
annot: no visible global function definition for ‘flush.console’
annot: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  flush.console read.table write.table
Consider adding
  importFrom("utils", "flush.console", "read.table", "write.table")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from ‘anoint’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
Package suggested but not available for checking: ‘rhdf5’
aw_map: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
'library' or 'require' call to ‘boot’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  print.wald.test
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
varbin: no visible global function definition for ‘boot’
Undefined global functions or variables:
  boot
Packages in Depends field not imported from:
  ‘boot’ ‘lme4’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
TSPM: no visible global function definition for ‘glm’
TSPM: no visible binding for global variable ‘poisson’
TSPM: no visible global function definition for ‘hatvalues’
TSPM: no visible global function definition for ‘residuals’
TSPM: no visible global function definition for ‘deviance’
TSPM: no visible global function definition for ‘qchisq’
TSPM: no visible global function definition for ‘qf’
TSPM: no visible global function definition for ‘pf’
TSPM: no visible global function definition for ‘pchisq’
TSPM: no visible global function definition for ‘p.adjust’
norm.inttable: no visible global function definition for ‘median’
norm.inttable : <anonymous>: no visible global function definition for
  ‘quantile’
saint_permF: no visible global function definition for ‘read.table’
saint_permF: no visible global function definition for ‘write.table’
saint_permF: no visible global function definition for ‘write.csv2’
tspm_apms: no visible global function definition for ‘read.table’
varFilter : <anonymous>: no visible global function definition for
  ‘median’
varFilter: no visible global function definition for ‘median’
varFilter: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  deviance glm hatvalues median p.adjust pchisq pf poisson qchisq qf
  quantile read.table residuals write.csv2 write.table
Consider adding
  importFrom("stats", "deviance", "glm", "hatvalues", "median",
             "p.adjust", "pchisq", "pf", "poisson", "qchisq", "qf",
             "quantile", "residuals")
  importFrom("utils", "read.table", "write.csv2", "write.table")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘examples’
apple: no visible global function definition for ‘ginv’
apple: no visible global function definition for ‘runif’
deri: no visible global function definition for ‘ginv’
logit: no visible global function definition for ‘qlogis’
plot.apple: no visible global function definition for ‘matplot’
plot.apple: no visible global function definition for ‘lines’
y.app: no visible global function definition for ‘ginv’
Undefined global functions or variables:
  ginv lines matplot qlogis runif
Consider adding
  importFrom("graphics", "lines", "matplot")
  importFrom("stats", "qlogis", "runif")
to your NAMESPACE file.
prepare_Rd: plot.apple.Rd:51-53: Dropping empty section \examples
runAPSIM: warning in scan(reports_file[i], "", sep = "", skip =
  length(temp), nline = 1): partial argument match of ‘nline’ to
  ‘nlines’
runAPSIM: no visible global function definition for ‘write.table’
runAPSIM: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘apsrtable-Ex.R’
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.
kristen.colors: no visible global function definition for
  ‘colorRampPalette’
kristen.colors: no visible global function definition for ‘grey’
plot3d.points: no visible global function definition for ‘heat.colors’
plot3d.points: no visible global function definition for ‘plot’
ragged.image: no visible global function definition for ‘heat.colors’
ragged.image: no visible global function definition for ‘image’
scatterplot.density: no visible global function definition for ‘grey’
scatterplot.density: no visible global function definition for ‘image’
scatterplot.density: no visible global function definition for ‘abline’
scatterplot.density: no visible global function definition for ‘lm’
scatterplot.density: no visible global function definition for ‘legend’
vertical.image.legend: no visible global function definition for ‘par’
vertical.image.legend: no visible global function definition for
  ‘image’
vertical.image.legend: no visible global function definition for ‘axis’
vertical.image.legend: no visible global function definition for ‘box’
Undefined global functions or variables:
  abline axis box colorRampPalette grey heat.colors image legend lm par
  plot
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey", "heat.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "legend",
             "par", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
Found the following significant warnings:
  am.c:275:9: warning: comparison of array 'readByte' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/aqr.Rcheck/00install.out’ for details.
aqDayOfWeekStat: no visible global function definition for ‘index’
aqDropHour: no visible global function definition for ‘index’
aqFilterOHLCSD: no visible binding for global variable ‘sd’
aqHourIndex: no visible global function definition for ‘index’
aqHourlyStat: no visible global function definition for ‘index’
aqLoadOHLC: no visible global function definition for ‘read.csv’
aqLoadSeriesField: no visible global function definition for ‘read.csv’
aqLoadXtsFromCsv: no visible global function definition for ‘read.csv2’
aqLoadYahooEOD: no visible global function definition for ‘read.csv’
aqSaveXtsToCsv: no visible global function definition for ‘write.csv2’
aqStoreSeriesField: no visible global function definition for ‘index’
aqStoreSeriesField: no visible global function definition for
  ‘capture.output’
aqStoreSeriesField: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  capture.output index read.csv read.csv2 sd write.csv2 write.table
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "capture.output", "read.csv", "read.csv2",
             "write.csv2", "write.table")
to your NAMESPACE file.
AR1seg_func: no visible global function definition for ‘median’
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘MASS’ ‘TSP’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
ardec: no visible global function definition for ‘filter’
ardec.lm: no visible global function definition for ‘ar’
ardec.lm: no visible global function definition for ‘lm’
Undefined global functions or variables:
  ar filter lm
Consider adding
  importFrom("stats", "ar", "filter", "lm")
to your NAMESPACE file.
arfimaOLS: no visible global function definition for ‘lm’
arfimaPrep: no visible global function definition for ‘aggregate’
arfimaPrep: no visible global function definition for ‘arima’
arfimaPrep: no visible global function definition for ‘lm’
arfimaPrep: no visible global function definition for ‘residuals’
Undefined global functions or variables:
  aggregate arima lm residuals
Consider adding
  importFrom("stats", "aggregate", "arima", "lm", "residuals")
to your NAMESPACE file.
Rd file 'sdafilter.Rd':
  \examples lines wider than 100 characters:
     plot(lon,lat,col="lightgrey",type="l",xlim=c(5,18), ylim=c(77.1,79.1),xlab="Longitude",ylab="Latitude")

Rd file 'vmask.Rd':
  \examples lines wider than 100 characters:
     plot(lon,lat,col="lightgrey",type="l",xlim=c(5,18), ylim=c(77.1,79.1),xlab="Longitude",ylab="Latitude")

These lines will be truncated in the PDF manual.
Packages suggested but not available for checking:
  'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Found the following significant warnings:
  arrApply.cpp:189:29: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/arrApply.Rcheck/00install.out’ for details.
binarize.array: no visible binding for global variable ‘sd’
mskmeans: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  kmeans sd
Consider adding
  importFrom("stats", "kmeans", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: ‘cacheSweave’
Warning: no function found corresponding to methods exports from ‘ascii’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
'library' or 'require' calls in package code:
  ‘cacheSweave’ ‘weaver’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘utils:::RtangleSetup’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘survival:::survmean’ ‘utils:::.SweaveValidFilenameRegexp’
  ‘utils:::RtangleFinish’ ‘utils:::RtangleRuncode’
  ‘utils:::SweaveParseOptions’
  See the note in ?`:::` about the use of this operator.
Unavailable namespace imported from by a ':::' call: ‘cacheSweave’
  See the note in ?`:::` about the use of this operator.
Found the following apparent S3 methods exported but not registered:
  cbind.ascii
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'cbind.ascii':
  ‘cbind.ascii’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking: 'REBayes', 'Rmosek'
Problems with news in ‘inst/NEWS.Rd’:
  Malformed NEWS.Rd file:
  Chunk starting
    \itemize{
    This is the first documented NEWS release of ASM
  contains no \item.
'library' or 'require' calls to packages already attached by Depends:
  ‘Hmisc’ ‘splancs’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Hmisc’ ‘shapefiles’ ‘splancs’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'calc_box.Rd':
  \examples lines wider than 100 characters:
     ## plot_box by default takes as input the result produced from the calc_box, read from the current workspace. 

Rd file 'calc_sdd.Rd':
  \examples lines wider than 100 characters:
     ## plot_sdd by default takes as input the result produced from the calc_sdd, read from the current workspace. 

Rd file 'calc_sde.Rd':
  \examples lines wider than 100 characters:
     ## plot_sde by default takes as input the result produced from the calc_sde, read from the current workspace. 

Rd file 'centre.Rd':
  \examples lines wider than 100 characters:
     ## plot_centres by default takes as input the result produced from mean_centre, median centre, CF, CF2PTS, and CMD, read from the curre ... [TRUNCATED]

Rd file 'plot_box.Rd':
  \examples lines wider than 100 characters:
     ## plot_box by default takes as input the result produced from the calc_box, read from the current workspace. 

Rd file 'plot_centres.Rd':
  \examples lines wider than 100 characters:
     ## plot_centres by default takes as input the result produced from CF, CF2PTS, and CMD, read from the current workspace. 

Rd file 'plot_sdd.Rd':
  \examples lines wider than 100 characters:
     ## plot_sdd by default takes as input the result produced from the calc_sdd, read from the current workspace. 

Rd file 'plot_sde.Rd':
  \examples lines wider than 100 characters:
     ## plot_sde by default takes as input the result produced from the calc_sde, read from the current workspace. 

These lines will be truncated in the PDF manual.
ASP.Score: no visible global function definition for ‘pnorm’
Graphs.Bayesian: no visible global function definition for ‘dev.new’
colorhex: no visible global function definition for ‘gray’
colorhex: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  dev.new gray pnorm rgb
Consider adding
  importFrom("grDevices", "dev.new", "gray", "rgb")
  importFrom("stats", "pnorm")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘asreml’
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(devtools)
  > library(assertive.data)
  > 
  > with_envvar(
  +   c(LANG = "en_US"),
  +   test_check("assertive.data")
  + )
  Error in with_envvar(c(LANG = "en_US"), test_check("assertive.data")) : 
    could not find function "with_envvar"
  Execution halted
':::' call which should be '::': ‘assertive.base:::print_and_capture’
  See the note in ?`:::` about the use of this operator.
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(devtools)
  > library(assertive.matrices)
  > 
  > with_envvar(
  +   c(LANG = "en_US"),
  +   test_check("assertive.matrices")
  + )
  Error in with_envvar(c(LANG = "en_US"), test_check("assertive.matrices")) : 
    could not find function "with_envvar"
  Execution halted
Package in Depends field not imported from: ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CALPHA: no visible global function definition for ‘dbinom’
CALPHA: no visible global function definition for ‘pchisq’
CAST: no visible global function definition for ‘fisher.test’
CAST: no visible global function definition for ‘chisq.test’
CMC: no visible global function definition for ‘pf’
MULTI: no visible global function definition for ‘complete.cases’
RVT1: no visible global function definition for ‘pchisq’
RVT2: no visible global function definition for ‘pchisq’
RWAS: no visible global function definition for ‘pnorm’
SKAT: no visible global function definition for ‘dbeta’
SKAT: no visible global function definition for ‘pchisq’
TTEST: no visible global function definition for ‘complete.cases’
TTEST: no visible global function definition for ‘pf’
WST: no visible global function definition for ‘mvfft’
WST: no visible global function definition for ‘pnorm’
my_cmc_method: no visible global function definition for
  ‘complete.cases’
my_getUV: no visible global function definition for ‘complete.cases’
my_orwss_method: no visible global function definition for ‘sd’
my_rarecov_method: no visible global function definition for
  ‘chisq.test’
my_rbt_method: no visible global function definition for ‘ppois’
my_score_method: no visible global function definition for ‘pchisq’
my_ssu_method: no visible global function definition for ‘pchisq’
my_ssuw_method: no visible global function definition for ‘pchisq’
my_sum_method: no visible global function definition for ‘pchisq’
my_uminp_method: no visible global function definition for ‘pchisq’
my_uminp_method: no visible global function definition for ‘pmvnorm’
Undefined global functions or variables:
  chisq.test complete.cases dbeta dbinom fisher.test mvfft pchisq pf
  pmvnorm pnorm ppois sd
Consider adding
  importFrom("stats", "chisq.test", "complete.cases", "dbeta", "dbinom",
             "fisher.test", "mvfft", "pchisq", "pf", "pnorm", "ppois",
             "sd")
to your NAMESPACE file.
beamDiskOverlap: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
fm_unred: no visible global function definition for ‘spline’
galage: no visible global function definition for ‘integrate’
lumdist: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate spline
Consider adding
  importFrom("stats", "integrate", "spline")
to your NAMESPACE file.
Dependence on R version ‘3.4.2’ not with patchlevel 0
VPC.graph : findQuantile: no visible global function definition for
  ‘quantile’
VPC.graph : findQuantileCI : <anonymous>: no visible global function
  definition for ‘quantile’
asVPC.binW: no visible global function definition for ‘median’
asVPC.binW : <anonymous>: no visible global function definition for
  ‘quantile’
asVPC.binW: no visible global function definition for ‘quantile’
asVPC.distanceW: no visible global function definition for ‘median’
asVPC.distanceW : <anonymous>: no visible global function definition
  for ‘quantile’
asVPC.distanceW: no visible global function definition for ‘quantile’
makeCOVbin: no visible global function definition for ‘quantile’
makeCOVbin: no visible global function definition for ‘median’
read_Simdata: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  median quantile read.table
Consider adding
  importFrom("stats", "median", "quantile")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘cairoDevice’ ‘gWidgetsRGtk2’ ‘partitions’ ‘proto’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
get.est.ATT: no visible global function definition for ‘tail’
get.est.MT: no visible global function definition for ‘tail’
get.est.simple: no visible global function definition for ‘tail’
newton.r: no visible global function definition for ‘tail’
plot.ATE: no visible global function definition for ‘par’
plot.ATE: no visible global function definition for ‘plot’
plot.ATE: no visible global function definition for ‘axis’
plot.ATE: no visible global function definition for ‘abline’
plot.ATE: no visible global function definition for ‘lines’
plot.ATE: no visible global function definition for ‘legend’
plot.ATE: no visible global function definition for ‘points’
print.summary.ATE: no visible global function definition for
  ‘printCoefmat’
summary.ATE: no visible global function definition for ‘qnorm’
summary.ATE: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline axis legend lines par plot pnorm points printCoefmat qnorm
  tail
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "points")
  importFrom("stats", "pnorm", "printCoefmat", "qnorm")
  importFrom("utils", "tail")
to your NAMESPACE file.
atmcmc : rmvtnorm: no visible global function definition for ‘rnorm’
atmcmc: no visible global function definition for ‘rnorm’
atmcmc: no visible global function definition for ‘runif’
atmcmc: no visible global function definition for ‘par’
atmcmc: no visible global function definition for ‘lm’
atmcmc: no visible global function definition for ‘lines’
atmcmc: no visible global function definition for ‘var’
atmcmc: no visible global function definition for ‘cov’
atmcmc: no visible global function definition for ‘quantile’
atmcmc: no visible global function definition for ‘sd’
plotmcmc: no visible global function definition for ‘pdf’
plotmcmc: no visible global function definition for ‘par’
plotmcmc: no visible global function definition for ‘dev.new’
plotmcmc: no visible global function definition for ‘png’
plotmcmc: no visible global function definition for ‘hist’
plotmcmc: no visible global function definition for ‘dev.off’
plotmcmc: no visible global function definition for ‘plot’
plotmcmc: no visible global function definition for ‘lines’
Undefined global functions or variables:
  cov dev.new dev.off hist lines lm par pdf plot png quantile rnorm
  runif sd var
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf", "png")
  importFrom("graphics", "hist", "lines", "par", "plot")
  importFrom("stats", "cov", "lm", "quantile", "rnorm", "runif", "sd",
             "var")
to your NAMESPACE file.
LHSdesign: no visible global function definition for ‘qnorm’
LHSdesign: no visible global function definition for ‘qunif’
LHSdesign: no visible global function definition for ‘qt’
MCdesign: no visible global function definition for ‘rnorm’
MCdesign: no visible global function definition for ‘runif’
MCdesign: no visible global function definition for ‘rt’
Undefined global functions or variables:
  qnorm qt qunif rnorm rt runif
Consider adding
  importFrom("stats", "qnorm", "qt", "qunif", "rnorm", "rt", "runif")
to your NAMESPACE file.
PlotAtm.lin : scale_image: no visible global function definition for
  ‘heat.colors’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘par’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘sd’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘approx’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘image’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘axis’
PlotAtm.lin : scale_image: no visible global function definition for
  ‘mtext’
PlotAtm.lin: no visible global function definition for ‘arrows’
PlotAtm.lin: no visible global function definition for ‘text’
PlotAtm.lin: no visible global function definition for ‘polygon’
sky.colors: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  approx arrows axis heat.colors image mtext par polygon rgb sd text
Consider adding
  importFrom("grDevices", "heat.colors", "rgb")
  importFrom("graphics", "arrows", "axis", "image", "mtext", "par",
             "polygon", "text")
  importFrom("stats", "approx", "sd")
to your NAMESPACE file.
Rd file 'MakeArrivals.lin.Rd':
  \examples lines wider than 100 characters:
     MakeArrivals.lin(xs = c(100, 150), ys = c(100, 150), zs = c(100, 150), xr = 0, yr = 0, zr = 0, dt = 0.01, nt = 100, timing = c(0, 0), A ... [TRUNCATED]

Rd file 'MakeAtmList.lin.Rd':
  \usage lines wider than 90 characters:
     MakeAtmList.lin(z0 = 0, c0 = 343, gc = 0, wx0 = 0, gwx = 0, wy0 = 0, gwy = 0, rho0 = 1.2929 * exp(-z0/6800), grho = -0.0001901323 * exp ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following apparent S3 methods exported but not registered:
  summary.attribrisk
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
attribrisk: no visible global function definition for ‘terms’
attribrisk: no visible global function definition for ‘.getXlevels’
attribrisk: no visible global function definition for ‘model.response’
attribrisk: no visible global function definition for ‘model.weights’
attribrisk: no visible global function definition for ‘model.offset’
attribrisk: no visible global function definition for ‘model.matrix’
attribrisk: no visible global function definition for ‘model.frame’
attribrisk.fit: no visible global function definition for ‘glm.fit’
attribrisk.fit: no visible global function definition for ‘binomial’
attribrisk.fit: no visible global function definition for ‘glm.control’
attribrisk.fit: no visible global function definition for ‘coef’
attribrisk.fit: no visible global function definition for
  ‘coefficients’
attribrisk_boot: no visible global function definition for ‘var’
print.attribrisk: no visible global function definition for ‘qnorm’
summary.attribrisk: no visible global function definition for ‘hasArg’
summary.attribrisk: no visible global function definition for ‘var’
Undefined global functions or variables:
  .getXlevels binomial coef coefficients glm.control glm.fit hasArg
  model.frame model.matrix model.offset model.response model.weights
  qnorm terms var
Consider adding
  importFrom("methods", "hasArg")
  importFrom("stats", ".getXlevels", "binomial", "coef", "coefficients",
             "glm.control", "glm.fit", "model.frame", "model.matrix",
             "model.offset", "model.response", "model.weights", "qnorm",
             "terms", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
plot.AUC: no visible global function definition for ‘plot’
plot.AUC: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines plot
Consider adding
  importFrom("graphics", "lines", "plot")
to your NAMESPACE file.
AUCRFcv: no visible global function definition for ‘predict’
plot.AUCRF: no visible global function definition for ‘par’
plot.AUCRF: no visible global function definition for ‘dotchart’
plot.AUCRF: no visible global function definition for ‘title’
plot.AUCRF: no visible global function definition for ‘text’
Undefined global functions or variables:
  dotchart par predict text title
Consider adding
  importFrom("graphics", "dotchart", "par", "text", "title")
  importFrom("stats", "predict")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘RJSONIO’ ‘hexbin’ ‘plotrix’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
audioHist: no visible global function definition for ‘hist’
audioHist: no visible global function definition for ‘rescale’
audioHist: no visible global function definition for ‘toJSON’
audioScatter: no visible binding for global variable ‘formula’
audioScatter: no visible global function definition for ‘hexbinplot’
audioScatter: no visible global function definition for ‘cor’
audioScatter: no visible global function definition for ‘toJSON’
audioSplom: no visible global function definition for ‘hexplom’
audioSplom: no visible binding for global variable ‘BTY’
audioSplom: no visible binding for global variable ‘panel.hexboxplot’
audioSplom: no visible global function definition for ‘combn’
audioSplom : <anonymous>: no visible global function definition for
  ‘cor’
audioSplom : <anonymous>: no visible global function definition for
  ‘toJSON’
audiolyzRcheck: no visible global function definition for
  ‘download.file’
audiolyzRcheck: no visible global function definition for ‘unzip’
matricize: no visible global function definition for ‘hexbin’
panel.audiolyzR: no visible global function definition for
  ‘panel.hexbinplot’
Undefined global functions or variables:
  BTY combn cor download.file formula hexbin hexbinplot hexplom hist
  panel.hexbinplot panel.hexboxplot rescale toJSON unzip
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "cor", "formula")
  importFrom("utils", "combn", "download.file", "unzip")
to your NAMESPACE file.
Found the following significant warnings:
  pa.c:247:2: warning: incompatible pointer types initializing 'struct audio_instance *(*)(SEXP, float, int)' (aka 'struct audio_instance *(*)(struct SEXPREC *, float, int)') with an expression of type 'void *(SEXP, float, int)' (aka 'void *(struct SEXPREC *, float, int)') [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/audio.Rcheck/00install.out’ for details.
File ‘audio/libs/audio.so’:
  Found non-API call to R: ‘R_checkActivity’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Description field: should contain one or more complete sentences.
License components which are templates and need '+ file LICENSE':
  MIT
simulateD: no visible global function definition for ‘rgamma’
simulateT: no visible global function definition for ‘runif’
simulateT: no visible global function definition for ‘rbeta’
simulateT: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  rbeta rbinom rgamma runif
Consider adding
  importFrom("stats", "rbeta", "rbinom", "rgamma", "runif")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘ggplot2’ ‘gpclib’ ‘maptools’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
gLog.ep: no visible global function definition for ‘quantile’
gedestp: no visible global function definition for ‘na.omit’
gedestp: no visible global function definition for ‘optim’
gets.mean: no visible global function definition for ‘start’
gets.mean: no visible global function definition for ‘end’
gets.mean: no visible global function definition for ‘window’
gets.mean: no visible global function definition for ‘pt’
gets.mean: no visible global function definition for ‘Box.test’
gets.mean: no visible global function definition for ‘pchisq’
gets.vol: no visible global function definition for ‘start’
gets.vol: no visible global function definition for ‘end’
gets.vol: no visible global function definition for ‘window’
gets.vol: no visible global function definition for ‘pt’
gets.vol: no visible global function definition for ‘Box.test’
gets.vol: no visible global function definition for ‘pchisq’
jb.test: no visible global function definition for ‘pchisq’
skewness.test: no visible global function definition for ‘pchisq’
sm: no visible global function definition for ‘start’
sm: no visible global function definition for ‘end’
sm: no visible global function definition for ‘window’
sm: no visible global function definition for ‘pt’
sm: no visible global function definition for ‘pchisq’
sm: no visible global function definition for ‘Box.test’
Undefined global functions or variables:
  Box.test end na.omit optim pchisq pt quantile start window
Consider adding
  importFrom("stats", "Box.test", "end", "na.omit", "optim", "pchisq",
             "pt", "quantile", "start", "window")
to your NAMESPACE file.
CRexp_set: no visible global function definition for ‘runif’
b6e6rl: no visible global function definition for ‘runif’
derand_RL: no visible global function definition for ‘runif’
derandexp_RL: no visible global function definition for ‘runif’
nahvyb_expt: no visible global function definition for ‘runif’
roulete: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
.generateTransform: no visible global function definition for ‘sd’
.generateUnitHyperCube: no visible global function definition for
  ‘runif’
.makeBoundedSingleStep: no visible global function definition for
  ‘runif’
.makeBoundedStep: no visible global function definition for ‘runif’
.makeStep: no visible global function definition for ‘runif’
.staircaseSampling: no visible global function definition for ‘runif’
GaussianPrior: no visible global function definition for ‘qnorm’
LogNormalPrior: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm runif sd
Consider adding
  importFrom("stats", "qnorm", "runif", "sd")
to your NAMESPACE file.
BACprior.CV: no visible global function definition for ‘na.fail’
BACprior.CV: no visible global function definition for ‘plot’
BACprior.CV: no visible global function definition for ‘abline’
BACprior.boot: no visible global function definition for ‘na.fail’
BACprior.boot: no visible global function definition for ‘plot’
BACprior.boot: no visible global function definition for ‘abline’
BACprior.lm: no visible global function definition for ‘na.fail’
BACprior.lm: no visible global function definition for ‘coef’
BACprior.lm: no visible global function definition for ‘vcov’
Undefined global functions or variables:
  abline coef na.fail plot vcov
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("stats", "coef", "na.fail", "vcov")
to your NAMESPACE file.
'library' or 'require' call to ‘mvtnorm’ which was already attached by Depends.
  Please remove these calls from your code.
bagging: no visible global function definition for ‘predict’
samme: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
Running examples in ‘ballr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: NBAPlayerPerGameStats
> ### Title: NBA Player Career Statistics
> ### Aliases: NBAPlayerPerGameStats
> 
> ### ** Examples
> 
> NBAPlayerPerGameStats("/players/d/davisan02.html") # Anthony Davis
Error in rvest::html_table(pg, fill = T)[[2]] : subscript out of bounds
Calls: NBAPlayerPerGameStats
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 83-86 (use-ballr.Rmd) 
Error: processing vignette ‘use-ballr.Rmd’ failed with diagnostics:
subscript out of bounds
Execution halted
best_binomial_bandit : f: no visible global function definition for
  ‘dbeta’
best_binomial_bandit : f: no visible global function definition for
  ‘pbeta’
best_binomial_bandit: no visible global function definition for
  ‘integrate’
best_poisson_bandit : f: no visible global function definition for
  ‘dgamma’
best_poisson_bandit : f: no visible global function definition for
  ‘pgamma’
best_poisson_bandit: no visible global function definition for
  ‘integrate’
deseasonalized_trend: no visible global function definition for
  ‘predict’
distribution_estimate: no visible global function definition for
  ‘quantile’
distribution_estimate: no visible global function definition for
  ‘qbeta’
significance_analysis: no visible global function definition for
  ‘prop.test’
sim_post: no visible global function definition for ‘rbeta’
summarize_metrics: no visible global function definition for ‘median’
summarize_metrics: no visible global function definition for
  ‘prop.test’
Undefined global functions or variables:
  dbeta dgamma integrate median pbeta pgamma predict prop.test qbeta
  quantile rbeta
Consider adding
  importFrom("stats", "dbeta", "dgamma", "integrate", "median", "pbeta",
             "pgamma", "predict", "prop.test", "qbeta", "quantile",
             "rbeta")
to your NAMESPACE file.
extractAffybatch: no visible global function definition for ‘new’
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' calls to packages already attached by Depends:
  ‘grid’ ‘lattice’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘grid’ ‘lattice’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
barcode: no visible global function definition for ‘unit’
barcode: no visible global function definition for ‘grid.newpage’
barcode: no visible global function definition for ‘grid.text’
barcode: no visible global function definition for ‘gpar’
barcode: no visible global function definition for ‘pushViewport’
barcode: no visible global function definition for ‘viewport’
barcode: no visible global function definition for ‘convertHeight’
barcode: no visible global function definition for ‘convertWidth’
barcode: no visible global function definition for ‘grid.rect’
barcode: no visible global function definition for ‘popViewport’
barcode.panel: no visible global function definition for ‘unit’
barcode.panel: no visible global function definition for ‘hist’
barcode.panel: no visible global function definition for ‘pushViewport’
barcode.panel: no visible global function definition for ‘viewport’
barcode.panel: no visible global function definition for ‘grid.xaxis’
barcode.panel: no visible global function definition for ‘gpar’
barcode.panel: no visible global function definition for ‘grid.text’
barcode.panel: no visible global function definition for ‘popViewport’
barcode.panel: no visible global function definition for
  ‘grid.segments’
barcode.panel: no visible global function definition for ‘grid.points’
Undefined global functions or variables:
  convertHeight convertWidth gpar grid.newpage grid.points grid.rect
  grid.segments grid.text grid.xaxis hist popViewport pushViewport unit
  viewport
Consider adding
  importFrom("graphics", "hist")
to your NAMESPACE file.
Running ‘testthat.R’ [18s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BAS)
  > 
  > test_check("BAS")
  ── 1. Failure: shrinkage is less than or equal to 1 (@test-bas-lm.R#66)  ───────
  0 not equal to sum(hald_bas$shrinkage > 1).
  1/1 mismatches
  [1] 0 - NA == NA
  
  ── 2. Error: check non-full rank (@test-bas-lm.R#297)  ─────────────────────────
  NA/NaN/Inf in foreign function call (arg 11)
  1: update(basObj.eplogp, newprior = "EB-local") at testthat/test-bas-lm.R:297
  2: update.bas(basObj.eplogp, newprior = "EB-local")
  
  
   Marginal Posterior Summaries of Coefficients: 
  
   Using  BMA 
  
   Based on the top  16 models 
             post mean  post SD   post p(B != 0)
  Intercept  95.42308    0.67885   1.00000      
  X1          1.40116    0.35351   0.97454      
  X2          0.42326    0.38407   0.76017      
  X3         -0.03997    0.33398   0.30660      
  X4         -0.22077    0.36931   0.44354      
  
  Call:
  bas.lm(formula = Y ~ ., data = Hald, prior = "BIC", modelprior = uniform())
  
  
   Marginal Posterior Inclusion Probabilities: 
  Intercept         X1         X2         X3         X4  
     1.0000     0.9856     0.7921     0.4705     0.5220  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 149 SKIPPED: 0 FAILED: 2
  1. Failure: shrinkage is less than or equal to 1 (@test-bas-lm.R#66) 
  2. Error: check non-full rank (@test-bas-lm.R#297) 
  
  Error: testthat unit tests failed
  Execution halted
'library' or 'require' call to ‘hwriter’ which was already attached by Depends.
  Please remove these calls from your code.
prepare_Rd: mkhtml.Rd:31-33: Dropping empty section \details
prepare_Rd: mkhtml.Rd:43-45: Dropping empty section \note
prepare_Rd: mkhtml.Rd:40-42: Dropping empty section \author
prepare_Rd: mkhtml.Rd:37-39: Dropping empty section \references
prepare_Rd: mkhtml.Rd:49-51: Dropping empty section \seealso
gimli.16008hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
BayClone2: no visible global function definition for ‘rbeta’
fn.MCMC.CNV: no visible global function definition for ‘runif’
fn.Tr.CNV: no visible global function definition for ‘quantile’
fn.Tr.CNV: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  quantile rbeta rgamma runif
Consider adding
  importFrom("stats", "quantile", "rbeta", "rgamma", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  rcpparma_hello_world.cpp:930:4: warning: explicitly assigning value of variable of type 'arma::colvec' (aka 'Col<double>') to itself [-Wself-assign-overloaded]
  rcpparma_hello_world.cpp:930:12: warning: explicitly assigning value of variable of type 'arma::colvec' (aka 'Col<double>') to itself [-Wself-assign-overloaded]
  rcpparma_hello_world.cpp:939:4: warning: explicitly assigning value of variable of type 'arma::colvec' (aka 'Col<double>') to itself [-Wself-assign-overloaded]
  rcpparma_hello_world.cpp:939:12: warning: explicitly assigning value of variable of type 'arma::colvec' (aka 'Col<double>') to itself [-Wself-assign-overloaded]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BayesBD.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Blasso.cpp:451:51: warning: assigning field to itself [-Wself-assign-field]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/bayesCL.Rcheck/00install.out’ for details.
FECRT: no visible global function definition for ‘pdf’
FECRT: no visible global function definition for ‘hist’
FECRT: no visible global function definition for ‘abline’
FECRT: no visible global function definition for ‘dev.off’
FECRT.analysis: no visible global function definition for ‘pdf’
FECRT.analysis: no visible global function definition for ‘hist’
FECRT.analysis: no visible global function definition for ‘abline’
FECRT.analysis: no visible global function definition for ‘dev.off’
fecrt: no visible global function definition for ‘pdf’
fecrt: no visible global function definition for ‘hist’
fecrt: no visible global function definition for ‘abline’
fecrt: no visible global function definition for ‘dev.off’
fecrt.analysis: no visible global function definition for ‘pdf’
fecrt.analysis: no visible global function definition for ‘hist’
fecrt.analysis: no visible global function definition for ‘abline’
fecrt.analysis: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  abline dev.off hist pdf
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "hist")
to your NAMESPACE file.
Dependence on R version ‘3.4.1’ not with patchlevel 0
BugReports field is not a suitable URL but contains an email address
  which will be used as from R 3.4.0
BMAnimalTrack: no visible global function definition for ‘nlm’
BMAnimalTrack: no visible global function definition for ‘qnorm’
dataSim: no visible global function definition for ‘rnorm’
rBBridge: no visible global function definition for ‘rnorm’
rBMotion: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  nlm qnorm rnorm
Consider adding
  importFrom("stats", "nlm", "qnorm", "rnorm")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  print.Bayesianbetareg print.summary.Bayesianbetareg
  summary.Bayesianbetareg
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
BayesianbetaregEst: no visible global function definition for ‘runif’
BayesianbetaregEst: no visible global function definition for ‘as.ts’
BayesianbetaregEst: no visible global function definition for ‘dev.new’
BayesianbetaregEst: no visible global function definition for ‘ts.plot’
BayesianbetaregEst: no visible binding for global variable ‘sd’
BayesianbetaregEst: no visible global function definition for
  ‘quantile’
betaresiduals : lt: no visible global function definition for ‘dbeta’
diagnostics: no visible global function definition for ‘plot’
diagnostics: no visible global function definition for ‘abline’
diagnostics: no visible global function definition for ‘qqnorm’
diagnostics: no visible global function definition for ‘qqline’
dpostb: no visible global function definition for ‘dbeta’
dpostg: no visible global function definition for ‘dbeta’
plotresiduals: no visible global function definition for ‘plot’
print.summary.Bayesianbetareg: no visible global function definition
  for ‘printCoefmat’
summary.Bayesianbetareg: no visible global function definition for
  ‘coef’
Undefined global functions or variables:
  abline as.ts coef dbeta dev.new plot printCoefmat qqline qqnorm
  quantile runif sd ts.plot
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "plot")
  importFrom("stats", "as.ts", "coef", "dbeta", "printCoefmat", "qqline",
             "qqnorm", "quantile", "runif", "sd", "ts.plot")
to your NAMESPACE file.
noninform_prior : a : f1: no visible global function definition for
  ‘pbeta’
noninform_prior : a : f1: no visible global function definition for
  ‘dbeta’
noninform_prior : a: no visible global function definition for
  ‘integrate’
noninform_prior: no visible global function definition for ‘rbeta’
noninform_prior: no visible global function definition for ‘optim’
postNullFun : b : f1: no visible global function definition for ‘pbeta’
postNullFun : b : f1: no visible global function definition for ‘dbeta’
postNullFun : b: no visible global function definition for ‘integrate’
prior_prob : a : f1: no visible global function definition for ‘pbeta’
prior_prob : a : f1: no visible global function definition for ‘dbeta’
prior_prob : a: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  dbeta integrate optim pbeta rbeta
Consider adding
  importFrom("stats", "dbeta", "integrate", "optim", "pbeta", "rbeta")
to your NAMESPACE file.
MHratioPopPref: no visible global function definition for ‘runif’
MratioPopMult: no visible global function definition for ‘dunif’
MratioPopMult: no visible global function definition for ‘runif’
bayesPref: no visible global function definition for ‘runif’
calcP: no visible global function definition for ‘dunif’
calcP: no visible global function definition for ‘dmultinom’
calcdic: no visible global function definition for ‘median’
calcdic: no visible binding for global variable ‘median’
calcdic: no visible global function definition for ‘dmultinom’
calcdicExtern: no visible global function definition for ‘median’
calcdicExtern: no visible global function definition for ‘dmultinom’
calcdicExtern: no visible binding for global variable ‘median’
credibleIntervals: no visible global function definition for ‘quantile’
prefPlot: no visible global function definition for ‘postscript’
prefPlot: no visible global function definition for ‘plot’
prefPlot: no visible global function definition for ‘lines’
prefPlot: no visible global function definition for ‘density’
prefPlot: no visible global function definition for ‘median’
prefPlot: no visible global function definition for ‘legend’
prefPlot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  density dev.off dmultinom dunif legend lines median plot postscript
  quantile runif
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "density", "dmultinom", "dunif", "median",
             "quantile", "runif")
to your NAMESPACE file.
mlike.alt.g.AR: no visible global function definition for ‘integrate’
mlike.alt.gtheta.AR: no visible global function definition for ‘dbeta’
mlike.null.AR: no visible global function definition for ‘dbeta’
multilevel.Gibbs.AR: no visible global function definition for
  ‘txtProgressBar’
multilevel.Gibbs.AR : pbFun: no visible global function definition for
  ‘setTxtProgressBar’
trendtest.Gibbs.AR: no visible global function definition for
  ‘txtProgressBar’
trendtest.Gibbs.AR : pbFun: no visible global function definition for
  ‘setTxtProgressBar’
trendtest.Gibbs.AR: no visible global function definition for ‘dcauchy’
trendtest.Gibbs.AR: no visible global function definition for ‘pcauchy’
trendtest.MC.AR: no visible global function definition for
  ‘txtProgressBar’
trendtest.MC.AR : pbFun: no visible global function definition for
  ‘setTxtProgressBar’
trendtest.nullMargLikeAR: no visible global function definition for
  ‘integrate’
ttest.Gibbs.AR: no visible global function definition for
  ‘txtProgressBar’
ttest.Gibbs.AR : pbFun: no visible global function definition for
  ‘setTxtProgressBar’
ttest.Gibbs.AR: no visible global function definition for ‘dcauchy’
ttest.Gibbs.AR: no visible global function definition for ‘pcauchy’
ttest.MCGQ.AR: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  dbeta dcauchy integrate pcauchy setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "dbeta", "dcauchy", "integrate", "pcauchy")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘MASS’ ‘combinat’ ‘gplots’ ‘mnormt’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bayes.regress: no visible binding for global variable ‘var’
bayesregressB1S1: no visible global function definition for ‘rgamma’
bayesregressB1S2: no visible global function definition for ‘rgamma’
bayesregressB2S1: no visible global function definition for ‘rgamma’
bayesregressB2S2: no visible global function definition for ‘rgamma’
bayesregressB3S1: no visible global function definition for ‘rWishart’
bayesregressB3S1: no visible global function definition for ‘rgamma’
bayesregressB3S2: no visible global function definition for ‘rWishart’
bayesregressB3S2: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  rWishart rgamma var
Consider adding
  importFrom("stats", "rWishart", "rgamma", "var")
to your NAMESPACE file.
validate: no visible binding for global variable ‘qnorm’
validate: no visible global function definition for ‘pchisq’
validate: no visible global function definition for ‘qnorm’
validate: no visible global function definition for ‘plot’
validate: no visible global function definition for ‘axis’
validate: no visible global function definition for ‘points’
validate: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline axis pchisq plot points qnorm
Consider adding
  importFrom("graphics", "abline", "axis", "plot", "points")
  importFrom("stats", "pchisq", "qnorm")
to your NAMESPACE file.
Unexported object imported by a ':::' call: ‘boa:::boa.getparms’
  See the note in ?`:::` about the use of this operator.
Rd file 'BayHap-internal.Rd':
  \usage lines wider than 90 characters:
      expectedGenotypes(x, alleles = allele.names(x), ploidy = 2, sort = TRUE, haplotype = FALSE)  

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘coda’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Rd file 'BPSpostSample.Rd':
  \usage lines wider than 90 characters:
     BPSpostSample(hyp, times, obs = NULL, mclen = 10, burnin = 0, thin = 1, df = 10, etastar = NULL)
  \examples lines wider than 100 characters:
     post<-BPSpostSample(hypars, times = earthquakes$ti, obs = earthquakes$ob, etastar = postmode$etastar)

These lines will be truncated in the PDF manual.
'library' or 'require' call to ‘mvnmle’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
BilogData: no visible global function definition for ‘write.table’
CohensD.rawData: no visible global function definition for ‘var’
EtaSq: no visible global function definition for ‘summary.aov’
HedgesG.rawData: no visible global function definition for ‘var’
LittleMCAR: no visible global function definition for ‘mlest’
LittleMCAR: no visible global function definition for ‘pchisq’
PseudoR2: no visible global function definition for ‘predict’
Undefined global functions or variables:
  mlest pchisq predict summary.aov var write.table
Consider adding
  importFrom("stats", "pchisq", "predict", "summary.aov", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘fields’ ‘poibin’ ‘rjags’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
BMR.plot: no visible global function definition for ‘heat.colors’
BMR.plot: no visible global function definition for ‘image.plot’
BMR.plot: no visible global function definition for ‘title’
BMR.plot: no visible global function definition for ‘mtext’
BMR.plot: no visible global function definition for ‘par’
baysic.data: no visible global function definition for ‘layout’
baysic.data: no visible global function definition for ‘barplot’
baysic.data: no visible global function definition for ‘rainbow’
baysic.fit: no visible global function definition for ‘jags.model’
baysic.fit: no visible global function definition for ‘update’
baysic.fit: no visible global function definition for ‘coda.samples’
baysic.test: no visible global function definition for ‘ppois’
baysic.test : <anonymous>: no visible global function definition for
  ‘ppoibin’
baysic.test: no visible global function definition for ‘pbinom’
fuzzy.FDR.approx: no visible global function definition for ‘p.adjust’
fuzzy.FDR.approx: no visible global function definition for ‘runif’
Undefined global functions or variables:
  barplot coda.samples heat.colors image.plot jags.model layout mtext
  p.adjust par pbinom ppoibin ppois rainbow runif title update
Consider adding
  importFrom("grDevices", "heat.colors", "rainbow")
  importFrom("graphics", "barplot", "layout", "mtext", "par", "title")
  importFrom("stats", "p.adjust", "pbinom", "ppois", "runif", "update")
to your NAMESPACE file.
Rd file 'baysic.fit.Rd':
  \usage lines wider than 90 characters:
     baysic.fit(dat.out, snv.cat, covar = NULL, excl.list = NULL, burn.in = 10000,n.samp = 25000, fn.jags = "baysic.jags", prior = NULL)
  \examples lines wider than 100 characters:
     snv.cat.ex[[2]]<-unique(c(grep("TC.",colnames(ccds.19)[-c(1:2)]),grep(".CG",colnames(ccds.19)[-c(1:2)])))

Rd file 'baysic.test.Rd':
  \usage lines wider than 90 characters:
     baysic.test(dat.out, fit.out, fdr.level = 0.15, fuzzy.cnt = 10000, r = NULL,subtype = NULL, PB.approx = FALSE)
  \examples lines wider than 100 characters:
     snv.cat.ex[[2]]<-unique(c(grep("TC.",colnames(ccds.19)[-c(1:2)]),grep(".CG",colnames(ccds.19)[-c(1:2)])))

These lines will be truncated in the PDF manual.
BAYSTAR: no visible global function definition for ‘median’
BAYSTAR: no visible global function definition for ‘ar’
BAYSTAR: no visible global function definition for ‘quantile’
BAYSTAR: no visible global function definition for ‘dev.new’
BAYSTAR: no visible global function definition for ‘ts.plot’
BAYSTAR: no visible global function definition for ‘title’
BAYSTAR: no visible global function definition for ‘par’
BAYSTAR: no visible global function definition for ‘plot.ts’
BAYSTAR: no visible global function definition for ‘lines’
BAYSTAR: no visible global function definition for ‘acf’
TAR.lagd: no visible global function definition for ‘runif’
TAR.sigma: no visible global function definition for ‘rgamma’
TAR.simu: no visible global function definition for ‘rnorm’
TAR.summary: no visible global function definition for ‘quantile’
TAR.summary: no visible global function definition for ‘sd’
TAR.thres: no visible global function definition for ‘rnorm’
TAR.thres: no visible global function definition for ‘runif’
Undefined global functions or variables:
  acf ar dev.new lines median par plot.ts quantile rgamma rnorm runif
  sd title ts.plot
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "lines", "par", "title")
  importFrom("stats", "acf", "ar", "median", "plot.ts", "quantile",
             "rgamma", "rnorm", "runif", "sd", "ts.plot")
to your NAMESPACE file.
Package in Depends field not imported from: ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
LaplaceMetropolis_admkr: no visible binding for global variable
  ‘median’
LaplaceMetropolis_admkr: no visible global function definition for
  ‘mad’
LaplaceMetropolis_gaussian: no visible binding for global variable
  ‘median’
LaplaceMetropolis_gaussian: no visible global function definition for
  ‘mad’
cost_admkr: no visible global function definition for ‘sd’
cov_chol: no visible global function definition for ‘qchisq’
cov_chol_admkr: no visible global function definition for ‘qchisq’
gibbs_admkr_erro: no visible global function definition for ‘rnorm’
gibbs_admkr_erro: no visible global function definition for ‘runif’
gibbs_admkr_nw: no visible global function definition for ‘qnorm’
gibbs_admkr_nw: no visible global function definition for ‘rnorm’
gibbs_admkr_nw: no visible global function definition for ‘runif’
loglikelihood_admkr: no visible global function definition for ‘sd’
margin_like_admkr: no visible global function definition for ‘sd’
np_gibbs: no visible global function definition for ‘qnorm’
np_gibbs: no visible global function definition for ‘rnorm’
np_gibbs: no visible global function definition for ‘runif’
np_gibbs: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  mad median qchisq qnorm rgamma rnorm runif sd
Consider adding
  importFrom("stats", "mad", "median", "qchisq", "qnorm", "rgamma",
             "rnorm", "runif", "sd")
to your NAMESPACE file.
bbmm.contour: no visible global function definition for ‘na.omit’
bbmm.contour: no visible global function definition for ‘optimize’
bbmm.contour: no visible global function definition for ‘contour’
bbmm.contour: no visible global function definition for ‘points’
bbmm.contour: no visible global function definition for ‘lines’
brownian.bridge: no visible global function definition for ‘sd’
brownian.motion.variance: no visible global function definition for
  ‘optimize’
Undefined global functions or variables:
  contour lines na.omit optimize points sd
Consider adding
  importFrom("graphics", "contour", "lines", "points")
  importFrom("stats", "na.omit", "optimize", "sd")
to your NAMESPACE file.
bbo: no visible global function definition for ‘runif’
bbo: no visible global function definition for ‘tail’
plot.bbo: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot runif tail
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
  importFrom("utils", "tail")
to your NAMESPACE file.
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.
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 file.
'library' or 'require' call to ‘rgl’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
pairs.bce : panel.cor: no visible global function definition for ‘text’
pairs.bce : panel.cor: no visible global function definition for ‘cor’
pairs.bce : panel.hist: no visible global function definition for ‘par’
pairs.bce : panel.hist: no visible global function definition for
  ‘hist’
pairs.bce : panel.hist: no visible global function definition for
  ‘rect’
pairs.bce: no visible global function definition for ‘pairs’
panel.cor: no visible global function definition for ‘par’
panel.cor: no visible global function definition for ‘cor’
panel.cor: no visible global function definition for ‘strwidth’
panel.cor: no visible global function definition for ‘text’
rdirichlet2: no visible global function definition for ‘rgamma’
summary.bce: no visible global function definition for ‘cov’
summary.bce: no visible binding for global variable ‘sd’
summary.bce: no visible binding for global variable ‘quantile’
Undefined global functions or variables:
  cor cov hist pairs par quantile rect rgamma sd strwidth text
Consider adding
  importFrom("graphics", "hist", "pairs", "par", "rect", "strwidth",
             "text")
  importFrom("stats", "cor", "cov", "quantile", "rgamma", "sd")
to your NAMESPACE file.
Found the following significant warnings:
  sparseFactor.cpp:33:10: warning: explicitly assigning value of variable of type 'Rcpp::IntegerVector' (aka 'Vector<13>') to itself [-Wself-assign-overloaded]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BClustLonG.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘bcmaps.rdata’
plot.cvsvd: no visible binding for global variable ‘sd’
plot.cvsvd: no visible global function definition for ‘plot’
plot.cvsvd: no visible global function definition for ‘lines’
plot.cvsvd: no visible global function definition for ‘segments’
plot.cvsvd: no visible global function definition for ‘points’
print.cvsvd: no visible binding for global variable ‘sd’
summary.cvsvd: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  lines plot points sd segments
Consider adding
  importFrom("graphics", "lines", "plot", "points", "segments")
  importFrom("stats", "sd")
to your NAMESPACE file.
mise: no visible global function definition for ‘integrate’
density,BrVitale : density.vitale : <anonymous>: no visible global
  function definition for ‘dbeta’
density,Chen99Kernel : <anonymous>: no visible global function
  definition for ‘dbeta’
density,HirukawaJLNKernel : <anonymous>: no visible global function
  definition for ‘dbeta’
density,MicroBetaChen99Kernel : <anonymous>: no visible global function
  definition for ‘dbeta’
density,Vitale : <anonymous>: no visible global function definition for
  ‘dbeta’
distribution,BernsteinPolynomials : <anonymous>: no visible global
  function definition for ‘integrate’
distribution,KernelDensity : <anonymous>: no visible global function
  definition for ‘integrate’
print,BoundedDensity: no visible global function definition for ‘str’
print,KernelDensity: no visible global function definition for ‘str’
rsample,BoundedDensity: no visible global function definition for
  ‘runif’
setNormalizationConst,MacroBetaChen99Kernel: no visible global function
  definition for ‘integrate’
setNormalizationConst,MacroBetaHirukawaTSKernel: no visible global
  function definition for ‘integrate’
setNormalizationConstant,MacroBetaHirukawaJLNKernel: no visible global
  function definition for ‘integrate’
setNormalizationConstants,MicroBetaChen99Kernel :
  density.kernelFunction: no visible global function definition for
  ‘dbeta’
setNormalizationConstants,MicroBetaChen99Kernel : <anonymous>: no
  visible global function definition for ‘integrate’
show,BoundedDensity: no visible global function definition for ‘str’
show,KernelDensity: no visible global function definition for ‘str’
Undefined global functions or variables:
  dbeta integrate runif str
Consider adding
  importFrom("stats", "dbeta", "integrate", "runif")
  importFrom("utils", "str")
to your NAMESPACE file.
BDtest: no visible global function definition for ‘binom.test’
CIlnpv: no visible global function definition for ‘qnorm’
CIlnpvak: no visible global function definition for ‘qnorm’
CIlppv: no visible global function definition for ‘qnorm’
CIlppvak: no visible global function definition for ‘qnorm’
CIpvBI: no visible global function definition for ‘rbeta’
CIpvBI: no visible global function definition for ‘quantile’
CIpvBI: no visible global function definition for ‘median’
CIpvBII: no visible global function definition for ‘rbeta’
CIpvBII: no visible global function definition for ‘quantile’
CIpvBII: no visible global function definition for ‘median’
nNPV: no visible global function definition for ‘qnorm’
nPPV: no visible global function definition for ‘qnorm’
plotnPV: no visible global function definition for ‘na.omit’
plotnPV: no visible global function definition for ‘lines’
plotnPV2 : defplot: no visible global function definition for ‘plot’
plotnPV2 : defplot: no visible global function definition for ‘lines’
plotnPV2: no visible global function definition for ‘par’
plotnPV2: no visible global function definition for ‘layout’
simPV: no visible global function definition for ‘rbinom’
simPV: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  binom.test layout lines median na.omit par plot qnorm quantile rbeta
  rbinom
Consider adding
  importFrom("graphics", "layout", "lines", "par", "plot")
  importFrom("stats", "binom.test", "median", "na.omit", "qnorm",
             "quantile", "rbeta", "rbinom")
to your NAMESPACE file.
Package suggested but not available for checking: ‘lumi’
Packages in Depends field not imported from:
  ‘RColorBrewer’ ‘beadarray’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
beadtypeFilter: no visible global function definition for ‘na.omit’
beadtypeFilter: no visible global function definition for ‘exprs’
beadtypeFilter: no visible global function definition for ‘se.exprs’
beadtypeFilter: no visible global function definition for ‘beadNum’
beadtypeFilter: no visible global function definition for ‘fData’
emCDF: no visible global function definition for ‘brewer.pal’
emCDF: no visible global function definition for ‘plot’
emCDF: no visible global function definition for ‘ecdf’
emCDF: no visible global function definition for ‘legend’
emCDF: no visible global function definition for ‘lines’
emCDF: no visible global function definition for ‘text’
emCDF: no visible global function definition for ‘reshape’
iccFun : <anonymous>: no visible global function definition for
  ‘quantile’
varianceplot: no visible global function definition for ‘reshape’
varianceplot: no visible global function definition for ‘plot’
varianceplot: no visible global function definition for ‘points’
varianceplot: no visible global function definition for ‘legend’
Undefined global functions or variables:
  beadNum brewer.pal ecdf exprs fData legend lines na.omit plot points
  quantile reshape se.exprs text
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points", "text")
  importFrom("stats", "ecdf", "na.omit", "quantile", "reshape")
to your NAMESPACE file.
Rd file 'iccFun.Rd':
  \examples lines wider than 100 characters:
     aaa<-na.omit(data.frame(I(rownames(exprs(exampleSummaryDataNorm))),exprs(exampleSummaryDataNorm)))[1:40,]

These lines will be truncated in the PDF manual.
beqi2: no visible global function definition for ‘na.omit’
beqi2: no visible global function definition for ‘browseURL’
readAMBI: no visible global function definition for ‘read.csv’
readBEQI: no visible global function definition for ‘read.csv’
readERF: no visible global function definition for ‘read.csv’
readTWN: no visible global function definition for ‘read.csv’
read_ITI_FIBI: no visible global function definition for ‘read.csv’
Undefined global functions or variables:
  browseURL na.omit read.csv
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "browseURL", "read.csv")
to your NAMESPACE file.
'library' or 'require' call to ‘MASS’ which was already attached by Depends.
  Please remove these calls from your code.
ber: no visible global function definition for ‘model.matrix’
ber: no visible global function definition for ‘as.formula’
ber_bg: no visible global function definition for ‘model.matrix’
ber_bg: no visible global function definition for ‘as.formula’
combat_np: no visible global function definition for ‘as.formula’
combat_np: no visible global function definition for ‘model.matrix’
combat_p: no visible global function definition for ‘as.formula’
combat_p: no visible global function definition for ‘model.matrix’
combat_p: no visible binding for global variable ‘var’
combat_p: no visible global function definition for ‘par’
combat_p: no visible global function definition for ‘density’
combat_p: no visible global function definition for ‘plot’
combat_p: no visible global function definition for ‘lines’
combat_p: no visible global function definition for ‘dnorm’
combat_p: no visible global function definition for ‘qqnorm’
combat_p: no visible global function definition for ‘qqline’
combat_p: no visible global function definition for ‘rgamma’
combat_p: no visible global function definition for ‘qqplot’
combat_p: no visible global function definition for ‘title’
mean_centering: no visible global function definition for
  ‘model.matrix’
standardization: no visible global function definition for
  ‘model.matrix’
Undefined global functions or variables:
  as.formula density dnorm lines model.matrix par plot qqline qqnorm
  qqplot rgamma title var
Consider adding
  importFrom("graphics", "lines", "par", "plot", "title")
  importFrom("stats", "as.formula", "density", "dnorm", "model.matrix",
             "qqline", "qqnorm", "qqplot", "rgamma", "var")
to your NAMESPACE file.
Package in Depends field not imported from: ‘Rmpfr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bI: no visible global function definition for ‘is’
bI: no visible global function definition for ‘mpfr’
bI: no visible binding for global variable ‘slot’
bI: no visible global function definition for ‘as’
Undefined global functions or variables:
  as is mpfr slot
Consider adding
  importFrom("methods", "as", "is", "slot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Non-standard file/directory found at top level:
  ‘extdata’
betafam: no visible global function definition for ‘pnorm’
betafam: no visible global function definition for ‘pchisq’
betafam: no visible global function definition for ‘lm’
betafam: no visible global function definition for ‘coefficients’
betafam: no visible global function definition for ‘glm.fit’
betafam: no visible global function definition for ‘gaussian’
betafam: no visible global function definition for ‘glmnet’
Undefined global functions or variables:
  coefficients gaussian glm.fit glmnet lm pchisq pnorm
Consider adding
  importFrom("stats", "coefficients", "gaussian", "glm.fit", "lm",
             "pchisq", "pnorm")
to your NAMESPACE file.
Rd file 'betafam.Rd':
  \usage lines wider than 90 characters:
     betafam(ped,group.threshold=-1,fix.group.index=NULL, fix.weight=NULL,mute.SMM=TRUE,trait=c("binary","qtl"),LC.test=c("LC.true","LC","si ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Checking should be performed on sources prepared by ‘R CMD build’.
'library' or 'require' call to ‘vegan’ which was already attached by Depends.
  Please remove these calls from your code.
Found the following apparent S3 methods exported but not registered:
  cca.pertables plot.adonis.pertables plot.cca.pertables
  plot.mantel.pertables plot.rda.pertables print.adonis.pertables
  print.cca.pertables print.mantel.pertables print.pertables
  print.rda.pertables rda.pertables
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'cca.pertables':
  ‘cca.pertables’

S3 methods shown with full name in documentation object 'rda.pertables':
  ‘rda.pertables’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
betas.lm: no visible binding for global variable ‘sd’
betas.lm: no visible global function definition for ‘sd’
my.wtd.var: no visible global function definition for ‘var’
Undefined global functions or variables:
  sd var
Consider adding
  importFrom("stats", "sd", "var")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  print.summary.bezierArcLength print.summary.bezierCurveFit
  summary.bezierArcLength summary.bezierCurveFit
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
bezierArcLength: no visible global function definition for ‘sd’
bezierArcLength: no visible global function definition for ‘lm’
bezierCurveFit: no visible global function definition for ‘nls’
bezierCurveFit: no visible global function definition for ‘nls.control’
bezierCurveFit: no visible global function definition for ‘lm’
bezierCurveFit: no visible global function definition for ‘na.omit’
pointsOnBezier: no visible global function definition for ‘optim’
Undefined global functions or variables:
  lm na.omit nls nls.control optim sd
Consider adding
  importFrom("stats", "lm", "na.omit", "nls", "nls.control", "optim",
             "sd")
to your NAMESPACE file.
block.gibbs: no visible global function definition for ‘rmultinom’
rdirichlet: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  rgamma rmultinom
Consider adding
  importFrom("stats", "rgamma", "rmultinom")
to your NAMESPACE file.
global: no visible global function definition for ‘par’
global: no visible global function definition for ‘runif’
global: no visible global function definition for ‘cov’
mymcmc: no visible global function definition for ‘par’
mymcmc: no visible global function definition for ‘rnorm’
mymcmc: no visible global function definition for ‘runif’
mymcmc: no visible global function definition for ‘cov’
mymcmc: no visible global function definition for ‘lines’
plkhci: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  cov lines par qchisq rnorm runif
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "cov", "qchisq", "rnorm", "runif")
to your NAMESPACE file.
Package in Depends field not imported from: ‘betareg’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bias: no visible global function definition for ‘predict’
bias: no visible global function definition for ‘pnorm’
bias: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  model.matrix pnorm predict
Consider adding
  importFrom("stats", "model.matrix", "pnorm", "predict")
to your NAMESPACE file.
anon_matrix: no visible global function definition for
  ‘filebacked.big.matrix’
anon_matrix: no visible global function definition for ‘capture.output’
finalize_anon_matrix: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  capture.output filebacked.big.matrix
Consider adding
  importFrom("utils", "capture.output")
to your NAMESPACE file.
gimli.805hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.10970hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.18546hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.27124hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.19222hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.3564hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.27515hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.885hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.9443hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.19212hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.29089hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Non-standard file/directory found at top level:
  ‘test’
Packages in Depends field not imported from:
  ‘DBI’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Call with DUP:
   .Fortran("regcf", as.integer(p), as.integer(p * p/2), bigQR$D, 
       bigQR$rbar, bigQR$thetab, bigQR$tol, beta = numeric(p), nreq = as.integer(nvar), 
       ier = integer(1), DUP = FALSE)
DUP is no longer supported and will be ignored.
bigglm.RODBC: no visible global function definition for ‘odbcQuery’
bigglm.RODBC : chunk: no visible global function definition for
  ‘odbcQuery’
bigglm.RODBC : chunk: no visible global function definition for
  ‘sqlGetResults’
bigglm,ANY-DBIConnection: no visible global function definition for
  ‘dbSendQuery’
bigglm,ANY-DBIConnection: no visible global function definition for
  ‘dbClearResult’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘dbClearResult’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘dbSendQuery’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘fetch’
Undefined global functions or variables:
  dbClearResult dbSendQuery fetch odbcQuery sqlGetResults

Found the following calls to data() loading into the global environment:
File ‘biglm/R/bigglm.R’:
  data(reset = TRUE)
  data(reset = FALSE)
See section ‘Good practice’ in ‘?data’.
Running ‘testthat.R’ [69s/72s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BIGL)
  > 
  > test_check("BIGL")
  ── 1. Failure: statistics (@test_wrapper.R#14)  ────────────────────────────────
  rs$maxR not equal to maxR(...).
  Component "Ymean": Component "sign": 1 element mismatch
  Component "Ymean": Component "call": 1 string mismatch
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 180 SKIPPED: 0 FAILED: 1
  1. Failure: statistics (@test_wrapper.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
quickModel: no visible global function definition for ‘tail’
quickSource: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  tail write.table
Consider adding
  importFrom("utils", "tail", "write.table")
to your NAMESPACE file.
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars: it is not portable to include SHLIB_OPENMP_*' macros in PKG_CPPFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
PKG_CPPFLAGS is used for both C and C++ code so it is not portable to
use it for these macros.
Packages in Depends field not imported from:
  ‘gbm’ ‘glmnet’ ‘randomForest’ ‘tree’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
LDCAEst: no visible global function definition for ‘glmnet’
cv.LDCA: no visible global function definition for ‘cv.glmnet’
predict.LDCA: no visible global function definition for ‘predict’
predict.cv.LDCA: no visible global function definition for ‘predict’
predict.tsp.gbm: no visible global function definition for ‘predict’
predict.tsp.randomForest: no visible global function definition for
  ‘predict’
predict.tsp.tree: no visible global function definition for ‘predict’
tsp.gbm: no visible global function definition for ‘gbm.fit’
tsp.randomForest: no visible global function definition for
  ‘randomForest’
tsp.tree: no visible global function definition for ‘tree.control’
tsp.tree: no visible global function definition for ‘tree’
Undefined global functions or variables:
  cv.glmnet gbm.fit glmnet predict randomForest tree tree.control
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
Rd file 'predict.LDCA.Rd':
  \usage lines wider than 90 characters:
     predict(object, newx, s = NULL, type = c("link", "response", "coefficients", "nonzero", "class"), exact = FALSE, offset, ...)

Rd file 'predict.tsp.randomForest.Rd':
  \usage lines wider than 90 characters:
     predict(object, newdata, type = "response", norm.votes = TRUE, predict.all = FALSE, proximity = FALSE, nodes = FALSE, cutoff, ...)

Rd file 'predict.tsp.tree.Rd':
  \usage lines wider than 90 characters:
     predict(object, newdata, type = c("vector", "tree", "class", "where"), split = FALSE, nwts, eps = 0.001, ...)

Rd file 'tsp.gbm.Rd':
  \usage lines wider than 90 characters:
     tsp.gbm(x, y, offset = NULL, misc = NULL, distribution = "bernoulli", w = NULL, var.monotone = NULL, n.trees = 100, interaction.depth = ... [TRUNCATED]

Rd file 'tsp.randomForest.Rd':
  \usage lines wider than 90 characters:
     tsp.randomForest(x, y = NULL, xtest = NULL, ytest = NULL, ntree = 500, type = "classification", mtry = if (!is.null(y) && !is.factor(y) ... [TRUNCATED]

Rd file 'tsp.tree.Rd':
  \usage lines wider than 90 characters:
     tsp.tree(X, response, control = tree.control(dim(X)[1], ...), method = "recursive.partition", split = c("deviance", "gini"), x = FALSE, ... [TRUNCATED]

These lines will be truncated in the PDF manual.
plot,bild-missing: no visible global function definition for
  ‘dev.interactive’
plot,bild-missing: no visible global function definition for
  ‘devAskNewPage’
plot,bild-missing: no visible global function definition for
  ‘extendrange’
Undefined global functions or variables:
  dev.interactive devAskNewPage extendrange
Consider adding
  importFrom("grDevices", "dev.interactive", "devAskNewPage",
             "extendrange")
to your NAMESPACE file.
chisq.sim.factory : chisq.sim.func: no visible global function
  definition for ‘chisq.test’
rmultnom: no visible global function definition for ‘runif’
Undefined global functions or variables:
  chisq.test runif
Consider adding
  importFrom("stats", "chisq.test", "runif")
to your NAMESPACE file.
commonprob2sigma: no visible global function definition for ‘approxfun’
rmvbin: no visible global function definition for ‘qnorm’
simul.commonprob: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  approxfun qnorm
Consider adding
  importFrom("stats", "approxfun", "qnorm")
to your NAMESPACE file.
bin_ps: no visible global function definition for ‘runif’
bin_ps: no visible global function definition for ‘dbinom’
draw_i: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dbinom runif
Consider adding
  importFrom("stats", "dbinom", "runif")
to your NAMESPACE file.
IndivdRUMIndMH: no visible global function definition for
  ‘flush.console’
dRUMAuxMix: no visible global function definition for ‘flush.console’
dRUMHAM: no visible global function definition for ‘flush.console’
dRUMIndMH: no visible global function definition for ‘flush.console’
print.binomlogit: no visible global function definition for ‘is’
summary.binomlogit: no visible global function definition for ‘is’
Undefined global functions or variables:
  flush.console is
Consider adding
  importFrom("methods", "is")
  importFrom("utils", "flush.console")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' calls in package code:
  ‘ggplot2’ ‘lattice’ ‘polynom’ ‘tcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
bins.quantiles: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Package suggested but not available for checking: ‘BiocVersion’
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
'library' or 'require' calls to packages already attached by Depends:
  ‘ape’ ‘cladoRcpp’ ‘phylobase’ ‘rexpokit’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘ape’ ‘cladoRcpp’ ‘methods’ ‘phylobase’ ‘rexpokit’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  ‘ape:::floating.pie.asp’ ‘cladoRcpp:::areas_list_to_states_list_old’
  See the note in ?`:::` about the use of this operator.
Missing link or links in documentation object 'BioGeoBEARS-package.Rd':
  ‘[cladoRcpp]{cladoRcpp}’

Missing link or links in documentation object 'areas_list_to_states_list_new.Rd':
  ‘[cladoRcpp]{cladoRcpp}’

Missing link or links in documentation object 'calc_loglike_sp.Rd':
  ‘[cladoRcpp]{cladoRcpp}’

Missing link or links in documentation object 'calc_loglike_sp_prebyte.Rd':
  ‘[cladoRcpp]{cladoRcpp}’

Missing link or links in documentation object 'calc_loglike_sp_stratified.Rd':
  ‘[cladoRcpp]{cladoRcpp}’

Missing link or links in documentation object 'check_BioGeoBEARS_run.Rd':
  ‘[cladoRcpp]{cladoRcpp}’

Missing link or links in documentation object 'make_relprob_matrix_bi.Rd':
  ‘[cladoRcpp]{cladoRcpp}’

Missing link or links in documentation object 'make_spmat_row.Rd':
  ‘[cladoRcpp]{cladoRcpp}’

Missing link or links in documentation object 'meval.Rd':
  ‘[cladoRcpp]{cladoRcpp}’

Missing link or links in documentation object 'symbolic_cell_to_relprob_cell.Rd':
  ‘[cladoRcpp]{cladoRcpp}’

Missing link or links in documentation object 'symbolic_cell_to_relprob_cell_sp.Rd':
  ‘[cladoRcpp]{cladoRcpp}’

Missing link or links in documentation object 'symbolic_to_relprob_matrix_sp.Rd':
  ‘[cladoRcpp]{cladoRcpp}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
Missing or unexported object: ‘gam::step.gam’
'library' or 'require' call to ‘MGRASTer’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.onAttach: no visible global function definition for ‘packageVersion’
biom.matrix: no visible global function definition for ‘packageVersion’
Undefined global functions or variables:
  packageVersion
Consider adding
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
binom.ci : bc: no visible global function definition for ‘qf’
binom.ci : bc: no visible global function definition for ‘qnorm’
cvar: no visible global function definition for ‘sd’
eta2: no visible global function definition for ‘lm’
eta2: no visible global function definition for ‘as.formula’
gg_qqplot: no visible binding for global variable ‘qnorm’
gg_qqplot: no visible global function definition for ‘quantile’
panel.hist: no visible global function definition for ‘par’
panel.hist: no visible global function definition for ‘hist’
panel.hist: no visible global function definition for ‘rect’
plotcdf2: no visible global function definition for ‘colorRampPalette’
plotcdf2 : jet.colors: no visible global function definition for ‘gray’
plotcdf2: no visible global function definition for ‘persp’
poi.ci: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  as.formula colorRampPalette gray hist lm par persp qchisq qf qnorm
  quantile rect sd
Consider adding
  importFrom("grDevices", "colorRampPalette", "gray")
  importFrom("graphics", "hist", "par", "persp", "rect")
  importFrom("stats", "as.formula", "lm", "qchisq", "qf", "qnorm",
             "quantile", "sd")
to your NAMESPACE file.
bivarcalcn: no visible global function definition for ‘qnorm’
bivarcalcn: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
prepare_Rd: bivarcalcn.Rd:49-50: Dropping empty section \details
prepare_Rd: bivarcalcn.Rd:59-61: Dropping empty section \note
prepare_Rd: bivarcalcn.Rd:65-67: Dropping empty section \seealso
biwt.cor: no visible global function definition for ‘covMcd’
biwt.cor: no visible binding for global variable ‘mad’
biwt.est: no visible global function definition for ‘covMcd’
biwt.est: no visible global function definition for ‘mahalanobis’
chi.int: no visible global function definition for ‘pchisq’
chi.int.p: no visible global function definition for ‘dchisq’
chi.int2: no visible global function definition for ‘pchisq’
chi.int2.p: no visible global function definition for ‘dchisq’
rejpt.bw: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  covMcd dchisq mad mahalanobis pchisq
Consider adding
  importFrom("stats", "dchisq", "mad", "mahalanobis", "pchisq")
to your NAMESPACE file.
Package suggested but not available for checking: ‘bigrf’
Missing or unexported object: ‘xgboost::predict’
bglmer: no visible global function definition for ‘packageVersion’
getBglmerDevianceFunctionBody: no visible global function definition
  for ‘packageVersion’
getParInfo : <anonymous>: no visible global function definition for
  ‘sd’
makeRefitDevFun: no visible global function definition for
  ‘packageVersion’
mkBglmerDevfun: no visible global function definition for
  ‘packageVersion’
namedList: no visible global function definition for ‘setNames’
refit.bmerMod: no visible global function definition for
  ‘packageVersion’
refit.bmerMod: no visible global function definition for ‘model.frame’
refit.bmerMod: no visible global function definition for ‘family’
refit.bmerMod: no visible global function definition for ‘getCall’
Undefined global functions or variables:
  family getCall model.frame packageVersion sd setNames
Consider adding
  importFrom("stats", "family", "getCall", "model.frame", "sd",
             "setNames")
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
blockMessage : <anonymous>: no visible global function definition for
  ‘head’
blockMessage: no visible global function definition for ‘head’
blockMessage: no visible global function definition for ‘tail’
Undefined global functions or variables:
  head tail
Consider adding
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
blockmodelskmeans: no visible global function definition for ‘dist’
matrixplot: no visible global function definition for ‘image’
matrixplot: no visible global function definition for ‘hsv’
matrixplot: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis dist hsv image
Consider adding
  importFrom("grDevices", "hsv")
  importFrom("graphics", "axis", "image")
  importFrom("stats", "dist")
to your NAMESPACE file.
plotblockrand: no visible global function definition for ‘pdf’
plotblockrand: no visible global function definition for ‘dev.off’
plotblockrand: no visible global function definition for ‘par’
plotblockrand: no visible global function definition for ‘plot.new’
plotblockrand: no visible global function definition for ‘strheight’
plotblockrand: no visible global function definition for ‘strwidth’
plotblockrand: no visible global function definition for ‘text’
plotblockrand: no visible global function definition for ‘lines’
Undefined global functions or variables:
  dev.off lines par pdf plot.new strheight strwidth text
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot.new", "strheight",
             "strwidth", "text")
to your NAMESPACE file.
File
  inst/LICENCE
will install at top-level and is not mentioned in the DESCRIPTION file.
Package in Depends field not imported from: ‘drc’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bmd: no visible global function definition for ‘qnorm’
bmd: no visible global function definition for ‘predict’
bmd: no visible global function definition for ‘LL.2’
bmd: no visible global function definition for ‘LN.2’
bmd: no visible global function definition for ‘W1.2’
bmd: no visible global function definition for ‘W2.2’
bmd: no visible global function definition for ‘LL.5’
bmd: no visible global function definition for ‘LN.4’
bmd: no visible global function definition for ‘W1.4’
bmd: no visible global function definition for ‘W2.4’
bmd: no visible global function definition for ‘FPL.4’
bmd: no visible global function definition for ‘maED’
bmd: no visible global function definition for ‘ED’
Undefined global functions or variables:
  ED FPL.4 LL.2 LL.5 LN.2 LN.4 W1.2 W1.4 W2.2 W2.4 maED predict qnorm
Consider adding
  importFrom("stats", "predict", "qnorm")
to your NAMESPACE file.
Rd file 'bmd.Rd':
  \examples lines wider than 100 characters:
     efsa2009p41.LL2 <- drm(number/total~dose, weights=total, data=efsa2009p41, type="binomial", fct=LL.2())
     efsa2009p41.LL3u <- drm(number/total~dose, weights=total, data=efsa2009p41, type="binomial", fct=LL.3u())
     hwang2009 <- data.frame(dose = c(0, 2.68, 10.34, 37.03), number = c(1,0,2,9), total = c(50,50,50,50))
     hwang2009.LN2 <- drm(number/total ~ dose, weights = total, data = hwang2009, type = "binomial", fct = LN.2())

These lines will be truncated in the PDF manual.
Packages in Depends field not imported from:
  ‘Amelia’ ‘MASS’ ‘lavaan’ ‘sem’ ‘snowfall’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls to packages already attached by Depends:
  ‘coda’ ‘functional’ ‘plyr’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘coda’ ‘functional’ ‘plyr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HDistNoSize: no visible global function definition for ‘density’
HDistSize: no visible global function definition for ‘density’
bmkconverge: no visible global function definition for ‘Compose’
bmksensitive: no visible global function definition for ‘Compose’
bmksummary: no visible global function definition for ‘Compose’
bmksummary: no visible global function definition for ‘Curry’
bmksummary: no visible binding for global variable ‘quantile’
bmksummary : std.error: no visible global function definition for ‘var’
bmksummary: no visible global function definition for ‘mcmc’
bmksummary: no visible global function definition for ‘mcmc.list’
bmksummary: no visible global function definition for ‘median’
bmksummary: no visible global function definition for ‘effectiveSize’
bmksummary: no visible global function definition for ‘gelman.diag’
Undefined global functions or variables:
  Compose Curry density effectiveSize gelman.diag mcmc mcmc.list median
  quantile var
Consider adding
  importFrom("stats", "density", "median", "quantile", "var")
to your NAMESPACE file.
bmmix : LL.y: no visible global function definition for ‘dmultinom’
bmmix : LL.x : <anonymous>: no visible global function definition for
  ‘dmultinom’
bmmix : LPrior.alpha: no visible global function definition for ‘dexp’
bmmix : alpha.move: no visible global function definition for ‘rnorm’
bmmix : alpha.move: no visible global function definition for ‘runif’
bmmix : phi.move: no visible global function definition for ‘rnorm’
bmmix : phi.move: no visible global function definition for ‘runif’
bmmix: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  dexp dmultinom read.table rnorm runif
Consider adding
  importFrom("stats", "dexp", "dmultinom", "rnorm", "runif")
  importFrom("utils", "read.table")
to your NAMESPACE file.
make_topology: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
bnlr: no visible global function definition for ‘dnorm’
bnlr: no visible global function definition for ‘runif’
chainsum : <anonymous>: no visible global function definition for
  ‘quantile’
infocrit: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm quantile runif
Consider adding
  importFrom("stats", "dnorm", "quantile", "runif")
to your NAMESPACE file.
clusterplots: no visible global function definition for ‘par’
clusterplots: no visible global function definition for ‘rainbow’
clusterplots: no visible global function definition for ‘plot’
clusterplots: no visible global function definition for ‘axis’
clusterplots: no visible global function definition for ‘lines’
diagplots: no visible global function definition for ‘par’
diagplots: no visible global function definition for ‘plot’
diagplots: no visible global function definition for ‘hist’
tseriesca: no visible global function definition for ‘rgamma’
tseriesca: no visible global function definition for ‘runif’
tseriesca: no visible global function definition for ‘dbeta’
tseriesca: no visible global function definition for ‘dgamma’
tseriescm: no visible global function definition for ‘rgamma’
tseriescm: no visible global function definition for ‘runif’
tseriescm: no visible global function definition for ‘dbeta’
tseriescm: no visible global function definition for ‘dgamma’
tseriescq: no visible global function definition for ‘rgamma’
tseriescq: no visible global function definition for ‘runif’
tseriescq: no visible global function definition for ‘dbeta’
tseriescq: no visible global function definition for ‘dgamma’
Undefined global functions or variables:
  axis dbeta dgamma hist lines par plot rainbow rgamma runif
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "hist", "lines", "par", "plot")
  importFrom("stats", "dbeta", "dgamma", "rgamma", "runif")
to your NAMESPACE file.
BOGest: no visible global function definition for ‘read.table’
BOGstat: no visible global function definition for ‘phyper’
BOGstat: no visible global function definition for ‘wilcox.test’
BOGstat: no visible global function definition for ‘p.adjust’
gseaplot: no visible global function definition for ‘par’
gseaplot: no visible global function definition for ‘plot’
gseaplot: no visible global function definition for ‘points’
gseaplot: no visible global function definition for ‘axis’
gseaplot: no visible global function definition for ‘segments’
hgplot: no visible global function definition for ‘par’
hgplot: no visible global function definition for ‘barplot’
Undefined global functions or variables:
  axis barplot p.adjust par phyper plot points read.table segments
  wilcox.test
Consider adding
  importFrom("graphics", "axis", "barplot", "par", "plot", "points",
             "segments")
  importFrom("stats", "p.adjust", "phyper", "wilcox.test")
  importFrom("utils", "read.table")
to your NAMESPACE file.
src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but not in PKG_CFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
Found the following non-portable file paths:
  Boom/inst/include/Models/Hierarchical/PosteriorSamplers/HierarchicalGaussianRegressionAsisSampler.hpp
  Boom/inst/include/Models/PointProcess/PosteriorSamplers/HomogeneousPoissonProcessPosteriorSampler.hpp
  Boom/inst/include/Models/PointProcess/PosteriorSamplers/MarkovModulatedPoissonProcessPosteriorSampler.hpp

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
boostBackend: no visible global function definition for ‘model.frame’
findFormulaIn: no visible global function definition for ‘as.formula’
kFoldCV: no visible binding for global variable ‘par’
predictResponseFromWeightedAverage: no visible global function
  definition for ‘weighted.mean’
print.boostr: no visible global function definition for ‘str’
Undefined global functions or variables:
  as.formula model.frame par str weighted.mean
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "as.formula", "model.frame", "weighted.mean")
  importFrom("utils", "str")
to your NAMESPACE file.
'library' or 'require' call to ‘lpSolveAPI’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘genetics’ ‘lpSolveAPI’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
alleleEnrichment: no visible binding for global variable ‘na.omit’
alleleEnrichment: no visible binding for global variable ‘na.pass’
alleleEnrichment: no visible global function definition for
  ‘write.table’
alleleEnrichment.data.alleles: no visible binding for global variable
  ‘na.omit’
alleleEnrichment.data.alleles: no visible binding for global variable
  ‘na.pass’
alleleEnrichment.data.alleles : <anonymous>: no visible global function
  definition for ‘allele.count’
alleleEnrichment.data.alleles: no visible global function definition
  for ‘runif’
alleleEnrichment.data.pheno: no visible global function definition for
  ‘read.table’
alleleEnrichment.lp: no visible global function definition for
  ‘make.lp’
alleleEnrichment.lp : <anonymous>: no visible global function
  definition for ‘set.column’
alleleEnrichment.lp : <anonymous>: no visible global function
  definition for ‘set.type’
alleleEnrichment.lp: no visible global function definition for
  ‘set.objfn’
alleleEnrichment.lp: no visible global function definition for
  ‘set.constr.type’
alleleEnrichment.lp: no visible global function definition for
  ‘set.rhs’
alleleEnrichment.lp: no visible global function definition for
  ‘lp.control’
alleleEnrichment.lp: no visible global function definition for
  ‘get.variables’
getGenotypes : <anonymous>: no visible global function definition for
  ‘genotype’
getRefAlleles: no visible global function definition for ‘read.table’
getSnpWeights: no visible global function definition for ‘read.table’
readMapfile: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  allele.count genotype get.variables lp.control make.lp na.omit
  na.pass read.table runif set.column set.constr.type set.objfn set.rhs
  set.type write.table
Consider adding
  importFrom("stats", "na.omit", "na.pass", "runif")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
specdens: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Rd file 'specdens.Rd':
  \examples lines wider than 100 characters:
                                                                                         #the first 20 values of the 
                                                                                         #time series Nile and WWWusage

These lines will be truncated in the PDF manual.
boot.stepAIC: no visible global function definition for ‘update’
boot.stepAIC: no visible binding for global variable ‘coef’
boot.stepAIC : <anonymous>: no visible global function definition for
  ‘anova’
boot.stepAIC: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  anova coef pnorm update
Consider adding
  importFrom("stats", "anova", "coef", "pnorm", "update")
to your NAMESPACE file.
bootSVD: no visible global function definition for ‘object.size’
bootSVD : <anonymous> : <anonymous>: no visible global function
  definition for ‘quantile’
bootSVD_LD: no visible global function definition for ‘txtProgressBar’
bootSVD_LD: no visible global function definition for
  ‘setTxtProgressBar’
genQ: no visible global function definition for ‘rnorm’
getHDpercentiles : <anonymous>: no visible global function definition
  for ‘quantile’
getMomentsAndMomentCI: no visible binding for global variable ‘var’
os: no visible global function definition for ‘object.size’
simEEG: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  object.size quantile rnorm setTxtProgressBar txtProgressBar var
Consider adding
  importFrom("stats", "quantile", "rnorm", "var")
  importFrom("utils", "object.size", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
boottol: no visible global function definition for ‘setNames’
boottol : shift: no visible global function definition for ‘tail’
boottol : shift: no visible global function definition for ‘head’
boottol: no visible global function definition for ‘na.omit’
vastol: no visible global function definition for ‘setNames’
vastol: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  head na.omit setNames tail
Consider adding
  importFrom("stats", "na.omit", "setNames")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Rd file 'beq.lin.Rd':
  \examples lines wider than 100 characters:
     plot(x,h_sol0,type="l",lty=1,main=paste("Water Surface Elevetion after",t,"days",sep=" "),xlab="x[m]",ylab="h[m]")

Rd file 'beq.song.Rd':
  \examples lines wider than 100 characters:
     plot(x,h_sol1,type="l",lty=1,main="Water Surface Elevetion (Song at's solution) ",xlab="x[m]",ylab="h[m]")

These lines will be truncated in the PDF manual.
bPeaksAnalysis: no visible global function definition for ‘write.table’
dataReading: no visible global function definition for ‘read.table’
dataSmoothing: no visible global function definition for ‘filter’
peakDetection: no visible global function definition for ‘quantile’
peakDetection: no visible global function definition for ‘pdf’
peakDetection: no visible global function definition for ‘par’
peakDetection: no visible global function definition for ‘plot’
peakDetection: no visible global function definition for ‘text’
peakDetection: no visible global function definition for ‘abline’
peakDetection: no visible global function definition for ‘points’
peakDetection: no visible global function definition for ‘dev.off’
peakDetection: no visible global function definition for ‘write.table’
peakDrawing: no visible global function definition for ‘par’
peakDrawing: no visible global function definition for ‘plot’
peakDrawing: no visible global function definition for ‘abline’
peakLocation: no visible global function definition for ‘read.table’
peakLocation: no visible global function definition for ‘pdf’
peakLocation: no visible global function definition for ‘barplot’
peakLocation: no visible global function definition for ‘dev.off’
peakLocation: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  abline barplot dev.off filter par pdf plot points quantile read.table
  text write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "barplot", "par", "plot", "points",
             "text")
  importFrom("stats", "filter", "quantile")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
M0: no visible global function definition for ‘fft’
M1: no visible global function definition for ‘fft’
bpk: no visible binding for global variable ‘dnorm’
bpkde: no visible binding for global variable ‘dnorm’
bpkde: no visible binding for global variable ‘bw.SJ’
bpkde: no visible global function definition for ‘rnorm’
bpkde: no visible global function definition for ‘fft’
bpkde: no visible global function definition for ‘optimize’
contour.discretize.kernel: no visible global function definition for
  ‘contour.default’
contour.mvkde: no visible global function definition for
  ‘contour.default’
image.discretize.kernel: no visible global function definition for
  ‘image.default’
image.discretize.kernel: no visible global function definition for
  ‘gray’
image.mvkde: no visible global function definition for ‘image.default’
image.mvkde: no visible global function definition for ‘gray’
image.mvlinbin: no visible global function definition for ‘image’
image.mvlinbin: no visible global function definition for ‘gray’
plot.discretize.kernel: no visible global function definition for
  ‘mtext’
plot.discretize.kernel: no visible global function definition for ‘par’
plot.mvkde: no visible global function definition for ‘mtext’
plot.mvkde: no visible global function definition for ‘par’
plot.mvlinbin: no visible global function definition for ‘plot’
plot.mvlinbin: no visible global function definition for ‘mtext’
plot.mvlinbin: no visible global function definition for ‘par’
Undefined global functions or variables:
  bw.SJ contour.default dnorm fft gray image image.default mtext
  optimize par plot rnorm
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "contour.default", "image", "image.default",
             "mtext", "par", "plot")
  importFrom("stats", "bw.SJ", "dnorm", "fft", "optimize", "rnorm")
to your NAMESPACE file.
Package suggested but not available for checking: ‘installr’
Package in Depends field not imported from: ‘waveslim’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
apply.breaks: no visible binding for global variable ‘median’
break.clust: no visible global function definition for ‘plot’
break.clust: no visible global function definition for ‘median’
breakage.plot: no visible binding for global variable ‘median’
breakage.plot: no visible global function definition for ‘plot’
breakage.plot: no visible global function definition for ‘abline’
breakage.plot: no visible global function definition for ‘lm’
find.bottom: no visible global function definition for ‘filter’
fit.breakage: no visible global function definition for ‘optim’
fit.breakage: no visible global function definition for ‘plot’
fit.breakage: no visible global function definition for ‘points’
fit.sensitivity.plot: no visible global function definition for
  ‘contour’
fit.sensitivity.plot: no visible global function definition for
  ‘points’
fit.sensitivity.plot: no visible global function definition for ‘text’
Undefined global functions or variables:
  abline contour filter lm median optim plot points text
Consider adding
  importFrom("graphics", "abline", "contour", "plot", "points", "text")
  importFrom("stats", "filter", "lm", "median", "optim")
to your NAMESPACE file.
Package suggested but not available for checking: ‘glmmADMB’
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
BSGS.Sample: no visible global function definition for ‘rgamma’
BSGS.Simple: no visible global function definition for ‘rgamma’
CompWiseGibbs: no visible global function definition for ‘runif’
CompWiseGibbs: no visible global function definition for ‘rnorm’
CompWiseGibbsSMP: no visible global function definition for ‘rbinom’
CompWiseGibbsSMP: no visible global function definition for ‘runif’
CompWiseGibbsSMP: no visible global function definition for ‘rnorm’
CompWiseGibbsSimple: no visible global function definition for ‘runif’
CompWiseGibbsSimple: no visible global function definition for ‘rnorm’
CompWiseGibbsSimple: no visible global function definition for ‘rgamma’
GroupMH: no visible global function definition for ‘runif’
GroupZ.MH: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rbinom rgamma rnorm runif
Consider adding
  importFrom("stats", "rbinom", "rgamma", "rnorm", "runif")
to your NAMESPACE file.
plot.bspec: no visible global function definition for ‘par’
plot.bspec: no visible global function definition for ‘plot’
plot.bspec: no visible global function definition for ‘matlines’
plot.bspec: no visible global function definition for ‘points’
plot.bspec: no visible global function definition for ‘axis’
plot.bspec: no visible global function definition for ‘mtext’
plot.bspec: no visible global function definition for ‘axTicks’
plot.bspec: no visible global function definition for ‘box’
plot.bspecACF: no visible global function definition for ‘plot’
plot.bspecACF: no visible global function definition for ‘abline’
plot.bspecACF: no visible global function definition for ‘matlines’
Undefined global functions or variables:
  abline axTicks axis box matlines mtext par plot points
Consider adding
  importFrom("graphics", "abline", "axTicks", "axis", "box", "matlines",
             "mtext", "par", "plot", "points")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  print.dir.cond print.dir.ord
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  helpers.c:365:19: warning: absolute value function 'fabsf' given an argument of type 'double' but has parameter of type 'float' which may cause truncation of value [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BSquare.Rcheck/00install.out’ for details.
'library' or 'require' calls to packages already attached by Depends:
  ‘VGAM’ ‘quadprog’ ‘quantreg’
  Please remove these calls from your code.
dqreg: no visible binding for global variable ‘median’
dqreg: no visible global function definition for ‘median’
log_pdf : q0: no visible global function definition for ‘qnorm’
log_pdf : d0: no visible global function definition for ‘dnorm’
log_pdf : q0: no visible global function definition for ‘qt’
log_pdf : d0: no visible global function definition for ‘dt’
log_pdf : q0: no visible global function definition for ‘qweibull’
log_pdf : d0: no visible global function definition for ‘dweibull’
log_pdf : q0: no visible global function definition for ‘qgamma’
log_pdf : d0: no visible global function definition for ‘dgamma’
make.B: no visible global function definition for ‘qnorm’
make.B: no visible global function definition for ‘qweibull’
make.B: no visible global function definition for ‘qgamma’
qr_plot: no visible global function definition for ‘gray’
qr_plot: no visible binding for global variable ‘quantile’
qr_plot: no visible global function definition for ‘polygon’
qr_plot: no visible global function definition for ‘lines’
qreg: no visible global function definition for ‘sd’
qreg: no visible global function definition for ‘lm’
qreg: no visible global function definition for ‘var’
qreg_spline: no visible global function definition for ‘rnorm’
qreg_spline: no visible global function definition for ‘var’
qreg_spline: no visible binding for global variable ‘quantile’
rootfind: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dgamma dnorm dt dweibull gray lines lm median polygon qgamma qnorm qt
  quantile qweibull rnorm runif sd var
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "lines", "polygon")
  importFrom("stats", "dgamma", "dnorm", "dt", "dweibull", "lm",
             "median", "qgamma", "qnorm", "qt", "quantile", "qweibull",
             "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
Found the following Makefile(s) without a final LF:
  src/Makevars
Some ‘make’ programs ignore lines not ending in LF.
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
alpha.proxy: no visible global function definition for ‘filled.contour’
alpha.proxy: no visible global function definition for ‘axis’
alpha.proxy: no visible global function definition for ‘contour’
factor.model.stat: no visible global function definition for ‘quantile’
factor.model.stat: no visible global function definition for ‘lsfit’
partial.rainbow: no visible binding for global variable ‘rainbow’
var.shrink.eqcor: no visible global function definition for ‘var’
var.shrink.eqcor: no visible global function definition for ‘quantile’
var.shrink.eqcor: no visible global function definition for ‘cov2cor’
Undefined global functions or variables:
  axis contour cov2cor filled.contour lsfit quantile rainbow var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "contour", "filled.contour")
  importFrom("stats", "cov2cor", "lsfit", "quantile", "var")
to your NAMESPACE file.
plot.bursts: no visible global function definition for ‘plot’
plot.bursts: no visible global function definition for ‘axis’
plot.bursts: no visible global function definition for ‘arrows’
Undefined global functions or variables:
  arrows axis plot
Consider adding
  importFrom("graphics", "arrows", "axis", "plot")
to your NAMESPACE file.
Rd file 'bvenn.Rd':
  \examples lines wider than 100 characters:
                     bvenn(list(Set1 = sample(letters, 16), Set2 = sample(letters, 3+ 3*j), Set3 = sample(letters, 7)), add = TRUE, fontsize ... [TRUNCATED]

These lines will be truncated in the PDF manual.
gimli.25001hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘haplo.stats’ ‘msm’
  Please remove these calls from your code.
fitBVS: no visible global function definition for ‘qnorm’
fitBVS: no visible global function definition for ‘model.matrix’
fitBVS: no visible global function definition for ‘as.formula’
fitBVS: no visible global function definition for ‘glm’
fitBVS: no visible global function definition for ‘deviance’
fitBVS: no visible global function definition for ‘pnorm’
plotBVS: no visible global function definition for ‘par’
plotBVS: no visible global function definition for ‘image’
plotBVS: no visible global function definition for ‘axis’
sampleBVS: no visible global function definition for ‘qnorm’
sampleBVS: no visible global function definition for ‘pnorm’
sampleBVS: no visible global function definition for ‘runif’
summaryBVS: no visible global function definition for ‘qnorm’
summaryBVS : inc.prob: no visible global function definition for
  ‘pnorm’
summaryBVS: no visible global function definition for ‘pnorm’
summaryBVS: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  as.formula axis deviance glm image model.matrix par pnorm qnorm runif
Consider adding
  importFrom("graphics", "axis", "image", "par")
  importFrom("stats", "as.formula", "deviance", "glm", "model.matrix",
             "pnorm", "qnorm", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  wgr20180916.cpp:1466:39: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  wgr20180916.cpp:1466:66: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  wgr20180916.cpp:1473:39: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  wgr20180916.cpp:1473:66: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/bWGR.Rcheck/00install.out’ for details.
makemim: no visible global function definition for ‘cor’
sigtestMTC: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  cor p.adjust
Consider adding
  importFrom("stats", "cor", "p.adjust")
to your NAMESPACE file.
cabootcrs: no visible global function definition for ‘read.table’
cabootcrs: no visible global function definition for ‘rmultinom’
cabootcrs: no visible global function definition for ‘rpois’
plotca : plotonepic: no visible global function definition for ‘qchisq’
plotca : plotonepic: no visible global function definition for
  ‘dev.new’
plotca : plotonepic: no visible global function definition for ‘plot’
plotca : plotonepic: no visible global function definition for ‘points’
plotca : plotonepic: no visible global function definition for ‘abline’
plotca : plotonepic: no visible global function definition for ‘legend’
plotca : plotonepic: no visible global function definition for ‘title’
plotca : plotonepic: no visible global function definition for ‘lines’
plotca : plotonepic: no visible global function definition for ‘text’
plotca: no visible global function definition for ‘colours’
plotca: no visible global function definition for ‘rainbow’
plotca: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  abline colours dev.new legend lines plot points qchisq rainbow
  read.table rmultinom rpois text title
Consider adding
  importFrom("grDevices", "colours", "dev.new", "rainbow")
  importFrom("graphics", "abline", "legend", "lines", "plot", "points",
             "text", "title")
  importFrom("stats", "qchisq", "rmultinom", "rpois")
  importFrom("utils", "read.table")
to your NAMESPACE file.
---- unloading

 *** caught segfault ***
address 0x7ffaf34f7af0, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
File ‘cairoDevice/libs/cairoDevice.so’:
  Found non-API call to R: ‘R_CStackLimit’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Cairo/libs/Cairo.so’:
  Found non-API calls to R: ‘R_InputHandlers’, ‘addInputHandler’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
calibrate: no visible global function definition for ‘lines’
calibrate: no visible global function definition for ‘text’
canocor: no visible global function definition for ‘cor’
circle: no visible global function definition for ‘points’
dlines: no visible global function definition for ‘lines’
origin: no visible global function definition for ‘par’
origin: no visible global function definition for ‘lines’
rda: no visible global function definition for ‘cor’
rda: no visible global function definition for ‘princomp’
rda: no visible global function definition for ‘var’
textxy: no visible global function definition for ‘text’
Undefined global functions or variables:
  cor lines par points princomp text var
Consider adding
  importFrom("graphics", "lines", "par", "points", "text")
  importFrom("stats", "cor", "princomp", "var")
to your NAMESPACE file.
EK.eqn10.supp: no visible global function definition for ‘integrate’
MH: no visible global function definition for ‘rmvnorm’
MH: no visible global function definition for ‘runif’
computer.model: no visible global function definition for ‘rmvnorm’
create.new.toy.datasets: no visible global function definition for
  ‘rnorm’
model.inadequacy: no visible global function definition for ‘rmvnorm’
prob.psi1: no visible global function definition for ‘dmvnorm’
prob.psi2: no visible global function definition for ‘dmvnorm’
prob.theta: no visible global function definition for ‘dmvnorm’
sample.theta: no visible global function definition for ‘rmvnorm’
stage1: no visible global function definition for ‘optim’
stage2: no visible global function definition for ‘optim’
stage3: no visible global function definition for ‘optim’
Undefined global functions or variables:
  dmvnorm integrate optim rmvnorm rnorm runif
Consider adding
  importFrom("stats", "integrate", "optim", "rnorm", "runif")
to your NAMESPACE file.
CAM: no visible global function definition for ‘object.size’
CAM: no visible global function definition for ‘as’
computeScoreMat: no visible global function definition for ‘combn’
computeScoreMat: no visible global function definition for ‘var’
computeScoreMatParallel: no visible global function definition for
  ‘var’
selLm: no visible global function definition for ‘lm’
selLm: no visible global function definition for ‘coef’
train_gam: no visible global function definition for ‘formula’
train_lasso: no visible global function definition for ‘predict’
train_linear: no visible global function definition for ‘lm’
Undefined global functions or variables:
  as coef combn formula lm object.size predict var
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "coef", "formula", "lm", "predict", "var")
  importFrom("utils", "combn", "object.size")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
bootstrapCapwire: no visible global function definition for ‘quantile’
drawCapRatesBeta : <anonymous>: no visible global function definition
  for ‘rbeta’
drawCapRatesExp : <anonymous>: no visible global function definition
  for ‘rexp’
drawCapRatesGamma : <anonymous>: no visible global function definition
  for ‘rgamma’
drawCapRatesGeom : <anonymous>: no visible global function definition
  for ‘rgeom’
drawCapRatesUnif : <anonymous>: no visible global function definition
  for ‘runif’
partitionCountData : find.3.way.partitions: no visible global function
  definition for ‘dmultinom’
Undefined global functions or variables:
  dmultinom quantile rbeta rexp rgamma rgeom runif
Consider adding
  importFrom("stats", "dmultinom", "quantile", "rbeta", "rexp", "rgamma",
             "rgeom", "runif")
to your NAMESPACE file.
Sub.pair: no visible global function definition for ‘qnorm’
as.record: no visible global function definition for ‘capture.output’
estN: no visible global function definition for ‘sd’
estN: no visible global function definition for ‘qnorm’
estN.bootstrap: no visible global function definition for ‘runif’
Undefined global functions or variables:
  capture.output qnorm runif sd
Consider adding
  importFrom("stats", "qnorm", "runif", "sd")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
abundance: no visible global function definition for ‘D’
Undefined global functions or variables:
  D
Consider adding
  importFrom("stats", "D")
to your NAMESPACE file.
barplotEQR: no visible global function definition for ‘barplot’
barplotEQR: no visible global function definition for ‘abline’
barplotEQR: no visible global function definition for ‘par’
barplotEQR: no visible global function definition for ‘text’
Undefined global functions or variables:
  abline barplot par text
Consider adding
  importFrom("graphics", "abline", "barplot", "par", "text")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘MASS’ ‘RSQLite’ ‘grid’ ‘sm’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
CARrampsOcl.fit: no visible global function definition for
  ‘coefficients’
CARrampsOcl.fit: no visible global function definition for ‘lm’
CARrampsOcl.fit: no visible global function definition for ‘runif’
CARrampsOcl.fit: no visible global function definition for
  ‘write.table’
CARrampsOcl.fit: no visible global function definition for ‘rgamma’
CARrampsOcl.fit: no visible global function definition for ‘rnorm’
multivspost2blogandtausqtot : genst: no visible global function
  definition for ‘rgamma’
optimizelogpost: no visible global function definition for ‘optim’
optimizelogpost: no visible global function definition for ‘optimize’
plot2Q: no visible global function definition for ‘terrain.colors’
plot2Q: no visible global function definition for ‘par’
plot3Q: no visible global function definition for ‘terrain.colors’
plot3Q: no visible global function definition for ‘par’
plot3Q: no visible global function definition for ‘dev.flush’
plotCAR1: no visible global function definition for ‘terrain.colors’
plotCAR1: no visible global function definition for ‘par’
plotCAR1plus1Q: no visible global function definition for
  ‘terrain.colors’
plotCAR1plus1Q: no visible global function definition for ‘par’
plotCAR1plus1Q: no visible global function definition for ‘dev.flush’
rdirichlet: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  coefficients dev.flush lm optim optimize par rgamma rnorm runif
  terrain.colors write.table
Consider adding
  importFrom("grDevices", "dev.flush", "terrain.colors")
  importFrom("graphics", "par")
  importFrom("stats", "coefficients", "lm", "optim", "optimize",
             "rgamma", "rnorm", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Package suggested but not available for checking: ‘lqa’
MDR.high.forward1: no visible global function definition for ‘combn’
MDR.sing.mod1: no visible global function definition for ‘combn’
MDR.sing.mod1: no visible global function definition for
  ‘complete.cases’
MDR.sing.mod1: no visible global function definition for ‘lm’
MDR.sing.mod1: no visible global function definition for ‘aov’
MDR.sing.mod1: no visible global function definition for ‘anova’
MDR.stage.forward1: no visible global function definition for ‘combn’
MDR.stage.forward1: no visible global function definition for
  ‘complete.cases’
MDR.stage.forward1: no visible global function definition for ‘lm’
MDR.stage.forward1: no visible global function definition for ‘resid’
MDR.stage.forward1: no visible global function definition for ‘pf’
MDR_forward1: no visible global function definition for
  ‘complete.cases’
MDR_forward1: no visible global function definition for ‘lm’
MDR_forward1: no visible global function definition for ‘aov’
low.anova: no visible global function definition for ‘complete.cases’
low.anova: no visible global function definition for ‘lm’
sing.mod1: no visible global function definition for ‘combn’
sing.mod1: no visible global function definition for ‘complete.cases’
sing.mod1: no visible global function definition for ‘lm’
sing.mod1: no visible global function definition for ‘pf’
Undefined global functions or variables:
  anova aov combn complete.cases lm pf resid
Consider adding
  importFrom("stats", "anova", "aov", "complete.cases", "lm", "pf",
             "resid")
  importFrom("utils", "combn")
to your NAMESPACE file.
mi.inference: no visible binding for global variable ‘var’
mi.inference: no visible global function definition for ‘qt’
mi.inference: no visible global function definition for ‘pt’
Undefined global functions or variables:
  pt qt var
Consider adding
  importFrom("stats", "pt", "qt", "var")
to your NAMESPACE file.
ctab: no visible global function definition for ‘xtabs’
mob.eqmain: no visible global function definition for ‘model.matrix’
mob.qi: no visible global function definition for ‘C’
mob.qi: no visible binding for global variable ‘contr.treatment’
mob.rc1: no visible global function definition for ‘C’
mob.rc1: no visible binding for global variable ‘contr.treatment’
mob.rc1: no visible global function definition for ‘model.matrix’
mob.symint: no visible global function definition for ‘model.matrix’
print.ctab: no visible global function definition for ‘ftable’
Undefined global functions or variables:
  C contr.treatment ftable model.matrix xtabs
Consider adding
  importFrom("stats", "C", "contr.treatment", "ftable", "model.matrix",
             "xtabs")
to your NAMESPACE file.
Rd file 'ctab.Rd':
  \usage lines wider than 90 characters:
     ctab(...,dec.places=NULL,digits=NULL,type=NULL,style=NULL,row.vars=NULL,col.vars=NULL,percentages=NULL,addmargins=NULL)

Rd file 'sqtab.Rd':
  \examples lines wider than 100 characters:
     OccFather<-gl(5,5,labels=c("Upper nonmanual","Lower nonmanual","Upper manual","Lower manual","Farm"))
     glm.q0<-glm(Freq~OccFather+OccSon+mob.qi(OccFather,OccSon,constrained=TRUE),family=poisson(),data=FHtab)
     glm.hrc1<-glm(Freq~OccFather+OccSon+mob.rc1(OccFather,OccSon,equal=TRUE),family=poisson(),data=FHtab)
     m2 <- mlogit(occupation ~ mob.qi(focc,alt)+mob.unif(focc,alt) | education+race,data=pc, reflevel = "farm")

These lines will be truncated in the PDF manual.
binParamPosteriorSampling: no visible global function definition for
  ‘rbeta’
bindagMonteCarloCausalEffect: no visible global function definition for
  ‘runif’
getBinDAGModelData: no visible global function definition for ‘runif’
logitDist: no visible global function definition for ‘runif’
logitDist: no visible global function definition for ‘rnorm’
simulateWitnessModel: no visible global function definition for ‘runif’
summary.covsearch: no visible global function definition for ‘quantile’
summary.iv: no visible global function definition for ‘quantile’
summary.wpp: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile rbeta rnorm runif
Consider adding
  importFrom("stats", "quantile", "rbeta", "rnorm", "runif")
to your NAMESPACE file.
ConstructModel: warning in AddDynamicRegression(ss, formula, data =
  data, sigma.mean.prior = sigma.mean.prior): partial argument match of
  ‘sigma.mean.prior’ to ‘sigma.mean.prior.DEPRECATED’
Non-standard file/directory found at top level:
  ‘integration_tests’
BinaryCut: no visible global function definition for ‘quantile’
CleanNaFromContinuousFunction: no visible global function definition
  for ‘median’
CleanNaFromContinuousFunction: no visible global function definition
  for ‘na.omit’
GetMetadata.Connect: no visible global function definition for
  ‘dbGetQuery’
GetRawData.Connect: no visible global function definition for
  ‘dbGetQuery’
Linearity: no visible global function definition for ‘median’
PredictivePowerCv: no visible global function definition for ‘sd’
ReadCausataCsv: no visible global function definition for ‘read.csv’
ToPmml.GlmnetModelDefinition: no visible global function definition for
  ‘coef’
ToPmml.GlmnetModelDefinition: no visible global function definition for
  ‘terms.formula’
ValidateModel: no visible global function definition for ‘predict’
predict.GlmnetModelDefinition: no visible global function definition
  for ‘model.matrix’
predict.GlmnetModelDefinition: no visible binding for global variable
  ‘contrasts’
predict.GlmnetModelDefinition: no visible global function definition
  for ‘predict’
Undefined global functions or variables:
  coef contrasts dbGetQuery median model.matrix na.omit predict
  quantile read.csv sd terms.formula
Consider adding
  importFrom("stats", "coef", "contrasts", "median", "model.matrix",
             "na.omit", "predict", "quantile", "sd", "terms.formula")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
estim.regul: warning in matrix(res, nc = length(grid2)): partial
  argument match of ‘nc’ to ‘ncol’
comput: no visible global function definition for ‘cor’
img.estim.regul: no visible global function definition for ‘par’
img.estim.regul: no visible global function definition for ‘image’
img.estim.regul: no visible global function definition for
  ‘heat.colors’
img.estim.regul: no visible global function definition for ‘axis’
img.estim.regul: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘par’
img.matcor: no visible global function definition for ‘image’
img.matcor: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘abline’
img.matcor: no visible global function definition for ‘layout’
loo: no visible global function definition for ‘cor’
matcor: no visible global function definition for ‘cor’
plt.cc: no visible global function definition for ‘par’
plt.cc: no visible global function definition for ‘layout’
plt.indiv: no visible global function definition for ‘plot’
plt.indiv: no visible global function definition for ‘text’
plt.indiv: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘plot’
plt.var: no visible global function definition for ‘points’
plt.var: no visible global function definition for ‘text’
plt.var: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘lines’
rcc: no visible global function definition for ‘var’
rcc: no visible global function definition for ‘cov’
Undefined global functions or variables:
  abline axis box cor cov heat.colors image layout lines par plot
  points text var
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "layout",
             "lines", "par", "plot", "points", "text")
  importFrom("stats", "cor", "cov", "var")
to your NAMESPACE file.
prepare_Rd: estim.regul.Rd:24-26: Dropping empty section \details
prepare_Rd: img.estim.regul.Rd:15-17: Dropping empty section \details
prepare_Rd: img.estim.regul.Rd:24-25: Dropping empty section \examples
ccd.sequential: no visible global function definition for ‘qchisq’
dominate.random.sample: no visible global function definition for
  ‘runif’
draw.circle: no visible global function definition for ‘polygon’
juggle2: no visible global function definition for ‘rbinom’
plot.cccd: no visible global function definition for ‘gray’
plot.cccd: no visible global function definition for ‘plot’
plot.cccd: no visible global function definition for ‘points’
plot.cccdClassifier: no visible global function definition for ‘points’
plot.cccdClassifier: no visible global function definition for ‘plot’
plot.ccd: no visible global function definition for ‘plot’
Undefined global functions or variables:
  gray plot points polygon qchisq rbinom runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "plot", "points", "polygon")
  importFrom("stats", "qchisq", "rbinom", "runif")
to your NAMESPACE file.
VD: no visible binding for global variable ‘var’
stratcc : <anonymous>: no visible global function definition for
  ‘hclust’
stratcc : <anonymous>: no visible global function definition for
  ‘cutree’
Undefined global functions or variables:
  cutree hclust var
Consider adding
  importFrom("stats", "cutree", "hclust", "var")
to your NAMESPACE file.
Rd file 'stratcc.Rd':
  \usage lines wider than 90 characters:
     stratcc(x, groups, alloc = "Pro", fraction = 0.1, clustering = FALSE, cluster_method = "ward")

These lines will be truncated in the PDF manual.
ccda.main: no visible global function definition for ‘hclust’
ccda.main: no visible global function definition for ‘dist’
ccda.main: no visible global function definition for ‘cutree’
ccda.main: no visible global function definition for ‘quantile’
percentage: no visible global function definition for ‘predict’
plotccda.cluster: no visible global function definition for ‘par’
plotccda.cluster: no visible global function definition for ‘plot’
plotccda.q95: no visible global function definition for ‘par’
plotccda.q95: no visible global function definition for ‘plot’
plotccda.q95: no visible global function definition for ‘density’
plotccda.q95: no visible global function definition for ‘abline’
plotccda.q95: no visible global function definition for ‘legend’
plotccda.q95: no visible global function definition for ‘strwidth’
plotccda.q95: no visible global function definition for ‘strheight’
plotccda.results: no visible global function definition for ‘par’
plotccda.results: no visible global function definition for ‘plot’
plotccda.results: no visible global function definition for ‘axis’
plotccda.results: no visible global function definition for ‘lines’
plotccda.results: no visible global function definition for ‘legend’
plotccda.results: no visible global function definition for ‘strwidth’
plotccda.results: no visible global function definition for ‘strheight’
Undefined global functions or variables:
  abline axis cutree density dist hclust legend lines par plot predict
  quantile strheight strwidth
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "strheight", "strwidth")
  importFrom("stats", "cutree", "density", "dist", "hclust", "predict",
             "quantile")
to your NAMESPACE file.
dcc.est: no visible global function definition for ‘cov’
dcc.estimation1: no visible global function definition for ‘optim’
dcc.estimation2: no visible global function definition for
  ‘constrOptim’
dlc: no visible global function definition for ‘cov’
eccc.estimation: no visible global function definition for ‘optim’
hh.test : uni.garch : uni.garch.est : garch.ll: no visible global
  function definition for ‘dnorm’
hh.test : uni.garch : uni.garch.est: no visible global function
  definition for ‘optim’
hh.test: no visible global function definition for ‘lm’
hh.test: no visible global function definition for ‘pchisq’
jb.test: no visible global function definition for ‘pchisq’
ljung.box.test: no visible global function definition for ‘pchisq’
nt.test : uni.garch : uni.garch.est : garch.ll: no visible global
  function definition for ‘dnorm’
nt.test : uni.garch : uni.garch.est: no visible global function
  definition for ‘optim’
nt.test: no visible global function definition for ‘lm’
nt.test: no visible global function definition for ‘pchisq’
rob.kr: no visible global function definition for ‘quantile’
rob.sk: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  constrOptim cov dnorm lm optim pchisq quantile
Consider adding
  importFrom("stats", "constrOptim", "cov", "dnorm", "lm", "optim",
             "pchisq", "quantile")
to your NAMESPACE file.
Found the following significant warnings:
  ./MCMC_prob.h:2091:41: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CCMnet.Rcheck/00install.out’ for details.
p.Roy: no visible global function definition for ‘pf’
p.asym: no visible global function definition for ‘pf’
p.perm: no visible global function definition for ‘cancor’
plt.asym: no visible global function definition for ‘qf’
plt.asym: no visible global function definition for ‘plot’
plt.asym: no visible global function definition for ‘df’
plt.asym: no visible global function definition for ‘abline’
plt.perm: no visible global function definition for ‘hist’
plt.perm: no visible global function definition for ‘mtext’
plt.perm: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline cancor df hist mtext pf plot qf
Consider adding
  importFrom("graphics", "abline", "hist", "mtext", "plot")
  importFrom("stats", "cancor", "df", "pf", "qf")
to your NAMESPACE file.
Rd file 'p.perm.Rd':
  \examples lines wider than 100 characters:
     ## Run permutation test using Wilks Lambda (default) as test statistic; include different numbers of canonical correlations:

Rd file 'plt.asym.Rd':
  \examples lines wider than 100 characters:
     ## Plot the F-approximation for the Hotelling-Lawley Trace, considering 3, 2, or 1 canonical correlation(s):

Rd file 'plt.perm.Rd':
  \examples lines wider than 100 characters:
     # plot the permutation distribution of an F approximation for Wilks' Lambda, considering 3 and 2 canonical correlations:
     # plot the permutation distribution of an F approximation for the Pillai-Bartlett Trace, considering 3, 2, and 1 canonical correlation( ... [TRUNCATED]

These lines will be truncated in the PDF manual.
'library' or 'require' call to ‘bitops’ which was already attached by Depends.
  Please remove these calls from your code.
bw: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  optimize
Consider adding
  importFrom("stats", "optimize")
to your NAMESPACE file.
CDFt: no visible global function definition for ‘ecdf’
CDFt: no visible global function definition for ‘quantile’
CDFt: no visible global function definition for ‘approx’
KolmogorovSmirnov: no visible global function definition for ‘ecdf’
KolmogorovSmirnov: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx ecdf quantile
Consider adding
  importFrom("stats", "approx", "ecdf", "quantile")
to your NAMESPACE file.
prepare_Rd: CramerVonMisesTwoSamples.Rd:23: Dropping empty section \examples
prepare_Rd: KolmogorovSmirnov.Rd:26: Dropping empty section \examples
Packages in Depends field not imported from:
  ‘gplots’ ‘minpack.lm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
erf: no visible global function definition for ‘pnorm’
fitVolDist: no visible global function definition for ‘nls.lm’
fitVolDist: no visible global function definition for ‘nls.lm.control’
fitVolDist: no visible global function definition for ‘optim’
fitVolDist: no visible global function definition for ‘relist’
print.fitVolDist: no visible global function definition for ‘coef’
print.fitVolDist: no visible global function definition for ‘deviance’
print.fitVolDist: no visible global function definition for ‘pt’
print.fitVolDist: no visible global function definition for
  ‘printCoefmat’
resFunChiSq: no visible global function definition for ‘relist’
volEq7: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  coef deviance integrate nls.lm nls.lm.control optim pnorm
  printCoefmat pt relist
Consider adding
  importFrom("stats", "coef", "deviance", "integrate", "optim", "pnorm",
             "printCoefmat", "pt")
  importFrom("utils", "relist")
to your NAMESPACE file.
cenNID: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Unexported objects imported by ':::' calls:
  ‘copula:::dCdu’ ‘copula:::fitCopStart’
  See the note in ?`:::` about the use of this operator.
MomNIT: no visible global function definition for ‘dnorm’
MomNIT: no visible global function definition for ‘pnorm’
cdfNI: no visible global function definition for ‘pnorm’
cdfNI: no visible global function definition for ‘pt’
em.cens: no visible global function definition for ‘lm’
em.cens: no visible global function definition for ‘coefficients’
em.cens : ft: no visible global function definition for ‘dt’
em.cens : ft: no visible global function definition for ‘pt’
em.cens: no visible global function definition for ‘optimize’
em.cens: no visible global function definition for ‘dnorm’
em.cens: no visible global function definition for ‘pnorm’
em.cens: no visible global function definition for ‘sd’
Undefined global functions or variables:
  coefficients dnorm dt lm optimize pnorm pt sd
Consider adding
  importFrom("stats", "coefficients", "dnorm", "dt", "lm", "optimize",
             "pnorm", "pt", "sd")
to your NAMESPACE file.
CM: no visible global function definition for ‘sd’
Erf: no visible global function definition for ‘pnorm’
Erfc: no visible global function definition for ‘pnorm’
boot.Cenarma: no visible global function definition for ‘coef’
boot.Cenarma: no visible global function definition for ‘arima.sim’
cenarma: no visible global function definition for ‘arima’
cenarma: no visible global function definition for ‘coef’
cenarma: no visible global function definition for ‘ARMAacf’
cenarma: no visible global function definition for ‘var’
plot.cents: no visible global function definition for ‘plot’
plot.cents: no visible global function definition for ‘segments’
plot.cents: no visible global function definition for ‘rgb’
plot.cents: no visible global function definition for ‘points’
rcarma: no visible global function definition for ‘arima.sim’
rcarma: no visible global function definition for ‘quantile’
scenNID: no visible global function definition for ‘sd’
se.Cenarma: no visible global function definition for ‘coef’
se.Cenarma: no visible global function definition for ‘sd’
Undefined global functions or variables:
  ARMAacf arima arima.sim coef plot pnorm points quantile rgb sd
  segments var
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "plot", "points", "segments")
  importFrom("stats", "ARMAacf", "arima", "arima.sim", "coef", "pnorm",
             "quantile", "sd", "var")
to your NAMESPACE file.
select_lambda: no visible global function definition for ‘median’
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but not in PKG_CFLAGS
  src/Makevars: it is not portable to include SHLIB_OPENMP_*' macros in PKG_CPPFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
PKG_CPPFLAGS is used for both C and C++ code so it is not portable to
use it for these macros.
cf_estimate_quantiles: no visible global function definition for
  ‘qnorm’
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
sw.plot : <anonymous>: no visible global function definition for
  ‘median’
sw.plot : <anonymous>: no visible global function definition for ‘mad’
sw.plot : my.line: no visible global function definition for ‘lines’
sw.plot : island.line: no visible global function definition for
  ‘lines’
sw.plot: no visible global function definition for ‘plot’
sw.plot: no visible global function definition for ‘rug’
sw.plot: no visible global function definition for ‘axis’
sw.plot: no visible global function definition for ‘mtext’
sw.plot: no visible global function definition for ‘abline’
sw.plot: no visible global function definition for ‘points’
sw.rob : <anonymous>: no visible global function definition for
  ‘median’
sw.rob : <anonymous>: no visible global function definition for ‘mad’
sw.threshold : <anonymous>: no visible global function definition for
  ‘median’
sw.threshold : <anonymous>: no visible global function definition for
  ‘mad’
Undefined global functions or variables:
  abline axis lines mad median mtext plot points rug
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "mtext", "plot",
             "points", "rug")
  importFrom("stats", "mad", "median")
to your NAMESPACE file.
Found the following significant warnings:
  costfunctions.c:33:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  costfunctions.c:57:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/changepoint.np.Rcheck/00install.out’ for details.
gimli.14060hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Hartree2Joule: no visible binding for global variable
  ‘universalConstants’
Hertz2Joule: no visible binding for global variable
  ‘universalConstants’
Joule2Hartree: no visible binding for global variable
  ‘universalConstants’
Joule2Hertz: no visible binding for global variable
  ‘universalConstants’
Joule2Kelvin: no visible binding for global variable
  ‘universalConstants’
Joule2centimeterMinusOne: no visible binding for global variable
  ‘universalConstants’
Joule2electronVolt: no visible binding for global variable
  ‘universalConstants’
Joule2kiloCaloriePerMole: no visible binding for global variable
  ‘universalConstants’
Joule2kiloJoulePerMole: no visible binding for global variable
  ‘universalConstants’
KMC: no visible global function definition for ‘runif’
Kelvin2Joule: no visible binding for global variable
  ‘universalConstants’
LandauZener: no visible binding for global variable
  ‘universalConstants’
LandauZenerProbability: no visible binding for global variable
  ‘universalConstants’
Marcus: no visible binding for global variable ‘universalConstants’
MarcusLevichJortner: no visible binding for global variable
  ‘universalConstants’
centimeterMinusOne2Joule: no visible binding for global variable
  ‘universalConstants’
electronVolt2Joule: no visible binding for global variable
  ‘universalConstants’
kiloCaloriePerMole2Joule: no visible binding for global variable
  ‘universalConstants’
kiloJoulePerMole2Joule: no visible binding for global variable
  ‘universalConstants’
Undefined global functions or variables:
  runif universalConstants
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
'library' or 'require' call to ‘RCurl’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RCurl’ ‘bitops’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
createDataset: no visible global function definition for ‘read.csv’
createInventory: no visible global function definition for ‘read.csv’
downloadMaster: no visible global function definition for
  ‘getURLContent’
downloadMaster: no visible global function definition for ‘read.csv’
downloadMaster: no visible global function definition for ‘write.csv’
getMissingScrape: no visible global function definition for ‘read.csv’
readLocalMaster: no visible global function definition for ‘read.csv’
readMonthlyCsv: no visible global function definition for ‘read.csv’
scrapeToCsv: no visible global function definition for ‘download.file’
writeData: no visible global function definition for ‘write.csv’
writeGhcn: no visible global function definition for ‘write.table’
writeInventory: no visible global function definition for ‘write.table’
writeMonthlyStations: no visible global function definition for
  ‘read.csv’
writeMonthlyStations: no visible global function definition for
  ‘write.csv’
Undefined global functions or variables:
  download.file getURLContent read.csv write.csv write.table
Consider adding
  importFrom("utils", "download.file", "read.csv", "write.csv",
             "write.table")
to your NAMESPACE file.
Rd file 'chebR.Rd':
  \examples lines wider than 100 characters:
     return(list(coefs=rlist$xx[1:n],resids=rlist$bb[1:m],rank=rlist$rank,iter=rlist$iter,ocode=rlist$ocode))

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: ‘ChemoSpec2D’
File
  LICENSE
is not mentioned in the DESCRIPTION file.
choicemodelr : drawDelta: no visible global function definition for
  ‘rnorm’
choicemodelr : mnlRwMetropOnce: no visible global function definition
  for ‘rnorm’
choicemodelr : mnlRwMetropOnce: no visible global function definition
  for ‘runif’
choicemodelr : rmultireg: no visible global function definition for
  ‘rnorm’
choicemodelr : rwishart: no visible global function definition for
  ‘rchisq’
choicemodelr : rwishart: no visible global function definition for
  ‘rnorm’
choicemodelr : fsh: no visible global function definition for
  ‘flush.console’
choicemodelr: no visible global function definition for ‘matplot’
choicemodelr: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  flush.console matplot rchisq rnorm runif write.table
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "rchisq", "rnorm", "runif")
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
Rd file 'choicemodelr.Rd':
  \examples lines wider than 100 characters:
     estbetas = cbind(estbetas[,1:4],0-apply(estbetas[,1:4],1,sum),estbetas[,5:6],0-apply(estbetas[,5:6],1,sum))
     estbetas = cbind(estbetas[,1:4],0-apply(estbetas[,1:4],1,sum),estbetas[,5:6],0-apply(estbetas[,5:6],1,sum))

These lines will be truncated in the PDF manual.
Qh.times.dhyper: no visible global function definition for ‘var’
Qh.times.dhyper: no visible global function definition for ‘pnorm’
Qh.times.dhyper: no visible global function definition for ‘dhyper’
TDiM: no visible global function definition for ‘sd’
choplump.default: no visible global function definition for
  ‘flush.console’
choplump.formula: no visible global function definition for ‘terms’
cm.compact: no visible global function definition for ‘dhyper’
Undefined global functions or variables:
  dhyper flush.console pnorm sd terms var
Consider adding
  importFrom("stats", "dhyper", "pnorm", "sd", "terms", "var")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
parse_counts: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
combineToSingleMatrix: no visible global function definition for
  ‘read.table’
combineToSingleMatrix: no visible global function definition for
  ‘write.table’
compareCIM: no visible global function definition for ‘sd’
correctData: no visible global function definition for ‘wd’
correctData: no visible global function definition for ‘threshold’
correctData: no visible binding for global variable ‘madmad’
correctData: no visible global function definition for ‘wr’
Undefined global functions or variables:
  madmad read.table sd threshold wd wr write.table
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
cin: no visible global function definition for ‘pnorm’
gammaHRF: no visible global function definition for ‘dgamma’
intertest: no visible global function definition for ‘pnorm’
truncSum: no visible global function definition for ‘spline’
Undefined global functions or variables:
  dgamma pnorm spline
Consider adding
  importFrom("stats", "dgamma", "pnorm", "spline")
to your NAMESPACE file.
cit.assignBcmst: no visible binding for global variable ‘citbcmst’
cit.assignBcmst : <anonymous>: no visible global function definition
  for ‘median’
cit.assignBcmst: no visible global function definition for ‘prcomp’
cit.assignBcmst: no visible global function definition for ‘par’
cit.assignBcmst: no visible global function definition for ‘lines’
cit.assignBcmst: no visible global function definition for ‘legend’
cit.centroids : <anonymous>: no visible global function definition for
  ‘median’
cit.centroids : <anonymous>: no visible global function definition for
  ‘var’
cit.dist: no visible global function definition for ‘dist’
cit.dist: no visible global function definition for ‘as.dist’
cit.dist: no visible global function definition for ‘cor’
cit.distToCentroids: no visible global function definition for
  ‘quantile’
cit.distToCentroids : <anonymous>: no visible global function
  definition for ‘median’
cit.distToCentroids : <anonymous>: no visible global function
  definition for ‘mad’
Undefined global functions or variables:
  as.dist citbcmst cor dist legend lines mad median par prcomp quantile
  var
Consider adding
  importFrom("graphics", "legend", "lines", "par")
  importFrom("stats", "as.dist", "cor", "dist", "mad", "median",
             "prcomp", "quantile", "var")
to your NAMESPACE file.
cit.assignCcmst: no visible binding for global variable ‘citccmst’
cit.assignCcmst : <anonymous>: no visible global function definition
  for ‘median’
cit.assignCcmst : median.na: no visible global function definition for
  ‘median’
cit.assignCcmst: no visible global function definition for ‘prcomp’
cit.assignCcmst: no visible global function definition for ‘par’
cit.assignCcmst: no visible global function definition for ‘lines’
cit.assignCcmst: no visible global function definition for ‘legend’
cit.centroids : <anonymous>: no visible global function definition for
  ‘median’
cit.centroids : <anonymous>: no visible global function definition for
  ‘var’
cit.dist: no visible global function definition for ‘dist’
cit.dist: no visible global function definition for ‘as.dist’
cit.dist: no visible global function definition for ‘cor’
cit.distToCentroids: no visible global function definition for
  ‘quantile’
cit.distToCentroids : <anonymous>: no visible global function
  definition for ‘median’
cit.distToCentroids : <anonymous>: no visible global function
  definition for ‘mad’
Undefined global functions or variables:
  as.dist citccmst cor dist legend lines mad median par prcomp quantile
  var
Consider adding
  importFrom("graphics", "legend", "lines", "par")
  importFrom("stats", "as.dist", "cor", "dist", "mad", "median",
             "prcomp", "quantile", "var")
to your NAMESPACE file.
CityPlot: no visible global function definition for ‘read.table’
CityPlot: no visible global function definition for ‘tail’
CityPlot: no visible global function definition for ‘pdf’
CityPlot: no visible global function definition for ‘split.screen’
CityPlot: no visible global function definition for ‘screen’
CityPlot: no visible global function definition for ‘par’
CityPlot: no visible global function definition for ‘plot’
CityPlot: no visible global function definition for ‘rect’
CityPlot: no visible global function definition for ‘text’
CityPlot: no visible global function definition for ‘lines’
CityPlot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off lines par pdf plot read.table rect screen split.screen tail
  text
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot", "rect", "screen",
             "split.screen", "text")
  importFrom("utils", "read.table", "tail")
to your NAMESPACE file.
'library' or 'require' call to ‘rggobi’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
generate_data : <anonymous>: no visible global function definition for
  ‘runif’
knnf: no visible global function definition for ‘terms’
rescaler.default: no visible global function definition for ‘sd’
rescaler.default: no visible global function definition for ‘median’
rescaler.default: no visible global function definition for ‘mad’
simvar.numeric: no visible global function definition for ‘runif’
Undefined global functions or variables:
  mad median runif sd terms
Consider adding
  importFrom("stats", "mad", "median", "runif", "sd", "terms")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  plot.classification plot.scores
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
classify.bug: no visible global function definition for
  ‘txtProgressBar’
classify.bug: no visible global function definition for
  ‘setTxtProgressBar’
plot.scores: no visible binding for global variable ‘quantile’
plot.scores: no visible global function definition for ‘runif’
plot.scores: no visible binding for global variable ‘median’
scores.gpcm.bug: no visible global function definition for
  ‘txtProgressBar’
scores.gpcm.bug: no visible global function definition for
  ‘setTxtProgressBar’
across.reps,classification: no visible global function definition for
  ‘sd’
Undefined global functions or variables:
  median quantile runif sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "median", "quantile", "runif", "sd")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
.boxRadial: no visible global function definition for ‘predict’
.radialSVM: no visible global function definition for ‘predict’
cfPredict: no visible global function definition for ‘predict’
getPerm5Num: no visible global function definition for ‘median’
getPerm5Num: no visible global function definition for ‘quantile’
ggClassPred: no visible global function definition for ‘ftable’
ggEnsHist: no visible global function definition for ‘sd’
ggPermHist: no visible global function definition for ‘sd’
Undefined global functions or variables:
  ftable median predict quantile sd
Consider adding
  importFrom("stats", "ftable", "median", "predict", "quantile", "sd")
to your NAMESPACE file.
clime: no visible global function definition for ‘cov’
cv.clime: no visible global function definition for ‘cov’
cv.clime: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  cov sd
Consider adding
  importFrom("stats", "cov", "sd")
to your NAMESPACE file.
gxe.cc: no visible global function definition for ‘qnorm’
gxe.coh: no visible global function definition for ‘qnorm’
utility.cc: no visible global function definition for ‘qnorm’
utility.coh: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
Found the following significant warnings:
  ./networkCliqueMSR.h:405:22: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ./networkCliqueMSR.h:414:17: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ./networkCliqueMSR.h:448:22: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ./networkCliqueMSR.h:466:17: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ./networkCliqueMSR.h:4:9: warning: 'NETWORKClIQUEMSR_H' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/cliqueMS.Rcheck/00install.out’ for details.
socp: no visible global function definition for ‘as’
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Rd file 'socp.Rd':
  \usage lines wider than 90 characters:
     socp(A, b, c, kvec, type = rep('q',length(kvec)), use_sparse=TRUE, gamma_fac=.95, delta0 = .75, sigma0 = .25, mu0 = 0.01, zero_tol = 1e ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Error in re-building vignettes:
  ...
Loading required package: dendextend

---------------------
Welcome to dendextend version 1.9.0
Type citation('dendextend') for how to cite the package.

Type browseVignettes(package = 'dendextend') for the package vignette.
The github page is: https://github.com/talgalili/dendextend/

Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
Or contact: <tal.galili@gmail.com>

	To suppress this message use:  suppressPackageStartupMessages(library(dendextend))
---------------------


Attaching package: ‘dendextend’

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

    cutree

Loading required package: devtools
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running ‘texi2dvi’ on ‘CluMix.tex’ failed.
LaTeX errors:
! Package inputenc Error: Unicode character ─ (U+2500)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode character ─ (U+2500)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode character ─ (U+2500)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode character ─ (U+2500)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode character ─ (U+2500)
(inputenc)                not se
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
'library' or 'require' call to ‘ggplot2’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
hopkins: no visible global function definition for ‘runif’
hopkins: no visible global function definition for ‘dist’
Undefined global functions or variables:
  dist runif
Consider adding
  importFrom("stats", "dist", "runif")
to your NAMESPACE file.
License components which are templates and need '+ file LICENSE':
  MIT
clustomit: no visible binding for global variable ‘weighted.mean’
sim_unif : multivariate_unif: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  runif weighted.mean
Consider adding
  importFrom("stats", "runif", "weighted.mean")
to your NAMESPACE file.
braycurtis: no visible global function definition for ‘as.dist’
czekanowski: no visible global function definition for ‘as.dist’
findComplementaryIndices: no visible global function definition for
  ‘na.omit’
genSimilarityProfile: no visible global function definition for ‘dist’
simprof: no visible global function definition for ‘dist’
simprof: no visible global function definition for ‘hclust’
simprof.plot : <local> : colorizer: no visible global function
  definition for ‘is.leaf’
simprof.plot: no visible global function definition for ‘rainbow’
simprof.plot: no visible global function definition for ‘dendrapply’
simprof.plot: no visible global function definition for ‘as.dendrogram’
Undefined global functions or variables:
  as.dendrogram as.dist dendrapply dist hclust is.leaf na.omit rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("stats", "as.dendrogram", "as.dist", "dendrapply", "dist",
             "hclust", "is.leaf", "na.omit")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘Biobase’ ‘GO.db’ ‘annotate’ ‘kohonen’ ‘mclust’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
cma_es: no visible global function definition for ‘rnorm’
f_rand: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
alpha.cronbach: no visible global function definition for ‘cov’
alpha.curve: no visible global function definition for ‘plot’
alpha.curve: no visible global function definition for ‘text’
Undefined global functions or variables:
  cov plot text
Consider adding
  importFrom("graphics", "plot", "text")
  importFrom("stats", "cov")
to your NAMESPACE file.
CMF: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
ComputeLambdaAndNuHat.shiftCMPest: no visible global function
  definition for ‘nlminb’
ControlCharts: no visible global function definition for
  ‘com.log.density’
ControlCharts: no visible global function definition for ‘plot’
ControlCharts: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline com.log.density nlminb plot
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("stats", "nlminb")
to your NAMESPACE file.
crr: no visible binding for global variable ‘na.omit’
crr: no visible global function definition for ‘approx’
cuminc: no visible binding for global variable ‘na.omit’
cuminc: no visible global function definition for ‘pchisq’
plot.cuminc: no visible global function definition for ‘par’
plot.cuminc: no visible global function definition for ‘plot’
plot.cuminc: no visible binding for global variable ‘legend’
plot.cuminc: no visible global function definition for ‘lines’
plot.predict.crr: no visible global function definition for ‘plot’
plot.predict.crr: no visible global function definition for ‘lines’
print.crr: no visible global function definition for ‘pnorm’
summary.crr: no visible global function definition for ‘pnorm’
summary.crr: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  approx legend lines na.omit par pchisq plot pnorm qnorm
Consider adding
  importFrom("graphics", "legend", "lines", "par", "plot")
  importFrom("stats", "approx", "na.omit", "pchisq", "pnorm", "qnorm")
to your NAMESPACE file.
copynumberBootstrap: no visible global function definition for
  ‘txtProgressBar’
copynumberBootstrap: no visible global function definition for
  ‘quantile’
copynumberBootstrap: no visible global function definition for
  ‘setTxtProgressBar’
gethits: no visible global function definition for ‘read.table’
normalizeGC: no visible global function definition for ‘median’
plotCNOGpro: no visible global function definition for ‘par’
plotCNOGpro: no visible global function definition for ‘plot’
plotCNOGpro: no visible global function definition for ‘rainbow’
plotCNOGpro: no visible global function definition for ‘density’
plotCNOGpro: no visible global function definition for ‘polygon’
plotCNOGpro: no visible global function definition for ‘lines’
plotCNOGpro: no visible global function definition for ‘legend’
plotCNOGpro: no visible global function definition for ‘boxplot’
sampleChromosome: no visible global function definition for ‘median’
sampleChromosome: no visible binding for global variable ‘var’
setupEmissionMatrix: no visible global function definition for ‘dgeom’
store: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  boxplot density dgeom legend lines median par plot polygon quantile
  rainbow read.table setTxtProgressBar txtProgressBar var write.table
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "boxplot", "legend", "lines", "par", "plot",
             "polygon")
  importFrom("stats", "density", "dgeom", "median", "quantile", "var")
  importFrom("utils", "read.table", "setTxtProgressBar",
             "txtProgressBar", "write.table")
to your NAMESPACE file.
CNclusterNcenter: no visible global function definition for ‘median’
CNclusterNcenter: no visible binding for global variable ‘var’
breakIntoGaps: no visible global function definition for ‘runif’
centerprob: no visible global function definition for ‘pnorm’
getz: no visible global function definition for ‘predict’
smad: no visible global function definition for ‘mad’
smedian: no visible global function definition for ‘median’
smedian.sample: no visible global function definition for ‘median’
smedmad: no visible global function definition for ‘median’
smedmad: no visible global function definition for ‘mad’
Undefined global functions or variables:
  mad median pnorm predict runif var
Consider adding
  importFrom("stats", "mad", "median", "pnorm", "predict", "runif",
             "var")
to your NAMESPACE file.
Error in .requirePackage(package) : 
    unable to find required package 'CGHbase'
  Calls: <Anonymous> ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
  Execution halted
coalescentMCMC: no visible global function definition for
  ‘packageVersion’
coalescentMCMC : getparams: no visible global function definition for
  ‘nlminb’
sim.coalescent: no visible global function definition for ‘plot’
sim.coalescent: no visible global function definition for ‘segments’
sim.coalescent: no visible global function definition for ‘points’
Undefined global functions or variables:
  nlminb packageVersion plot points segments
Consider adding
  importFrom("graphics", "plot", "points", "segments")
  importFrom("stats", "nlminb")
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘lars’ ‘randomForest’ ‘ridge’ ‘snowfall’ ‘tree’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package which this enhances but not available for checking: ‘rkward’
Package in Depends field not imported from: ‘coda’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'fast.flexsim.Rd':
  \usage lines wider than 90 characters:
     fast.flexsim(scale = 2, island,dispersalscale = 51, allee = 1, T = 1000, initp,parcombination, spnum = 2, sourcetype = "constant", type ... [TRUNCATED]

Rd file 'flexsim.Rd':
  \usage lines wider than 90 characters:
     flexsim(scale = 2, dispersalscale = 51, allee = 1, T = 1000, prange, initp,spnum = 2, island=10, sourcetype = "constant", type, path =  ... [TRUNCATED]

Rd file 'make.heatmap.Rd':
  \usage lines wider than 90 characters:
     make.heatmap(mat, type = "gray", xname = "x", yname = "y", xlab = NULL, ylab = NULL, title = NULL)

Rd file 'sim.coarse.Rd':
  \usage lines wider than 90 characters:
     sim.coarse(island=10,scale = 2, dispersalscale = 51, allee = 1, T = 1000, prange, type, initp, path = NULL)

These lines will be truncated in the PDF manual.
BMDE: no visible global function definition for ‘quantile’
BMDU: no visible global function definition for ‘runif’
BMDU: no visible global function definition for ‘quantile’
FS: no visible global function definition for ‘qnorm’
GM: no visible global function definition for ‘qchisq’
QH: no visible global function definition for ‘qchisq’
SG : sgp: no visible global function definition for ‘ppois’
SG : sgp: no visible global function definition for ‘dpois’
WALD: no visible global function definition for ‘qchisq’
WALDCC: no visible global function definition for ‘qchisq’
WS: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  dpois ppois qchisq qnorm quantile runif
Consider adding
  importFrom("stats", "dpois", "ppois", "qchisq", "qnorm", "quantile",
             "runif")
to your NAMESPACE file.
cICA: no visible global function definition for ‘mvfft’
cICA: no visible global function definition for ‘ar.yw’
cICA: no visible global function definition for ‘rnorm’
scICA: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  ar.yw mvfft rnorm
Consider adding
  importFrom("stats", "ar.yw", "mvfft", "rnorm")
to your NAMESPACE file.
Package in Depends field not imported from: ‘grid’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plotVenn2d : twoWayOverlap: no visible global function definition for
  ‘grid.polygon’
plotVenn2d : twoWayOverlap: no visible global function definition for
  ‘gpar’
plotVenn2d: no visible global function definition for ‘grid.text’
plotVenn2d: no visible global function definition for ‘gpar’
plotVenn2d: no visible global function definition for ‘grid.polygon’
plotVenn3d : twoWayOverlap: no visible global function definition for
  ‘grid.polygon’
plotVenn3d : twoWayOverlap: no visible global function definition for
  ‘gpar’
plotVenn3d: no visible global function definition for ‘grid.text’
plotVenn3d: no visible global function definition for ‘gpar’
plotVenn3d: no visible global function definition for ‘grid.polygon’
plotVenn4d : getCommonEllipse: no visible global function definition
  for ‘aggregate’
plotVenn4d : region.polygon: no visible global function definition for
  ‘head’
plotVenn4d : region.polygon: no visible global function definition for
  ‘grid.polygon’
plotVenn4d : region.polygon: no visible global function definition for
  ‘gpar’
plotVenn4d: no visible global function definition for ‘grid.text’
plotVenn4d: no visible global function definition for ‘gpar’
plotVenn4d: no visible global function definition for ‘pushViewport’
plotVenn4d: no visible global function definition for ‘viewport’
plotVenn4d: no visible global function definition for ‘grid.polygon’
plotVenn4d: no visible global function definition for ‘upViewport’
resizeCircles: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  aggregate gpar grid.polygon grid.text head pushViewport uniroot
  upViewport viewport
Consider adding
  importFrom("stats", "aggregate", "uniroot")
  importFrom("utils", "head")
to your NAMESPACE file.
generateMonochromaticColors: no visible global function definition for
  ‘col2rgb’
generateMonochromaticColors: no visible global function definition for
  ‘rgb’
generateMonochromaticColors: no visible global function definition for
  ‘tail’
hsv2rgb: no visible global function definition for ‘rgb’
rotational_dispersion: no visible global function definition for
  ‘col2rgb’
rotational_dispersion: no visible global function definition for
  ‘rgb2hsv’
tetradicColors: no visible global function definition for ‘head’
triadicColors: no visible global function definition for ‘head’
Undefined global functions or variables:
  col2rgb head rgb rgb2hsv tail
Consider adding
  importFrom("grDevices", "col2rgb", "rgb", "rgb2hsv")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
primary.colors: no visible global function definition for ‘rgb’
rgb.tables: no visible global function definition for ‘rgb’
ygobb: no visible global function definition for ‘approx’
ygobb: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  approx rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "approx")
to your NAMESPACE file.
competitive.test: no visible global function definition for ‘runif’
selfcontained.test : fun2: no visible global function definition for
  ‘qchisq’
selfcontained.test: no visible global function definition for ‘cov’
selfcontained.test: no visible global function definition for ‘qchisq’
selfcontained.test: no visible global function definition for ‘cor’
selfcontained.test: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  cor cov pchisq qchisq runif
Consider adding
  importFrom("stats", "cor", "cov", "pchisq", "qchisq", "runif")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘lattice’ ‘rgl’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  AIC.fmo Adj.Rsq.fmo Adj.Rsq.lm BIC.fmo Cp.fmo Cp.lm PRESS.fmo
  PRESS.lm fit.Models.glmFormula fit.Models.lmFormula fit.Models.tsm
  gen.Data.glmFormula gen.Data.lmFormula gen.Data.tsm
  gen.Params.lmFormula gen.Params.tsm holdout.Mean.Arima
  holdout.Mean.default holdout.Mean.fmo holdout.Mean.lm
  holdout.Med.Arima holdout.Med.default holdout.Med.fmo holdout.Med.lm
  holdout.SS.Arima holdout.SS.default holdout.SS.fmo holdout.SS.lm
  num.Terms.formula num.Terms.tsm plot.msc print.msc print.summary.msc
  print.tsm summary.msc
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'TMC.Rd':
  \usage lines wider than 90 characters:
     TMC(num.Iter = 50, data.Size = 100, make.Data = gen.Data, make.Params = gen.Params, model.List, weight.Vector = rep(1, times = length(m ... [TRUNCATED]
  \examples lines wider than 100 characters:
     result <- TMC(num.Iter = 3, model.List = make.Model.List.Reg(vars), msc.List = list(BIC, AIC, PRESS), var.Frame = vars)

Rd file 'make.Model.List.Reg.Rd':
  \usage lines wider than 90 characters:
     make.Model.List.Reg(fram, max.Size = min(8, dim(fram)[2]), no.Intercepts = FALSE, GLM = FALSE)

Rd file 'sarima.Sim.Rd':
  \usage lines wider than 90 characters:
     sarima.Sim(n = 20, period = 12, model, seasonal, rand.Gen.Fun = rnorm, rand.Gen.Seas = rnorm)

These lines will be truncated in the PDF manual.
p.Johansen: no visible global function definition for ‘pgamma’
plotComT: no visible global function definition for ‘axis’
plotComT: no visible global function definition for ‘title’
plotComT: no visible global function definition for ‘lines’
plotComT: no visible global function definition for ‘box’
q.Johansen: no visible global function definition for ‘qgamma’
Undefined global functions or variables:
  axis box lines pgamma qgamma title
Consider adding
  importFrom("graphics", "axis", "box", "lines", "title")
  importFrom("stats", "pgamma", "qgamma")
to your NAMESPACE file.
CommT.anova: no visible global function definition for ‘aov’
CommT.legendpos: no visible global function definition for ‘quantile’
CommT.plotcolors: no visible global function definition for ‘hcl’
Undefined global functions or variables:
  aov hcl quantile
Consider adding
  importFrom("grDevices", "hcl")
  importFrom("stats", "aov", "quantile")
to your NAMESPACE file.
addxaxis: no visible global function definition for ‘par’
addxaxis: no visible global function definition for ‘axis’
addxaxis: no visible global function definition for ‘mtext’
eplot: no visible global function definition for ‘plot’
eplot: no visible global function definition for ‘par’
eplot: no visible global function definition for ‘axis’
eplot: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  axis mtext par plot
Consider adding
  importFrom("graphics", "axis", "mtext", "par", "plot")
to your NAMESPACE file.
compareC: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
'library' or 'require' call to ‘XML’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘XML’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
compareODM: no visible global function definition for ‘xmlRoot’
compareODM: no visible global function definition for ‘xmlTreeParse’
compareODM: no visible global function definition for ‘xmlChildren’
compareODM: no visible global function definition for ‘xmlAttrs’
compareODM: no visible global function definition for ‘xmlValue’
Undefined global functions or variables:
  xmlAttrs xmlChildren xmlRoot xmlTreeParse xmlValue
two.level.comparison.items: no visible global function definition for
  ‘complete.cases’
two.level.components: no visible global function definition for
  ‘complete.cases’
plot,ece: no visible global function definition for ‘par’
plot,ece: no visible global function definition for ‘points’
plot,ece: no visible global function definition for ‘mtext’
plot,ece: no visible global function definition for ‘legend’
plot,ece: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline complete.cases legend mtext par points
Consider adding
  importFrom("graphics", "abline", "legend", "mtext", "par", "points")
  importFrom("stats", "complete.cases")
to your NAMESPACE file.
CIFplot: no visible global function definition for ‘plot’
CIFplot: no visible global function definition for ‘gray’
CIFplot: no visible global function definition for ‘lines’
iprop: no visible global function definition for ‘qnorm’
irates: no visible global function definition for ‘qnorm’
irates.ratio: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  gray lines plot qnorm
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "qnorm")
to your NAMESPACE file.
Rd file 'CIFplot.Rd':
  \usage lines wider than 90 characters:
     CIFplot(x, event.code = NULL, covar.code = NULL, indiv.times = NULL, indiv.events = NULL, indiv.covar = NULL, 

Rd file 'irates.Rd':
  \usage lines wider than 90 characters:
     irates(data, time.code = NULL, no.event.code = NULL, no.event.lab = NULL, event.lab = NULL, covar.lab = NULL, 

Rd file 'plot.irates.Rd':
  \usage lines wider than 90 characters:
     plot(x, covar.code = NULL, full.sample = FALSE, n.row = 1, viewport.size = list(w = 3.5, h = 2.5), 
     box.size = list(w = NULL, h = NULL), dist = 0.5, irates.vbw = NULL, arrow.maxlwd = 10, display.digits = 2, cex = 0.9, show.values = TRU ... [TRUNCATED]

Rd file 'print.iprop.Rd':
  \usage lines wider than 90 characters:
     print(x, event.code = NULL, covar.code = NULL, full.sample = FALSE, display.digits = 4, ...)

Rd file 'print.irates.Rd':
  \usage lines wider than 90 characters:
     print(x, event.code = NULL, covar.code = NULL, full.sample = FALSE, display.digits = 4, ...)

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: ‘inSilicoDb’
Package in Depends field not imported from: ‘numDeriv’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dcomplnorm: no visible global function definition for ‘grad’
dcomplnorm : f1: no visible global function definition for ‘dlnorm’
dcomplnorm : F1: no visible global function definition for ‘plnorm’
dcomplnorm : f1L: no visible global function definition for ‘dlnorm’
dcomplnorm : F1L: no visible global function definition for ‘plnorm’
pcomplnorm: no visible global function definition for ‘grad’
pcomplnorm : f1: no visible global function definition for ‘dlnorm’
pcomplnorm : F1: no visible global function definition for ‘plnorm’
pcomplnorm : F1L: no visible global function definition for ‘plnorm’
qcomplnorm: no visible global function definition for ‘grad’
qcomplnorm : f1: no visible global function definition for ‘dlnorm’
qcomplnorm : F1q: no visible global function definition for ‘qlnorm’
qcomplnorm : F1: no visible global function definition for ‘plnorm’
rcomplnorm: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dlnorm grad plnorm qlnorm runif
Consider adding
  importFrom("stats", "dlnorm", "plnorm", "qlnorm", "runif")
to your NAMESPACE file.
'library' or 'require' call to ‘hypergeo’ which was already attached by Depends.
  Please remove these calls from your code.
momentCompound: no visible global function definition for ‘integrate’
pgfIhypergeometric: no visible global function definition for ‘uniroot’
pgfIhyperpoisson: no visible global function definition for ‘uniroot’
pgfIkattitypeh1: no visible global function definition for ‘uniroot’
pgfIkattitypeh2: no visible global function definition for ‘uniroot’
pgfIneymantypeb: no visible global function definition for ‘uniroot’
pgfIneymantypec: no visible global function definition for ‘uniroot’
pgfIpoissonlindley: no visible global function definition for ‘uniroot’
pgfIthomas: no visible global function definition for ‘uniroot’
pgfIwaring: no visible global function definition for ‘uniroot’
pgfIyule: no visible global function definition for ‘uniroot’
rCompound: no visible global function definition for ‘runif’
Undefined global functions or variables:
  integrate runif uniroot
Consider adding
  importFrom("stats", "integrate", "runif", "uniroot")
to your NAMESPACE file.
Found the following significant warnings:
  Utility.c:162:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:187:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:211:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:392:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:417:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:442:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/CompRandFld.Rcheck/00install.out’ for details.
kef: no visible global function definition for ‘dgamma’
kef: no visible global function definition for ‘dlnorm’
simp_int: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx dgamma dlnorm
Consider adding
  importFrom("stats", "approx", "dgamma", "dlnorm")
to your NAMESPACE file.
prepare_Rd: concor.Rd:4: Dropping empty section \keyword
prepare_Rd: concor.Rd:5: Dropping empty section \keyword
prepare_Rd: concorcano.Rd:4: Dropping empty section \keyword
prepare_Rd: concorcano.Rd:5: Dropping empty section \keyword
prepare_Rd: concoreg.Rd:4: Dropping empty section \keyword
prepare_Rd: concoreg.Rd:5: Dropping empty section \keyword
prepare_Rd: concorgm.Rd:4: Dropping empty section \keyword
prepare_Rd: concorgm.Rd:5: Dropping empty section \keyword
prepare_Rd: concorgmcano.Rd:4: Dropping empty section \keyword
prepare_Rd: concorgmcano.Rd:5: Dropping empty section \keyword
prepare_Rd: concorgmreg.Rd:4: Dropping empty section \keyword
prepare_Rd: concorgmreg.Rd:5: Dropping empty section \keyword
prepare_Rd: concors.Rd:4: Dropping empty section \keyword
prepare_Rd: concors.Rd:5: Dropping empty section \keyword
prepare_Rd: concorscano.Rd:4: Dropping empty section \keyword
prepare_Rd: concorscano.Rd:5: Dropping empty section \keyword
prepare_Rd: concorsreg.Rd:4: Dropping empty section \keyword
prepare_Rd: concorsreg.Rd:5: Dropping empty section \keyword
prepare_Rd: svdbip.Rd:4: Dropping empty section \keyword
prepare_Rd: svdbip.Rd:5: Dropping empty section \keyword
prepare_Rd: svdbip2.Rd:4: Dropping empty section \keyword
prepare_Rd: svdbip2.Rd:5: Dropping empty section \keyword
prepare_Rd: svdbips.Rd:4: Dropping empty section \keyword
prepare_Rd: svdbips.Rd:5: Dropping empty section \keyword
prepare_Rd: svdcp.Rd:4: Dropping empty section \keyword
prepare_Rd: svdcp.Rd:5: Dropping empty section \keyword
K1.norm: no visible global function definition for ‘dnorm’
K1.norm: no visible global function definition for ‘pnorm’
K1.t3: no visible global function definition for ‘pt’
K2.norm: no visible global function definition for ‘dnorm’
K2.norm: no visible global function definition for ‘pnorm’
K2.t3: no visible global function definition for ‘pt’
Undefined global functions or variables:
  dnorm pnorm pt
Consider adding
  importFrom("stats", "dnorm", "pnorm", "pt")
to your NAMESPACE file.
Package in Depends field not imported from: ‘evd’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'condmixt.fit.Rd':
  \usage lines wider than 90 characters:
     condhparetomixt.dirac.fit.tailpen(theta,h,m,x,y,lambda=0,w=0.2,beta=50,mu=0.2,sigma=0.2, ...)

Rd file 'condmixt.train.Rd':
  \usage lines wider than 90 characters:
     condhparetomixt.train.tailpen(h,m,x,y,lambda=0,w=0.2,beta=50,mu=0.2,sigma=0.2, nstart = 1, ...)
     condhparetomixt.dirac.train.tailpen(h,m,x,y,lambda=0,w=0.2,beta=50,mu=0.2,sigma=0.2, nstart = 1, ...)

These lines will be truncated in the PDF manual.
ml_solver: no visible global function definition for ‘approx’
select_kmax: no visible global function definition for ‘median’
Undefined global functions or variables:
  approx median
Consider adding
  importFrom("stats", "approx", "median")
to your NAMESPACE file.
Running examples in ‘congressbr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sen_bills
> ### Title: Downloads and tidies information on the legislation in the
> ###   Federal Senate
> ### Aliases: sen_bills
> 
> ### ** Examples
> 
> pls_5_2010 <- sen_bills(type = "PLS", number = 5, year = 2010)
Error: Column `bill_indexing` must be a 1d atomic vector or a list
Execution halted
conicPlot: no visible global function definition for ‘palette’
conicPlotAsymptotes: no visible global function definition for
  ‘palette’
conicPlotAsymptotes: no visible global function definition for ‘abline’
conicPlotAxes: no visible global function definition for ‘palette’
conicPlotAxes: no visible global function definition for ‘abline’
plotDegenerateConic: no visible global function definition for ‘plot’
plotDegenerateConic: no visible global function definition for ‘points’
plotDegenerateConic: no visible global function definition for ‘abline’
plotEllipsis: no visible global function definition for ‘lines’
plotEllipsis: no visible global function definition for ‘plot’
plotEllipsis: no visible global function definition for ‘points’
plotHyperbola: no visible global function definition for ‘lines’
plotHyperbola: no visible global function definition for ‘plot’
plotHyperbola: no visible global function definition for ‘points’
plotParabola: no visible global function definition for ‘lines’
plotParabola: no visible global function definition for ‘plot’
Undefined global functions or variables:
  abline lines palette plot points
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "abline", "lines", "plot", "points")
to your NAMESPACE file.
'library' or 'require' call to ‘parallel’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘Rmpi’ ‘snow’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ConjointChecks: no visible global function definition for ‘makeCluster’
ConjointChecks: no visible global function definition for
  ‘clusterSetRNGStream’
ConjointChecks: no visible global function definition for
  ‘clusterApply’
ConjointChecks: no visible global function definition for ‘stopCluster’
omni.check: no visible global function definition for ‘runif’
omni.check: no visible global function definition for ‘quantile’
plot.checks: no visible global function definition for ‘mtext’
plot.checks: no visible global function definition for ‘text’
Undefined global functions or variables:
  clusterApply clusterSetRNGStream makeCluster mtext quantile runif
  stopCluster text
Consider adding
  importFrom("graphics", "mtext", "text")
  importFrom("stats", "quantile", "runif")
to your NAMESPACE file.
maCooperative: no visible global function definition for ‘points’
maCooperative: no visible global function definition for ‘legend’
maPessimistic: no visible global function definition for ‘combn’
maRules: no visible global function definition for ‘capture.output’
mstCooperative: no visible global function definition for ‘points’
mstCooperative: no visible global function definition for ‘legend’
mstOptimistic: no visible global function definition for ‘combn’
mstPessimistic: no visible global function definition for ‘combn’
mstRules: no visible global function definition for ‘capture.output’
plotCoreSet: no visible global function definition for ‘points’
plotCoreSet: no visible global function definition for ‘polygon’
plotImputationSet: no visible global function definition for ‘par’
plotImputationSet: no visible global function definition for ‘plot’
plotImputationSet: no visible global function definition for ‘box’
plotImputationSet: no visible global function definition for ‘polygon’
plotImputationSet: no visible global function definition for ‘text’
shapleyValue: no visible global function definition for ‘combn’
Undefined global functions or variables:
  box capture.output combn legend par plot points polygon text
Consider adding
  importFrom("graphics", "box", "legend", "par", "plot", "points",
             "polygon", "text")
  importFrom("utils", "capture.output", "combn")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  predict.copreg
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
density_conditional: no visible global function definition for ‘ppois’
density_joint: no visible global function definition for ‘ppois’
dgam: no visible global function definition for ‘dgamma’
dpolicy_loss: no visible global function definition for ‘ppois’
dztp: no visible global function definition for ‘dpois’
epolicy_loss: no visible global function definition for ‘integrate’
mle_joint: no visible global function definition for ‘optim’
mle_marginal: no visible global function definition for ‘glm’
mle_marginal: no visible global function definition for ‘Gamma’
mle_marginal: no visible global function definition for ‘vcov’
mle_marginal: no visible global function definition for ‘poisson’
mle_marginal: no visible global function definition for ‘coef’
mle_marginal: no visible global function definition for ‘ppois’
mle_marginal: no visible global function definition for ‘optim’
pgam: no visible global function definition for ‘pgamma’
ppolicy_loss: no visible global function definition for ‘integrate’
pztp: no visible global function definition for ‘ppois’
qpolicy_loss: no visible global function definition for ‘uniroot’
rgam: no visible global function definition for ‘rgamma’
vuongtest: no visible global function definition for ‘sd’
ztp.glm: no visible global function definition for ‘coef’
ztp.glm: no visible global function definition for ‘glm’
ztp.glm: no visible binding for global variable ‘poisson’
ztp.glm: no visible global function definition for ‘optim’
Undefined global functions or variables:
  Gamma coef dgamma dpois glm integrate optim pgamma poisson ppois
  rgamma sd uniroot vcov
Consider adding
  importFrom("stats", "Gamma", "coef", "dgamma", "dpois", "glm",
             "integrate", "optim", "pgamma", "poisson", "ppois",
             "rgamma", "sd", "uniroot", "vcov")
to your NAMESPACE file.
advanceRNG: no visible global function definition for ‘runif’
randomEventMoves: no visible global function definition for ‘runif’
randomRescaledEventMoves: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
coreTDT_geneset: no visible global function definition for
  ‘write.table’
pvalue_calculator: no visible global function definition for ‘dbinom’
Undefined global functions or variables:
  dbinom write.table
Consider adding
  importFrom("stats", "dbinom")
  importFrom("utils", "write.table")
to your NAMESPACE file.
compute.llh: no visible global function definition for ‘dnorm’
compute.u.hat.simple: no visible global function definition for ‘dnorm’
fit.CLM.1u.simple.start: no visible global function definition for
  ‘kmeans’
fit.CLMM.simple.start: no visible global function definition for
  ‘kmeans’
fit.CLMM.simple.start.NA: no visible global function definition for
  ‘kmeans’
Undefined global functions or variables:
  dnorm kmeans
Consider adding
  importFrom("stats", "dnorm", "kmeans")
to your NAMESPACE file.
CBData: no visible global function definition for ‘aggregate’
CMData: no visible global function definition for ‘aggregate’
GEE.trend.test: no visible binding for global variable ‘binomial’
GEE.trend.test: no visible global function definition for ‘pnorm’
RS.trend.test: no visible global function definition for ‘pnorm’
SO.mc.est: no visible global function definition for ‘xtabs’
SO.trend.test : boot.LRT.fun: no visible global function definition for
  ‘aggregate’
jointprobs: no visible global function definition for ‘xtabs’
mc.test.chisq.CBData: no visible global function definition for
  ‘pchisq’
mc.test.chisq.CMData : get.T: no visible global function definition for
  ‘weighted.mean’
mc.test.chisq.CMData: no visible global function definition for
  ‘pchisq’
mg.DirMult : <anonymous>: no visible global function definition for
  ‘rmultinom’
mg.LogitNorm : <anonymous>: no visible global function definition for
  ‘rmultinom’
mg.MixMult : <anonymous>: no visible global function definition for
  ‘rmultinom’
mg.Resample: no visible global function definition for ‘rmultinom’
ran.CBData : ran.gen: no visible global function definition for
  ‘rmultinom’
read.CBData: no visible global function definition for ‘read.table’
read.CBData: no visible global function definition for ‘aggregate’
read.CMData: no visible global function definition for ‘read.table’
trend.test : boot.LRT.fun: no visible global function definition for
  ‘aggregate’
unwrap.CMData: no visible global function definition for ‘reshape’
Undefined global functions or variables:
  aggregate binomial pchisq pnorm read.table reshape rmultinom
  weighted.mean xtabs
Consider adding
  importFrom("stats", "aggregate", "binomial", "pchisq", "pnorm",
             "reshape", "rmultinom", "weighted.mean", "xtabs")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Package in Depends field not imported from: ‘calibrate’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
correlogram: no visible global function definition for ‘par’
correlogram: no visible global function definition for ‘plot’
correlogram: no visible global function definition for ‘points’
correlogram: no visible global function definition for ‘textxy’
correlogram: no visible global function definition for ‘arrows’
correlogram: no visible global function definition for ‘circle’
fit_angles: no visible global function definition for ‘runif’
fit_angles: no visible global function definition for ‘nlminb’
linangplot: no visible global function definition for ‘cor’
linangplot: no visible global function definition for ‘rad2degree’
linangplot: no visible global function definition for ‘ginv’
linangplot: no visible global function definition for ‘par’
linangplot: no visible global function definition for ‘plot’
linangplot: no visible global function definition for ‘calibrate’
linangplot: no visible global function definition for ‘var’
pfa: no visible global function definition for ‘cor’
Undefined global functions or variables:
  arrows calibrate circle cor ginv nlminb par plot points rad2degree
  runif textxy var
Consider adding
  importFrom("graphics", "arrows", "par", "plot", "points")
  importFrom("stats", "cor", "nlminb", "runif", "var")
to your NAMESPACE file.
corr.Qmatrix: no visible global function definition for ‘cor’
corr.Qmatrix: no visible global function definition for ‘cor.test’
summarise.Fst: no visible global function definition for ‘cor’
summarise.Fst: no visible global function definition for ‘sd’
summarise.lnPD: no visible global function definition for ‘sd’
Undefined global functions or variables:
  cor cor.test sd
Consider adding
  importFrom("stats", "cor", "cor.test", "sd")
to your NAMESPACE file.
Rd file 'corr.Qmatrix.Rd':
  \usage lines wider than 90 characters:
     corr.Qmatrix(filepath = "./", instruct = FALSE, rowncol = TRUE, avmax = TRUE, pvalue = FALSE, raw = TRUE, r = 0.99, p = 0.05)

Rd file 'rowncolMatrix-method.Rd':
  \examples lines wider than 100 characters:
     test <- rowncolMatrix(K = 3, filtermatrix = table(matrix(c("Y","Y","Y",NA,"Y","Y",NA,NA,"Y"),ncol = 3, byrow = TRUE)))

These lines will be truncated in the PDF manual.
dist: no visible global function definition for ‘quantile’
edgecount: no visible global function definition for ‘reshape’
edgecutoff: no visible global function definition for ‘boxplot’
edgecutoff: no visible global function definition for ‘sd’
edgecutoff: no visible global function definition for ‘median’
edgecutoff: no visible global function definition for ‘IQR’
Undefined global functions or variables:
  IQR boxplot median quantile reshape sd
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "IQR", "median", "quantile", "reshape", "sd")
to your NAMESPACE file.
GA_search : subset_score: no visible global function definition for
  ‘combn’
choose_lambda : subset_score: no visible global function definition for
  ‘combn’
cond.fyx: no visible global function definition for ‘var’
cond.fyx: no visible global function definition for ‘cor’
diff_gen_PPI: no visible global function definition for ‘cov’
diff_gen_PPI: no visible global function definition for ‘sd’
f.test: no visible binding for global variable ‘var’
get_quantiles : node_edge: no visible global function definition for
  ‘combn’
score_scaling: no visible global function definition for ‘hist’
score_scaling: no visible global function definition for ‘sd’
Undefined global functions or variables:
  combn cor cov hist sd var
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "cor", "cov", "sd", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
cosinor.lm: no visible binding for global variable ‘na.omit’
cosinor.lm: no visible global function definition for ‘terms’
cosinor.lm: no visible global function definition for ‘as.formula’
cosinor.lm: no visible global function definition for ‘lm’
cosinor_analyzer: no visible binding for global variable ‘vitamind’
cosinor_analyzer : <anonymous>: no visible global function definition
  for ‘as.formula’
ggplot.cosinor.lm: no visible global function definition for ‘predict’
predict.cosinor.lm: no visible global function definition for ‘fitted’
predict.cosinor.lm: no visible global function definition for ‘predict’
simulate_cosinor: no visible global function definition for ‘runif’
simulate_cosinor: no visible global function definition for ‘rbinom’
simulate_cosinor: no visible global function definition for ‘rnorm’
summary.cosinor.lm: no visible global function definition for ‘vcov’
summary.cosinor.lm: no visible global function definition for ‘qnorm’
summary.cosinor.lm: no visible global function definition for ‘pnorm’
test_cosinor: no visible global function definition for ‘pchisq’
test_cosinor: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as.formula fitted lm na.omit pchisq pnorm predict qnorm rbinom rnorm
  runif terms vcov vitamind
Consider adding
  importFrom("stats", "as.formula", "fitted", "lm", "na.omit", "pchisq",
             "pnorm", "predict", "qnorm", "rbinom", "rnorm", "runif",
             "terms", "vcov")
to your NAMESPACE file.
D.M: no visible global function definition for ‘integrate’
lookbackTime: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
Rd file 'mass.CO.Rd':
  \usage lines wider than 90 characters:
     mass.CO(intInt, z, alpha = 0.8, f.rest = 115.27, omega.m = 0.27, omega.lambda = 0.73, H.0 = 71)

These lines will be truncated in the PDF manual.
Packages in Depends field not imported from:
  ‘Rglpk’ ‘glmnet’ ‘parallel’ ‘quadprog’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls to packages already attached by Depends:
  ‘Matrix’ ‘mlogit’ ‘poLCA’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Matrix’ ‘mlogit’ ‘poLCA’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
covLCA: no visible global function definition for ‘model.response’
covLCA: no visible global function definition for ‘model.frame’
covLCA: no visible global function definition for ‘model.matrix’
covLCA: no visible global function definition for ‘rnorm’
covLCA: no visible global function definition for ‘flush.console’
covLCA: no visible global function definition for ‘ginv’
covLCA.initialAlphaGamma: no visible global function definition for
  ‘as.formula’
covLCA.initialAlphaGamma: no visible global function definition for
  ‘mlogit.data’
covLCA.initialAlphaGamma: no visible global function definition for
  ‘mlogit’
covLCA.initialBeta: no visible global function definition for
  ‘as.formula’
covLCA.initialBeta: no visible global function definition for ‘poLCA’
covLCA.initialBeta: no visible global function definition for
  ‘mlogit.data’
covLCA.initialBeta: no visible global function definition for ‘mlogit’
covLCA.paramVariance: no visible global function definition for ‘ginv’
covLCA.varianceFirst: no visible global function definition for ‘bdiag’
Undefined global functions or variables:
  as.formula bdiag flush.console ginv mlogit mlogit.data model.frame
  model.matrix model.response poLCA rnorm
Consider adding
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response", "rnorm")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
covreg.mcmc: no visible global function definition for ‘model.frame’
covreg.mcmc: no visible global function definition for ‘model.matrix’
covreg.mcmc: no visible global function definition for ‘model.response’
covreg.mcmc: no visible global function definition for ‘lm’
covreg.mcmc: no visible global function definition for ‘rnorm’
covreg.mcmc: no visible global function definition for ‘cov’
rmn: no visible global function definition for ‘rnorm’
rwish: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  cov lm model.frame model.matrix model.response rnorm
Consider adding
  importFrom("stats", "cov", "lm", "model.frame", "model.matrix",
             "model.response", "rnorm")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘DESCRIPTION.old’
Found the following apparent S3 methods exported but not registered:
  predict.lars.en predict.lars.glm
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
calcz02: no visible global function definition for ‘coxph’
calcz02: no visible global function definition for ‘residuals’
covTest: no visible global function definition for ‘Surv’
covTest: no visible global function definition for ‘predict’
covTest: no visible global function definition for ‘update’
covTest: no visible global function definition for ‘lsfit’
covTest: no visible global function definition for ‘pexp’
covTest: no visible global function definition for ‘pf’
lars.en: no visible binding for global variable ‘var’
predict.lars.en: no visible global function definition for ‘predict’
Undefined global functions or variables:
  Surv coxph lsfit pexp pf predict residuals update var
Consider adding
  importFrom("stats", "lsfit", "pexp", "pf", "predict", "residuals",
             "update", "var")
to your NAMESPACE file.
Rd file 'lars.glm.Rd':
  \usage lines wider than 90 characters:
     lars.glm(x, y, status = NULL, family = c("binomial", "cox"), standardize=TRUE,frac.arclength=.1)

These lines will be truncated in the PDF manual.
Non-standard file/directory found at top level:
  ‘changeLog’
'library' or 'require' calls in package code:
  ‘parallel’ ‘snowfall’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Matrix’ ‘prodlim’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CoxBoost: no visible global function definition for ‘Matrix’
CoxBoost: no visible binding for global variable ‘sd’
CoxBoost: no visible global function definition for ‘predict’
cv.CoxBoost : eval.fold: no visible global function definition for
  ‘predict’
cv.CoxBoost: no visible global function definition for ‘mclapply’
cv.CoxBoost: no visible binding for global variable ‘sd’
estimPVal: no visible global function definition for ‘mclapply’
iCoxBoost: no visible global function definition for ‘terms’
iCoxBoost: no visible global function definition for ‘model.response’
iCoxBoost: no visible global function definition for ‘model.frame’
iCoxBoost: no visible global function definition for ‘model.matrix’
iCoxBoost: no visible global function definition for ‘Matrix’
plot.CoxBoost: no visible global function definition for ‘plot’
plot.CoxBoost: no visible global function definition for ‘lines’
plot.CoxBoost: no visible global function definition for ‘text’
predict.iCoxBoost: no visible global function definition for
  ‘model.response’
predict.iCoxBoost: no visible global function definition for
  ‘model.frame’
predict.iCoxBoost: no visible global function definition for
  ‘model.matrix’
Undefined global functions or variables:
  Matrix lines mclapply model.frame model.matrix model.response plot
  predict sd terms text
Consider adding
  importFrom("graphics", "lines", "plot", "text")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "predict", "sd", "terms")
to your NAMESPACE file.
coxaalen: no visible global function definition for ‘terms’
coxaalen: no visible global function definition for ‘model.matrix’
coxaalen: no visible binding for global variable ‘frame’
coxaalen: no visible global function definition for ‘update.formula’
coxaalen: no visible global function definition for ‘capture.output’
coxdual: no visible global function definition for ‘terms’
coxdual: no visible global function definition for ‘model.matrix’
coxdual: no visible binding for global variable ‘frame’
coxdual: no visible global function definition for ‘update.formula’
coxdual: no visible global function definition for ‘as.formula’
coxdual: no visible global function definition for ‘capture.output’
frame.assign: no visible global function definition for ‘model.matrix’
linapprox: no visible global function definition for ‘approx’
print.coxinterval: no visible global function definition for ‘pchisq’
print.summary.coxinterval : f: no visible global function definition
  for ‘printCoefmat’
step2stepfun : f: no visible global function definition for ‘stepfun’
summary.coxinterval : f: no visible global function definition for
  ‘pchisq’
summary.coxinterval : f: no visible global function definition for
  ‘qnorm’
Undefined global functions or variables:
  approx as.formula capture.output frame model.matrix pchisq
  printCoefmat qnorm stepfun terms update.formula
Consider adding
  importFrom("graphics", "frame")
  importFrom("stats", "approx", "as.formula", "model.matrix", "pchisq",
             "printCoefmat", "qnorm", "stepfun", "terms",
             "update.formula")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
comp.graph: no visible global function definition for ‘qnorm’
comp.graph: no visible global function definition for ‘plot’
comp.graph: no visible global function definition for ‘polygon’
comp.graph: no visible global function definition for ‘lines’
cox.ridge: no visible global function definition for ‘terms’
cox.ridge: no visible global function definition for ‘model.extract’
cox.ridge: no visible global function definition for ‘model.matrix’
cox.ridge: no visible binding for global variable ‘hat’
Undefined global functions or variables:
  hat lines model.extract model.matrix plot polygon qnorm terms
Consider adding
  importFrom("graphics", "lines", "plot", "polygon")
  importFrom("stats", "hat", "model.extract", "model.matrix", "qnorm",
             "terms")
to your NAMESPACE file.
Package in Depends field not imported from: ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
coxr: no visible global function definition for ‘model.extract’
coxr: no visible global function definition for ‘model.matrix’
coxr.draw: no visible global function definition for ‘plot’
coxr.draw: no visible global function definition for ‘lines’
coxr.draw: no visible global function definition for ‘points’
coxr.fit: no visible global function definition for ‘quantile’
gen_data: no visible global function definition for ‘rnorm’
gen_data: no visible global function definition for ‘rexp’
plot.coxr: no visible global function definition for ‘quantile’
plot.coxr: no visible global function definition for ‘par’
plot.coxr: no visible global function definition for ‘mtext’
plot.coxr: no visible global function definition for ‘title’
plot.coxr: no visible global function definition for ‘split.screen’
plot.coxr: no visible global function definition for ‘screen’
plot.coxr: no visible global function definition for ‘close.screen’
print.coxr: no visible global function definition for ‘pnorm’
print.coxr: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  close.screen lines model.extract model.matrix mtext par pchisq plot
  pnorm points quantile rexp rnorm screen split.screen title
Consider adding
  importFrom("graphics", "close.screen", "lines", "mtext", "par", "plot",
             "points", "screen", "split.screen", "title")
  importFrom("stats", "model.extract", "model.matrix", "pchisq", "pnorm",
             "quantile", "rexp", "rnorm")
to your NAMESPACE file.
CumInt : fn: no visible global function definition for ‘integrate’
RND0: no visible global function definition for ‘runif’
coxseiInt: no visible global function definition for ‘approxfun’
coxseiInt : js: no visible global function definition for ‘tail’
coxseiest: no visible global function definition for ‘approxfun’
coxseiest : loglik : ll: no visible global function definition for
  ‘tail’
coxseiest: no visible global function definition for ‘optim’
coxseiest2: no visible global function definition for ‘approxfun’
coxseiest2: no visible global function definition for ‘optim’
coxseiest3: no visible global function definition for ‘approxfun’
coxseiest3: no visible global function definition for ‘optim’
coxseiexp: no visible global function definition for ‘approxfun’
coxseiexp: no visible global function definition for ‘optim’
coxseiexp : js: no visible global function definition for ‘tail’
coxseiexp: no visible global function definition for ‘pnorm’
coxseiexp: no visible global function definition for ‘stepfun’
coxseifit.ex: no visible global function definition for ‘approxfun’
coxseifit.ex: no visible global function definition for ‘optim’
coxseifit.ex : js: no visible global function definition for ‘tail’
coxseifit.ex: no visible global function definition for ‘pnorm’
coxseifit.ex: no visible global function definition for ‘stepfun’
coxseisim : int.at.lasttm: no visible global function definition for
  ‘tail’
plot.coxsei: no visible global function definition for ‘plot’
print.summary.coxsei: no visible global function definition for
  ‘printCoefmat’
summary.coxsei: no visible global function definition for ‘coef’
Undefined global functions or variables:
  approxfun coef integrate optim plot pnorm printCoefmat runif stepfun
  tail
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "approxfun", "coef", "integrate", "optim", "pnorm",
             "printCoefmat", "runif", "stepfun")
  importFrom("utils", "tail")
to your NAMESPACE file.
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
src/Makevars: incorrect macro SHLIB_OPENMP_CFLAGS included in PKG_CXXFLAGS
  src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but not in PKG_CFLAGS
  src/Makevars.win: incorrect macro SHLIB_OPENMP_CFLAGS included in PKG_CXXFLAGS
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but not in PKG_CFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
Package required but not available: ‘tpr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
distance.comoving: no visible global function definition for
  ‘integrate’
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  print.cramertest
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
.cramer.kritwertfft: no visible global function definition for ‘fft’
Undefined global functions or variables:
  fft
Consider adding
  importFrom("stats", "fft")
to your NAMESPACE file.
crantastic.submitInstalledPackages: no visible global function
  definition for ‘installed.packages’
postData: no visible global function definition for ‘make.socket’
postData: no visible global function definition for ‘write.socket’
postData: no visible global function definition for ‘read.socket’
postData: no visible global function definition for ‘close.socket’
Undefined global functions or variables:
  close.socket installed.packages make.socket read.socket write.socket
Consider adding
  importFrom("utils", "close.socket", "installed.packages",
             "make.socket", "read.socket", "write.socket")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  print.crblocks_output
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
catrandpvalue: no visible global function definition for ‘read.table’
catrandpvalue: no visible global function definition for ‘rmultinom’
catrandpvaluepermute: no visible global function definition for
  ‘read.table’
catrandstat: no visible global function definition for ‘stack’
catrandstat: no visible global function definition for ‘pchisq’
catrandstat: no visible binding for global variable ‘var’
Undefined global functions or variables:
  pchisq read.table rmultinom stack var
Consider adding
  importFrom("stats", "pchisq", "rmultinom", "var")
  importFrom("utils", "read.table", "stack")
to your NAMESPACE file.
cm.CVaR: no visible global function definition for ‘quantile’
cm.hist: no visible global function definition for ‘hist’
cm.quantile: no visible global function definition for ‘qnorm’
cm.rnorm: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  hist qnorm quantile rnorm
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "qnorm", "quantile", "rnorm")
to your NAMESPACE file.
makeX_eset: no visible global function definition for ‘model.matrix’
normFit: no visible binding for global variable ‘lm’
normFit: no visible binding for global variable ‘sd’
normFit: no visible global function definition for ‘lm’
normPred: no visible binding for global variable ‘predict’
normPred: no visible global function definition for ‘predict’
normPred: no visible binding for global variable ‘median’
plot.nFit: no visible global function definition for ‘par’
plot.nFit: no visible global function definition for ‘barplot’
plot.nFit: no visible global function definition for ‘legend’
show_nfit: no visible global function definition for ‘anova’
show_nfit: no visible global function definition for ‘residuals’
show_nfit: no visible global function definition for ‘fitted’
standardsFit: no visible binding for global variable ‘lm’
standardsFit: no visible global function definition for ‘resid’
standardsFit: no visible global function definition for
  ‘compareVersion’
standardsPred: no visible global function definition for ‘predict’
makeX,ExpressionSet-character: no visible global function definition
  for ‘model.matrix’
plot,nFit: no visible global function definition for ‘par’
plot,nFit: no visible global function definition for ‘barplot’
plot,nFit: no visible global function definition for ‘legend’
show,nFit: no visible global function definition for ‘anova’
show,nFit: no visible global function definition for ‘residuals’
show,nFit: no visible global function definition for ‘fitted’
Undefined global functions or variables:
  anova barplot compareVersion fitted legend lm median model.matrix par
  predict resid residuals sd
Consider adding
  importFrom("graphics", "barplot", "legend", "par")
  importFrom("stats", "anova", "fitted", "lm", "median", "model.matrix",
             "predict", "resid", "residuals", "sd")
  importFrom("utils", "compareVersion")
to your NAMESPACE file.
'library' or 'require' call to ‘RCurl’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RCurl’ ‘chron’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
collateDaily: no visible global function definition for ‘read.table’
collateDaily: no visible global function definition for ‘write.table’
collateHourly: no visible global function definition for ‘read.table’
collateHourly: no visible global function definition for ‘write.table’
downloadCRN: no visible global function definition for ‘download.file’
getUrlsCRN: no visible global function definition for ‘getURL’
writeDataset: no visible global function definition for ‘read.table’
writeDataset: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  download.file getURL read.table write.table
Consider adding
  importFrom("utils", "download.file", "read.table", "write.table")
to your NAMESPACE file.
Rd file 'downloadCRN.Rd':
  \usage lines wider than 90 characters:
     downloadCRN(url = CRN.DAILY.URL, directory = DAILY_DIR, years = seq(from = 2000, to = 2011, by = 1))

These lines will be truncated in the PDF manual.
get.plan: no visible global function definition for ‘menu’
Undefined global functions or variables:
  menu
Consider adding
  importFrom("utils", "menu")
to your NAMESPACE file.
crossmatchtest: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
BootC : BSs: no visible global function definition for ‘lm’
BootC : BSs: no visible global function definition for ‘vcov’
BootC: no visible global function definition for ‘boot’
BootC: no visible global function definition for ‘boot.ci’
DeltaC: no visible global function definition for ‘lm’
DeltaC: no visible global function definition for ‘vcov’
FiellerC: no visible global function definition for ‘lm’
FiellerC: no visible global function definition for ‘vcov’
nonLinearC: no visible global function definition for ‘nls’
Undefined global functions or variables:
  boot boot.ci lm nls vcov
Consider adding
  importFrom("stats", "lm", "nls", "vcov")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from ‘CR’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
curerate : cr: no visible global function definition for ‘rbinom’
curerate : cr: no visible global function definition for ‘rexp’
curerate : cr: no visible global function definition for ‘runif’
curerate: no visible global function definition for ‘new’
showcr: no visible global function definition for ‘show’
Undefined global functions or variables:
  new rbinom rexp runif show
Consider adding
  importFrom("methods", "new", "show")
  importFrom("stats", "rbinom", "rexp", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
crrp: no visible global function definition for ‘approx’
gcrrp: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx
Consider adding
  importFrom("stats", "approx")
to your NAMESPACE file.
crrc: no visible binding for global variable ‘na.omit’
crrs: no visible binding for global variable ‘na.omit’
mycrr: no visible binding for global variable ‘na.omit’
mycrr.test: no visible binding for global variable ‘na.omit’
print.crrs: no visible global function definition for ‘pnorm’
psh.test: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  na.omit pchisq pnorm
Consider adding
  importFrom("stats", "na.omit", "pchisq", "pnorm")
to your NAMESPACE file.
crrstep : crr.makecov1: no visible global function definition for
  ‘model.matrix’
crrstep : crr.dropterm: no visible global function definition for
  ‘terms’
crrstep : crr.dropterm: no visible global function definition for
  ‘as.formula’
crrstep : crr.addterm: no visible global function definition for
  ‘terms’
crrstep : crr.addterm: no visible global function definition for
  ‘as.formula’
crrstep: no visible global function definition for ‘as.formula’
crrstep: no visible global function definition for ‘terms’
crrstep: no visible global function definition for ‘model.frame’
crrstep: no visible binding for global variable ‘na.pass’
crrstep: no visible global function definition for ‘update’
crrstep: no visible global function definition for ‘drop.terms’
Undefined global functions or variables:
  as.formula drop.terms model.frame model.matrix na.pass terms update
Consider adding
  importFrom("stats", "as.formula", "drop.terms", "model.frame",
             "model.matrix", "na.pass", "terms", "update")
to your NAMESPACE file.
pielou: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘test.html’
Package in Depends field not imported from: ‘compiler’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
csSAM: no visible binding for global variable ‘quantile’
csSAM: no visible global function definition for ‘median’
csfit: no visible global function definition for ‘lsfit’
csfit: no visible global function definition for ‘ls.diag’
plotCsSAM: no visible global function definition for ‘pdf’
plotCsSAM: no visible global function definition for ‘par’
plotCsSAM: no visible global function definition for ‘plot’
plotCsSAM: no visible global function definition for ‘title’
plotCsSAM: no visible global function definition for ‘dev.off’
runSAM: no visible binding for global variable ‘median’
runSAM: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  dev.off ls.diag lsfit median par pdf plot quantile title
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par", "plot", "title")
  importFrom("stats", "ls.diag", "lsfit", "median", "quantile")
to your NAMESPACE file.
cstar: no visible global function definition for ‘vcov’
cstar : utility: no visible global function definition for ‘dt’
cstar : maximand: no visible global function definition for ‘integrate’
cstar: no visible global function definition for ‘uniroot’
cstari : utility: no visible global function definition for ‘dt’
cstari : maximand: no visible global function definition for
  ‘integrate’
cstari: no visible global function definition for ‘uniroot’
cstarme : utility: no visible global function definition for ‘density’
cstarme : maximand: no visible global function definition for
  ‘integrate’
cstarme : maximand: no visible global function definition for ‘sd’
cstarme: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  density dt integrate sd uniroot vcov
Consider adding
  importFrom("stats", "density", "dt", "integrate", "sd", "uniroot",
             "vcov")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  [.int64 [<-.int64 [[.int64
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
map.coltypes: no visible global function definition for ‘read.csv’
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Package suggested but not available for checking: ‘R2Cuba’
Running ‘testthat.R’ [21s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(cubature)
  > 
  > test_check("cubature")
  ── 1. Error: Test Wang-Landau sampling 2d example (@test_integration.R#426)  ───
  all(scale > 0) is not TRUE
  1: testthat::expect_equal(expected, result$integral, tolerance = tol, scale = result$integral, 
         info = "Relative error not reached") at testthat/test_integration.R:426
  2: compare(act$val, exp$val, ...)
  3: compare.numeric(act$val, exp$val, ...)
  4: all.equal(x, y, tolerance = tolerance, check.attributes = check.attributes, ...)
  5: all.equal.numeric(x, y, tolerance = tolerance, check.attributes = check.attributes, 
         ...)
  6: stopifnot(all(scale > 0))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 64 SKIPPED: 0 FAILED: 1
  1. Error: Test Wang-Landau sampling 2d example (@test_integration.R#426) 
  
  Error: testthat unit tests failed
  Execution halted
gimli.32517hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but not in PKG_CFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
Found the following apparent S3 methods exported but not registered:
  plot.bayesm.mat plot.hcoef.post
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Found the following hidden files and directories:
  .gitignore
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Malformed Title field: should not end in a period.
License components which are templates and need '+ file LICENSE':
  MIT
Non-standard files/directories found at top level:
  ‘BUGS.md’ ‘TODO.md’ ‘benchmarks’ ‘build_script.sh’ ‘doc’
  ‘iddply_dt.R’ ‘profiling’
'library' or 'require' call to ‘lars’ which was already attached by Depends.
  Please remove these calls from your code.
Found the following apparent S3 methods exported but not registered:
  plot.aCGHsegmented
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
jumpoints : seg.lm.fit0: no visible global function definition for
  ‘lm.fit’
jumpoints : seg.lm.fit0: no visible global function definition for
  ‘coef’
jumpoints: no visible global function definition for ‘quantile’
jumpoints: no visible global function definition for ‘coef’
plot.aCGHsegmented: no visible global function definition for ‘plot’
plot.aCGHsegmented: no visible global function definition for ‘grey’
plot.aCGHsegmented: no visible global function definition for ‘abline’
plot.aCGHsegmented: no visible global function definition for ‘points’
plot.aCGHsegmented: no visible global function definition for
  ‘segments’
plot.aCGHsegmented: no visible global function definition for ‘par’
Undefined global functions or variables:
  abline coef grey lm.fit par plot points quantile segments
Consider adding
  importFrom("grDevices", "grey")
  importFrom("graphics", "abline", "par", "plot", "points", "segments")
  importFrom("stats", "coef", "lm.fit", "quantile")
to your NAMESPACE file.
Package unavailable to check Rd xrefs: ‘tilingArray’
File ‘curl/libs/curl.so’:
  Found non-API call to R: ‘R_new_custom_connection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
cci.nostrat: no visible global function definition for ‘quantile’
cci.nostrat: no visible global function definition for ‘plot’
cci.nostrat: no visible global function definition for ‘axis’
cci.nostrat: no visible global function definition for ‘lines’
cci.nostrat: no visible global function definition for ‘legend’
cci.strat: no visible global function definition for ‘plot’
cci.strat: no visible global function definition for ‘axis’
cci.strat: no visible global function definition for ‘lines’
cci.strat: no visible global function definition for ‘legend’
clfs.nostrat: no visible global function definition for ‘quantile’
clfs.nostrat: no visible global function definition for ‘plot’
clfs.nostrat: no visible global function definition for ‘axis’
clfs.nostrat: no visible global function definition for ‘lines’
clfs.nostrat: no visible global function definition for ‘legend’
clfs.strat: no visible global function definition for ‘plot’
clfs.strat: no visible global function definition for ‘axis’
clfs.strat: no visible global function definition for ‘lines’
clfs.strat: no visible global function definition for ‘legend’
pvals.2cat: no visible global function definition for ‘pchisq’
pvals.cat: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  axis legend lines pchisq plot quantile
Consider adding
  importFrom("graphics", "axis", "legend", "lines", "plot")
  importFrom("stats", "pchisq", "quantile")
to your NAMESPACE file.
Cut: no visible global function definition for ‘cor’
MissSimulation: no visible global function definition for ‘rbinom’
cutoff: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor rbinom
Consider adding
  importFrom("stats", "cor", "rbinom")
to your NAMESPACE file.
delta.glm: no visible global function definition for ‘glm’
delta.glm: no visible global function definition for ‘residuals’
delta.glm: no visible global function definition for ‘fitted’
delta.glm: no visible global function definition for ‘predict.glm’
two.stage.model.outputs: no visible global function definition for ‘sd’
Undefined global functions or variables:
  fitted glm predict.glm residuals sd
Consider adding
  importFrom("stats", "fitted", "glm", "predict.glm", "residuals", "sd")
to your NAMESPACE file.
ci.cvAUC: no visible global function definition for ‘qnorm’
ci.pooled.cvAUC: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
calfun: no visible global function definition for ‘optim’
calfun: no visible global function definition for ‘cov’
calfun: no visible global function definition for ‘var’
Undefined global functions or variables:
  cov optim var
Consider adding
  importFrom("stats", "cov", "optim", "var")
to your NAMESPACE file.
func.constructRegressionFormula: no visible global function definition
  for ‘as.formula’
func.crossValidationAnalysis: no visible global function definition for
  ‘glm’
func.crossValidationAnalysis: no visible global function definition for
  ‘predict’
func.crossValidationAnalysis: no visible global function definition for
  ‘write.table’
func.externalValidationAnalysis: no visible global function definition
  for ‘predict’
func.externalValidationAnalysis: no visible global function definition
  for ‘write.table’
func.linearRegressionAnalysis: no visible global function definition
  for ‘glm’
func.linearRegressionAnalysis: no visible global function definition
  for ‘predict’
func.linearRegressionAnalysis: no visible global function definition
  for ‘write.table’
func.sortDataColumns: no visible global function definition for
  ‘write.table’
mainfunc.q2: no visible global function definition for ‘write.table’
mainfunc.q2: no visible global function definition for ‘new’
mainfunc.stats: no visible global function definition for ‘write.table’
mainfunc.stats: no visible global function definition for ‘new’
Undefined global functions or variables:
  as.formula glm new predict write.table
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "as.formula", "glm", "predict")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
cvimpute.by.wavelet: no visible global function definition for ‘sd’
cvimpute.by.wavelet: no visible global function definition for ‘mad’
cvimpute.image.by.wavelet: no visible global function definition for
  ‘sd’
cvimpute.image.by.wavelet: no visible global function definition for
  ‘mad’
cvwavelet.image.after.impute: no visible global function definition for
  ‘sd’
cvwavelet.image.after.impute: no visible global function definition for
  ‘mad’
Undefined global functions or variables:
  mad sd
Consider adding
  importFrom("stats", "mad", "sd")
to your NAMESPACE file.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’ ‘robustbase’
A package should be listed in only one of these fields.
random.CV: no visible global function definition for ‘var’
regular.CV: no visible global function definition for ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
create_clustering_problem: no visible global function definition for
  ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
.mixgauss_init: no visible global function definition for ‘cov’
.mixgauss_init: no visible global function definition for ‘var’
Undefined global functions or variables:
  cov var
Consider adding
  importFrom("stats", "cov", "var")
to your NAMESPACE file.
cxxfun.from.dll: no visible global function definition for ‘new’
cxxfun.from.dso.bin: no visible global function definition for ‘new’
cxxfunctionplus: no visible global function definition for ‘getPlugin’
cxxfunctionplus: no visible global function definition for
  ‘cxxfunction’
cxxfunctionplus: no visible global function definition for ‘new’
show,cxxdso: no visible global function definition for ‘object.size’
Undefined global functions or variables:
  cxxfunction getPlugin new object.size
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "object.size")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package in Depends field not imported from: ‘fda’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
check.for.sequence.endpoint.breaks: no visible global function
  definition for ‘na.omit’
get.breaks.vector: no visible global function definition for ‘na.omit’
get.cycle.breaks: no visible global function definition for ‘na.omit’
get.cycle.counts: no visible global function definition for ‘na.omit’
get.cycle.matrix: no visible global function definition for ‘na.omit’
get.cycle.minimums: no visible global function definition for ‘na.omit’
get.peaks: no visible global function definition for ‘embed’
get.trans: no visible global function definition for
  ‘create.bspline.basis’
get.trans: no visible global function definition for ‘smooth.basis’
get.trans: no visible global function definition for ‘deriv.fd’
get.trans: no visible global function definition for ‘eval.fd’
get.transition.locations: no visible global function definition for
  ‘na.omit’
get.transition.locations.FDiff: no visible global function definition
  for ‘na.omit’
get.window: no visible global function definition for ‘sd’
Undefined global functions or variables:
  create.bspline.basis deriv.fd embed eval.fd na.omit sd smooth.basis
Consider adding
  importFrom("stats", "embed", "na.omit", "sd")
to your NAMESPACE file.
cytoDiv: no visible global function definition for ‘colorRampPalette’
cytoDiv: no visible global function definition for ‘persp’
Undefined global functions or variables:
  colorRampPalette persp
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "persp")
to your NAMESPACE file.
Rd file 'cytoDiv.Rd':
  \usage lines wider than 90 characters:
     cytoDiv(df, x.var="fsc_small", y.var="chl_small", Ncat = 16, Nbit = 16, do.plot=FALSE, ...)
  \examples lines wider than 100 characters:
     rainbow.cols <- colorRampPalette(c("#00007F", "blue", "#007FFF", "cyan", "#7FFF7F", "yellow","#FF7F00", "red", "#7F0000"))
     plot(cleaned.df[,2], cleaned.df[,3], col= densCols(cleaned.df[,2], cleaned.df[,3], colramp = rainbow.cols))

These lines will be truncated in the PDF manual.
compareModels: no visible binding for global variable ‘fgl’
compareModels: no visible global function definition for ‘rlm’
compareModels: no visible global function definition for ‘lm’
compareModels: no visible global function definition for ‘predict’
compareModels: no visible global function definition for ‘resid’
plotSampDist: no visible global function definition for ‘par’
plotSampDist: no visible global function definition for ‘density’
plotSampDist: no visible global function definition for ‘plot’
plotSampDist: no visible global function definition for ‘lines’
plotSampDist: no visible global function definition for ‘legend’
plotSampDist: no visible global function definition for ‘qqnorm’
plotSampDist: no visible global function definition for ‘points’
plotSampDist: no visible global function definition for ‘mtext’
simulateSampDist: no visible binding for global variable ‘rnorm’
Undefined global functions or variables:
  density fgl legend lines lm mtext par plot points predict qqnorm
  resid rlm rnorm
Consider adding
  importFrom("graphics", "legend", "lines", "mtext", "par", "plot",
             "points")
  importFrom("stats", "density", "lm", "predict", "qqnorm", "resid",
             "rnorm")
to your NAMESPACE file.
Package in Depends field not imported from: ‘s20x’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'intPlot.Rd':
  \usage lines wider than 90 characters:
      intPlot(y, fac1 = NULL, fac2 = NULL, xlab = NULL, xlab2 = NULL, ylab = NULL, data.order=TRUE, exlim=0.1, jitter=0.02, conf.level=0.95, ... [TRUNCATED]
      intPlot(y, data, xlab = NULL, xlab2 = NULL, ylab = NULL, data.order = TRUE, exlim=0.1, jitter=0.02, conf.level=0.95, interval.type="tu ... [TRUNCATED]

These lines will be truncated in the PDF manual.
allCombs: no visible global function definition for ‘combn’
brute.search: no visible global function definition for ‘na.omit’
dag.draw: no visible global function definition for ‘plot’
dag.draw: no visible global function definition for ‘text’
dag.init: no visible global function definition for
  ‘installed.packages’
dag.legend: no visible global function definition for ‘text’
dag.letter: no visible global function definition for ‘text’
dag.move: no visible global function definition for ‘identify’
dag.move: no visible global function definition for ‘locator’
dag.sim: no visible global function definition for ‘rnorm’
dag.sim: no visible global function definition for ‘rbinom’
dag.sim : <anonymous>: no visible global function definition for
  ‘rbinom’
garrows: no visible global function definition for ‘arrows’
smoothArc: no visible global function definition for ‘points’
summary_dagRdag: no visible global function definition for ‘na.omit’
viv: no visible global function definition for ‘na.omit’
write.paths: no visible global function definition for ‘text’
Undefined global functions or variables:
  arrows combn identify installed.packages locator na.omit plot points
  rbinom rnorm text
Consider adding
  importFrom("graphics", "arrows", "identify", "locator", "plot",
             "points", "text")
  importFrom("stats", "na.omit", "rbinom", "rnorm")
  importFrom("utils", "combn", "installed.packages")
to your NAMESPACE file.
Package in Depends field not imported from: ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  roc.area
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
DAMOCLES_ML: no visible global function definition for ‘flush.console’
DAMOCLES_bootstrap: no visible global function definition for
  ‘cophenetic’
DAMOCLES_bootstrap: no visible global function definition for ‘sd’
DAMOCLES_bootstrap: no visible global function definition for
  ‘quantile’
DAMOCLES_sim: no visible global function definition for ‘na.omit’
DAMOCLES_sim: no visible global function definition for ‘runif’
DAMOCLES_sim: no visible global function definition for ‘lines’
DAMOCLES_sim: no visible global function definition for ‘rnorm’
DAMOCLES_sim: no visible global function definition for ‘dexp’
DAMOCLES_sim: no visible global function definition for ‘dist’
DAMOCLES_simplex: no visible global function definition for
  ‘flush.console’
Undefined global functions or variables:
  cophenetic dexp dist flush.console lines na.omit quantile rnorm runif
  sd
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "cophenetic", "dexp", "dist", "na.omit",
             "quantile", "rnorm", "runif", "sd")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
drawAimSpot: no visible global function definition for ‘points’
drawBoard: no visible global function definition for ‘par’
drawBoard: no visible global function definition for ‘plot’
drawBoard: no visible global function definition for ‘points’
drawBoard: no visible global function definition for ‘text’
drawHeatmap: no visible global function definition for ‘heat.colors’
drawHeatmap: no visible global function definition for ‘par’
drawHeatmap: no visible global function definition for ‘image’
drawHeatmap: no visible global function definition for ‘rect’
generalExpScores: no visible global function definition for ‘fft’
simpleExpScores: no visible global function definition for ‘mvfft’
simpleExpScores: no visible global function definition for ‘fft’
Undefined global functions or variables:
  fft heat.colors image mvfft par plot points rect text
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "image", "par", "plot", "points", "rect",
             "text")
  importFrom("stats", "fft", "mvfft")
to your NAMESPACE file.
dashboard_open: no visible global function definition for ‘write.csv’
dashboard_open: no visible global function definition for
  ‘capture.output’
dctable: no visible global function definition for ‘capture.output’
Undefined global functions or variables:
  capture.output write.csv
Consider adding
  importFrom("utils", "capture.output", "write.csv")
to your NAMESPACE file.
datadict.profile: no visible global function definition for
  ‘txtProgressBar’
datadict.profile: no visible global function definition for
  ‘setTxtProgressBar’
datadict_profile: no visible global function definition for
  ‘txtProgressBar’
datadict_profile: no visible global function definition for
  ‘setTxtProgressBar’
heatmap.quality: no visible global function definition for
  ‘colorRampPalette’
heatmap.quality: no visible global function definition for ‘heatmap’
heatmap_quality: no visible global function definition for
  ‘colorRampPalette’
heatmap_quality: no visible global function definition for ‘heatmap’
is.oneOf: no visible global function definition for ‘read.csv’
is_one_of: no visible global function definition for ‘read.csv’
pkg.version: no visible global function definition for ‘citation’
pkg_version: no visible global function definition for ‘citation’
ruleCoverage: no visible global function definition for ‘dotchart’
ruleCoverage: no visible global function definition for ‘abline’
rule_coverage: no visible global function definition for ‘dotchart’
rule_coverage: no visible global function definition for ‘abline’
scoreSum: no visible global function definition for ‘plot’
score_sum: no visible global function definition for ‘plot’
shortSummary: no visible global function definition for ‘sd’
short_summary: no visible global function definition for ‘sd’
Undefined global functions or variables:
  abline citation colorRampPalette dotchart heatmap plot read.csv sd
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "abline", "dotchart", "plot")
  importFrom("stats", "heatmap", "sd")
  importFrom("utils", "citation", "read.csv", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
Package suggested but not available for checking: ‘Rhipe’
Found the following assignments to the global environment:
File ‘DataEntry/R/Export.R’:
  assign(svalue(edObnm), d, envir = .GlobalEnv)
Package in Depends field not imported from: ‘DBI’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.onLoad : <anonymous>: no visible global function definition for
  ‘read.table’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbConnect’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbListTables’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbExistsTable’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbReadTable’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbWriteTable’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbDisconnect’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbRemoveTable’
Undefined global functions or variables:
  dbConnect dbDisconnect dbExistsTable dbListTables dbReadTable
  dbRemoveTable dbWriteTable read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.

Found the following calls to attach():
File ‘datamap/R/datamap.R’:
  attach(.Call("CreateUserDB", map, PACKAGE = "datamap"), pos, 
    name, warn.conflicts)
See section ‘Good practice’ in ‘?attach’.
checkDataQuality: no visible binding for global variable ‘quantile’
checkDataQuality: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  quantile write.csv
Consider adding
  importFrom("stats", "quantile")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
browse: no visible global function definition for ‘slot’
browse: no visible global function definition for ‘page’
default.options: no visible binding for global variable ‘object.size’
heat.view: no visible global function definition for ‘head’
heat.view: no visible global function definition for ‘tail’
whos: no visible global function definition for ‘slotNames’
whos : <anonymous> : <anonymous>: no visible global function definition
  for ‘slot’
Undefined global functions or variables:
  head object.size page slot slotNames tail
Consider adding
  importFrom("methods", "slot", "slotNames")
  importFrom("utils", "head", "object.size", "page", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').

Found the following calls to attach():
File ‘dataview/R/browse.R’:
  attach(x)
File ‘dataview/R/entry_view.R’:
  attach(x)
See section ‘Good practice’ in ‘?attach’.
Depends: includes the non-default packages:
  'xtable', 'akima', 'R.oo', 'R.methodsS3', 'matlab', 'lattice',
  'locfit', 'grid'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  ‘R.methodsS3’ ‘R.oo’ ‘akima’ ‘graphics’ ‘grid’ ‘lattice’ ‘locfit’
  ‘matlab’ ‘xtable’
  Please remove these calls from your code.
'library' or 'require' call to ‘R.matlab’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘R.methodsS3’ ‘R.oo’ ‘akima’ ‘grid’ ‘lattice’ ‘locfit’ ‘matlab’
  ‘xtable’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
DAT : DATrun : calch: no visible global function definition for
  ‘preplot’
DAT : DATrun: no visible global function definition for ‘rot90’
DAT : DATrun: no visible global function definition for ‘median’
DAT : DATrun: no visible global function definition for ‘locfit.robust’
DAT : DATrun: no visible global function definition for ‘preplot’
DAT : DATrun: no visible global function definition for ‘dev.new’
DAT : DATrun: no visible global function definition for ‘image’
DAT : DATrun: no visible global function definition for ‘palette’
DAT : DATrun: no visible global function definition for
  ‘colorRampPalette’
DAT : DATrun: no visible global function definition for ‘text’
DAT : DATrun: no visible global function definition for ‘dev.set’
DAT : DATrun: no visible global function definition for ‘locator’
DAT : DATrun: no visible global function definition for ‘graphics.off’
DAT : DATrun: no visible global function definition for ‘pdf’
DAT : DATrun: no visible global function definition for ‘layout’
DAT : DATrun: no visible global function definition for ‘par’
DAT : DATrun: no visible global function definition for ‘plot’
DAT : DATrun: no visible global function definition for ‘frame’
DAT : DATrun: no visible global function definition for ‘lines’
DAT : DATrun: no visible global function definition for ‘dev.off’
DAT : DATrun: no visible global function definition for ‘writeMat’
DAT: no visible binding for global variable ‘DAT.simData’
Undefined global functions or variables:
  DAT.simData colorRampPalette dev.new dev.off dev.set frame
  graphics.off image layout lines locator locfit.robust median palette
  par pdf plot preplot rot90 text writeMat
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.new", "dev.off",
             "dev.set", "graphics.off", "palette", "pdf")
  importFrom("graphics", "frame", "image", "layout", "lines", "locator",
             "par", "plot", "text")
  importFrom("stats", "median", "preplot")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘RMySQL’ ‘gWidgets’
  Please remove these calls from your code.
dbEmpLikeGOF: no visible global function definition for ‘runif’
dbEmpLikeGOF: no visible global function definition for ‘var’
dbEmpLikeGOF: no visible global function definition for ‘rnorm’
emplikeGOFinternal: no visible global function definition for ‘var’
getCutoff: no visible binding for global variable ‘unifCut’
getCutoff: no visible binding for global variable ‘normCut’
getCutoff: no visible global function definition for ‘lm’
getCutoff: no visible binding for global variable ‘distEqCut’
getPval: no visible binding for global variable ‘unifCut’
getPval: no visible binding for global variable ‘normCut’
getPval: no visible global function definition for ‘lm’
getPval: no visible binding for global variable ‘distEqCut’
helperPval: no visible global function definition for ‘lm’
returnCutoff: no visible global function definition for ‘quantile’
testfun2: no visible global function definition for ‘runif’
testfun2: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  distEqCut lm normCut quantile rnorm runif unifCut var
Consider adding
  importFrom("stats", "lm", "quantile", "rnorm", "runif", "var")
to your NAMESPACE file.
computePval: no visible global function definition for ‘lm’
computeQhat: no visible global function definition for ‘pnorm’
dbELnorm: no visible global function definition for ‘rnorm’
getCutoffTableThree: no visible global function definition for ‘lm’
getCutoffTableTwo: no visible global function definition for ‘lm’
getCutoffValue: no visible global function definition for ‘lm’
helperGetTstat: no visible global function definition for ‘rnorm’
returnCutoffValue: no visible global function definition for ‘rnorm’
returnCutoffValue: no visible global function definition for ‘quantile’
varianceEstimator: no visible global function definition for ‘density’
varianceEstimator: no visible global function definition for ‘ecdf’
Undefined global functions or variables:
  density ecdf lm pnorm quantile rnorm
Consider adding
  importFrom("stats", "density", "ecdf", "lm", "pnorm", "quantile",
             "rnorm")
to your NAMESPACE file.
'library' or 'require' call to ‘fdrtool’ which was already attached by Depends.
  Please remove these calls from your code.
avelinkdis: no visible global function definition for ‘sd’
avelinkdis: no visible global function definition for ‘dist’
centdis: no visible global function definition for ‘sd’
centdis: no visible global function definition for ‘dist’
distable: no visible global function definition for ‘write.table’
functionall: no visible global function definition for ‘read.table’
randdis: no visible global function definition for ‘write.table’
valuep: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  dist read.table sd write.csv write.table
Consider adding
  importFrom("stats", "dist", "sd")
  importFrom("utils", "read.table", "write.csv", "write.table")
to your NAMESPACE file.
Rd file 'distable.Rd':
  \examples lines wider than 100 characters:
     ##before using "b1.txt" data, we need to find "b1.txt" in the data file and  put it in the work space of R

Rd file 'functionall.Rd':
  \examples lines wider than 100 characters:
     ##before running this funtion, we need to find out "b1.txt" data file, and put it into the R workspace.
     functionall(system.file("data","b1.txt",package="DBGSA"),10,avelinkdis,"euclidean","distance",afExp,2000,10,"rand.txt","pvalue.txt")

These lines will be truncated in the PDF manual.
Found the following apparent S3 methods exported but not registered:
  as.data.frame.dbkGrad
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
.CA.fast2: no visible global function definition for ‘lsfit’
.T2.fast: no visible global function definition for ‘txtProgressBar’
.T2.fast: no visible global function definition for ‘setTxtProgressBar’
.dcemri.bayes: no visible global function definition for ‘median’
.dcemri.bayes: no visible global function definition for ‘sd’
.dcemri.map : posterior: no visible global function definition for
  ‘dnorm’
.dcemri.map : posterior: no visible global function definition for
  ‘dgamma’
.dcemri.map : posterior: no visible global function definition for
  ‘dbeta’
.dcemri.map.single: no visible global function definition for ‘optim’
.dcemri.spline: no visible binding for global variable ‘median’
.dcemri.spline: no visible global function definition for ‘median’
.dcemri.spline.single: no visible binding for global variable
  ‘quantile’
.dcemri.spline.single: no visible binding for global variable ‘median’
.dcemri.spline.single: no visible global function definition for
  ‘median’
.ftm: no visible global function definition for ‘fft’
.ftm: no visible global function definition for ‘matplot’
.ftm: no visible global function definition for ‘legend’
compartmentalModel : <anonymous>: no visible global function definition
  for ‘approx’
convFFT: no visible global function definition for ‘fft’
extractAIF : c.start: no visible global function definition for ‘sd’
extractAIF : c.start: no visible global function definition for ‘cor’
Undefined global functions or variables:
  approx cor dbeta dgamma dnorm fft legend lsfit matplot median optim
  quantile sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "matplot")
  importFrom("stats", "approx", "cor", "dbeta", "dgamma", "dnorm", "fft",
             "lsfit", "median", "optim", "quantile", "sd")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘lattice’ ‘latticeExtra’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
test.LM: no visible global function definition for ‘lm’
Undefined global functions or variables:
  lm
Consider adding
  importFrom("stats", "lm")
to your NAMESPACE file.
getDelimiter: no visible global function definition for ‘read.csv’
setupfile: no visible global function definition for ‘read.csv’
treatPath: no visible global function definition for ‘file_test’
Undefined global functions or variables:
  file_test read.csv
Consider adding
  importFrom("utils", "file_test", "read.csv")
to your NAMESPACE file.
ifft: no visible global function definition for ‘fft’
lines.deamer: no visible global function definition for ‘lines’
plot.deamer: no visible global function definition for ‘plot’
rlaplace: no visible global function definition for ‘runif’
Undefined global functions or variables:
  fft lines plot runif
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "fft", "runif")
to your NAMESPACE file.
compare.relimp: no visible global function definition for ‘qchisq’
compare.relimp: no visible global function definition for ‘pchisq’
plot_transition: no visible global function definition for ‘dnorm’
plot_transition: no visible global function definition for ‘par’
plot_transition: no visible global function definition for ‘plot’
plot_transition: no visible global function definition for ‘lines’
plot_transition: no visible global function definition for ‘plogis’
plot_transition: no visible global function definition for ‘axis’
plot_transition: no visible global function definition for ‘mtext’
relative.importance: no visible global function definition for ‘glm’
relative.importance: no visible global function definition for ‘sd’
relative.importance : tr.pr: no visible global function definition for
  ‘pnorm’
relative.importance: no visible global function definition for ‘vcov’
Undefined global functions or variables:
  axis dnorm glm lines mtext par pchisq plogis plot pnorm qchisq sd
  vcov
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "par", "plot")
  importFrom("stats", "dnorm", "glm", "pchisq", "plogis", "pnorm",
             "qchisq", "sd", "vcov")
to your NAMESPACE file.
DeconCPdf: no visible global function definition for ‘bw.nrd0’
DeconCPdf: no visible global function definition for ‘bw.nrd’
DeconCPdf: no visible global function definition for ‘bw.ucv’
DeconCPdf: no visible global function definition for ‘bw.bcv’
DeconCPdf: no visible global function definition for ‘bw.SJ’
DeconCPdf: no visible global function definition for ‘density’
DeconCPdf: no visible global function definition for ‘dnorm’
bw.dboot2 : suppL2: no visible global function definition for ‘density’
bw.dboot2 : suppL2: no visible global function definition for ‘rnorm’
bw.dboot2 : gaussL2: no visible global function definition for
  ‘density’
bw.dboot2 : gaussL2: no visible global function definition for ‘rnorm’
bw.dmise: no visible global function definition for ‘var’
plot.Decon: no visible global function definition for ‘plot.default’
plot.Decon: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline bw.SJ bw.bcv bw.nrd bw.nrd0 bw.ucv density dnorm plot.default
  rnorm var
Consider adding
  importFrom("graphics", "abline", "plot.default")
  importFrom("stats", "bw.SJ", "bw.bcv", "bw.nrd", "bw.nrd0", "bw.ucv",
             "density", "dnorm", "rnorm", "var")
to your NAMESPACE file.
'library' or 'require' call to ‘irr’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘rgl’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  predict.kmeans
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
.make3dScatterPlotDialog: no visible global function definition for
  ‘install.packages’
.makePackageDataDialog: no visible global function definition for
  ‘data’
.makeVignetteDialog: no visible global function definition for
  ‘vignette’
.onLoad: no visible binding for global variable ‘jgr.addMenuItem’
.onLoad : gui.addSeperator: no visible global function definition for
  ‘jgr.addMenuSeparator’
applyModel: no visible global function definition for ‘predict’
predict.kmeans : <anonymous>: no visible global function definition for
  ‘dist’
Undefined global functions or variables:
  data dist install.packages jgr.addMenuItem jgr.addMenuSeparator
  predict vignette
Consider adding
  importFrom("stats", "dist", "predict")
  importFrom("utils", "data", "install.packages", "vignette")
to your NAMESPACE file.
Package in Depends field not imported from: ‘Deducer’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Depends: includes the non-default packages:
  'Deducer', 'psych', 'GPArotation', 'mvnormtest', 'irr', 'klaR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' call to ‘klaR’ which was already attached by Depends.
  Please remove these calls from your code.
.makeICCDialog: no visible global function definition for ‘J’
.makeICCDialog: no visible global function definition for ‘new’
.makeICCDialog: no visible global function definition for ‘.jnull’
.makeNewFactorAnalysisDialog: no visible global function definition for
  ‘new’
.makeNewFactorAnalysisDialog: no visible global function definition for
  ‘J’
.makeNewFactorAnalysisDialog: no visible global function definition for
  ‘toJava’
.makeNewLDADialog: no visible global function definition for ‘new’
.makeNewLDADialog: no visible global function definition for ‘J’
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for ‘new’
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for ‘toJava’
.makeNewLDADialog: no visible global function definition for ‘toJava’
.makeNewReliabilityDialog: no visible global function definition for
  ‘new’
.makeNewReliabilityDialog: no visible global function definition for
  ‘toJava’
.onLoad: no visible global function definition for ‘.jnull’
.onLoad: no visible global function definition for ‘jgr.getMenuNames’
.onLoad: no visible global function definition for ‘jgr.insertMenu’
.onLoad: no visible global function definition for ‘jgr.addMenu’
.onLoad: no visible global function definition for ‘jgr.addMenuItem’
Undefined global functions or variables:
  .jnull J jgr.addMenu jgr.addMenuItem jgr.getMenuNames jgr.insertMenu
  new toJava
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Depends: includes the non-default packages:
  'JavaGD', 'Deducer', 'sp', 'maptools', 'OpenStreetMap', 'scales',
  'rgdal'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘UScensus2010’
A package should be listed in only one of these fields.
Non-standard file/directory found at top level:
  ‘org’
'library' or 'require' call to ‘UScensus2010’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘JavaGD’ ‘OpenStreetMap’ ‘maptools’ ‘rgdal’ ‘scales’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'loadCensusData.Rd':
  \usage lines wider than 90 characters:
                     year=c("2010","2000"), verbose=TRUE, osmTransform=TRUE, envir = .GlobalEnv)

Rd file 'spatialTextPlot.Rd':
  \examples lines wider than 100 characters:
     plot.window(c(-1.3160249151515616E7,-1.3155204307648793E7),c(3992993.9205893227,3996691.5618326175), xaxs = 'i', yaxs = 'i')
     plot(openmap(c(33.760525217369974,-118.22052955627441),c(33.73290566922855,-118.17521095275879),14,'bing'),add=TRUE)

These lines will be truncated in the PDF manual.
.makeQuickWordcloud: no visible global function definition for ‘J’
.makeQuickWordcloud: no visible global function definition for ‘new’
.makeQuickWordcloud: no visible global function definition for ‘.jnull’
.makeTextPlot: no visible global function definition for ‘J’
.makeTextPlot: no visible global function definition for ‘new’
.makeTextPlot: no visible global function definition for ‘.jnull’
.onLoad: no visible global function definition for ‘.jpackage’
.onLoad: no visible global function definition for ‘.jnew’
.onLoad: no visible global function definition for ‘J’
make.color.scale: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  .jnew .jnull .jpackage J new rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
binary.state: no visible global function definition for ‘runif’
dbn.dnn.train: no visible global function definition for ‘runif’
dropout.mask: no visible global function definition for ‘runif’
nn.train: no visible global function definition for ‘runif’
rbm.train: no visible global function definition for ‘runif’
sae.dnn.train: no visible global function definition for ‘runif’
show.digit: no visible global function definition for ‘gray’
show.digit: no visible global function definition for ‘image’
Undefined global functions or variables:
  gray image runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "image")
  importFrom("stats", "runif")
to your NAMESPACE file.
DEEPR : perm_function: no visible global function definition for ‘head’
DEEPR : perm_function: no visible global function definition for ‘tail’
simCophy: no visible global function definition for ‘rpois’
simCophy: no visible global function definition for ‘rmultinom’
Undefined global functions or variables:
  head rmultinom rpois tail
Consider adding
  importFrom("stats", "rmultinom", "rpois")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
kern: no visible global function definition for ‘var’
kern: no visible global function definition for ‘dnorm’
pdeg: no visible global function definition for ‘var’
pdeg: no visible global function definition for ‘dnorm’
z.b: no visible binding for global variable ‘var’
z.s: no visible binding for global variable ‘var’
Undefined global functions or variables:
  dnorm var
Consider adding
  importFrom("stats", "dnorm", "var")
to your NAMESPACE file.
src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_CFLAGS but not in PKG_LIBS
  src/Makevars: SHLIB_OPENMP_FFLAGS is included in PKG_FFLAGS but not SHLIB_OPENMP_CFLAGS in PKG_LIBS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
Found an obsolete/platform-specific call in the following function:
  ‘dr_df’
Found the platform-specific device:
  ‘x11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
bootbagg: no visible global function definition for ‘runif’
bootworpl: no visible global function definition for ‘runif’
des12: no visible global function definition for ‘rnorm’
des12: no visible global function definition for ‘runif’
eval.stage.gauss: no visible global function definition for ‘var’
plotparti: no visible global function definition for ‘plot’
plotparti: no visible global function definition for ‘lines’
plotpartilev: no visible global function definition for ‘plot’
plotpartilev: no visible global function definition for ‘polygon’
plotpartilev: no visible global function definition for ‘points’
simesi: no visible global function definition for ‘runif’
simesi3d: no visible global function definition for ‘runif’
simfssk: no visible global function definition for ‘rnorm’
simfssk: no visible global function definition for ‘runif’
simmix.delt: no visible global function definition for ‘rnorm’
simmix.delt: no visible global function definition for ‘runif’
simpp: no visible global function definition for ‘rnorm’
simpp: no visible global function definition for ‘runif’
simutree: no visible global function definition for ‘runif’
stage.gaussR: no visible global function definition for ‘var’
unidis: no visible global function definition for ‘runif’
Undefined global functions or variables:
  lines plot points polygon rnorm runif var
Consider adding
  importFrom("graphics", "lines", "plot", "points", "polygon")
  importFrom("stats", "rnorm", "runif", "var")
to your NAMESPACE file.
Bootstrapping.CI: no visible global function definition for ‘quantile’
D.Jost: no visible global function definition for ‘read.table’
D.Jost: no visible global function definition for ‘write.table’
Dv.locis.corrected.calc: no visible global function definition for
  ‘p.adjust’
Gst.Nei: no visible global function definition for ‘read.table’
Gst.Nei: no visible global function definition for ‘write.table’
H.out: no visible global function definition for ‘write.table’
Hardy.calc: no visible global function definition for ‘chisq.test’
critical.ci.values: no visible global function definition for
  ‘quantile’
inputformat: no visible global function definition for ‘read.table’
inputformat: no visible global function definition for ‘write.table’
over.all.pops: no visible global function definition for ‘write.table’
p.value.correcture: no visible global function definition for
  ‘p.adjust’
pair.pops: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  chisq.test p.adjust quantile read.table write.table
Consider adding
  importFrom("stats", "chisq.test", "p.adjust", "quantile")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.

Found the following calls to attach():
File ‘DEMEtics/R/inputformat.r’:
  attach(y)
See section ‘Good practice’ in ‘?attach’.
DEMIPathway: no visible global function definition for ‘dhyper’
DEMIPathway: no visible global function definition for ‘p.adjust’
calcHypergeoExon: no visible global function definition for ‘dhyper’
calcHypergeoProb: no visible global function definition for ‘dhyper’
demi: no visible global function definition for ‘write.table’
demi.t.test: no visible global function definition for ‘t.test’
demi.wilcox.test: no visible global function definition for
  ‘wilcox.test’
demi.wilcox.test.fast: no visible global function definition for
  ‘wilcox.test’
demiequal: no visible global function definition for ‘wilcox.test’
wprob: no visible global function definition for ‘combn’
diffexp,DEMIDiff: no visible global function definition for ‘median’
diffexp,DEMIDiff: no visible global function definition for ‘p.adjust’
loadAnnotation,DEMIExperiment-environment: no visible global function
  definition for ‘data’
loadBlat,DEMIExperiment-environment: no visible global function
  definition for ‘data’
loadCytoband,DEMIExperiment-environment: no visible global function
  definition for ‘data’
loadPathway,DEMIExperiment-environment: no visible global function
  definition for ‘data’
Undefined global functions or variables:
  combn data dhyper median p.adjust t.test wilcox.test write.table
Consider adding
  importFrom("stats", "dhyper", "median", "p.adjust", "t.test",
             "wilcox.test")
  importFrom("utils", "combn", "data", "write.table")
to your NAMESPACE file.
DendSer: no visible global function definition for ‘getFromNamespace’
crit2cost : <anonymous>: no visible global function definition for
  ‘as.dist’
dser.dist: no visible global function definition for ‘hclust’
dser.matrix: no visible global function definition for ‘dist’
plotAsColor: no visible global function definition for ‘image’
plotAsColor: no visible global function definition for ‘box’
plotAsColor: no visible global function definition for ‘axis’
seriation_method_dist_dser: no visible global function definition for
  ‘hclust’
seriation_method_dist_dser: no visible global function definition for
  ‘modifyList’
seriation_method_leafsort: no visible global function definition for
  ‘modifyList’
Undefined global functions or variables:
  as.dist axis box dist getFromNamespace hclust image modifyList
Consider adding
  importFrom("graphics", "axis", "box", "image")
  importFrom("stats", "as.dist", "dist", "hclust")
  importFrom("utils", "getFromNamespace", "modifyList")
to your NAMESPACE file.
Package suggested but not available for checking: ‘Rdonlp2’
MBD: no visible global function definition for ‘par’
MBD: no visible global function definition for ‘gray’
MBD: no visible global function definition for ‘matplot’
MBD: no visible global function definition for ‘polygon’
MBD: no visible global function definition for ‘lines’
MBD: no visible global function definition for ‘legend’
MBD: no visible global function definition for ‘matlines’
R.test: no visible global function definition for ‘runif’
R.test: no visible global function definition for ‘wilcox.test’
centralPlot: no visible global function definition for ‘par’
centralPlot: no visible global function definition for
  ‘colorRampPalette’
centralPlot: no visible global function definition for ‘matplot’
centralPlot: no visible global function definition for ‘matlines’
centralPlot: no visible global function definition for ‘legend’
scalecurve: no visible global function definition for ‘plot’
scalecurve: no visible global function definition for ‘lines’
scalecurve: no visible global function definition for ‘legend’
tmean: no visible global function definition for ‘matplot’
tmean: no visible global function definition for ‘matlines’
tmean: no visible global function definition for ‘lines’
tmean: no visible global function definition for ‘legend’
tmean: no visible global function definition for ‘colorRampPalette’
Undefined global functions or variables:
  colorRampPalette gray legend lines matlines matplot par plot polygon
  runif wilcox.test
Consider adding
  importFrom("grDevices", "colorRampPalette", "gray")
  importFrom("graphics", "legend", "lines", "matlines", "matplot", "par",
             "plot", "polygon")
  importFrom("stats", "runif", "wilcox.test")
to your NAMESPACE file.
Package suggested but not available for checking: ‘RDCOMClient’
ds: no visible global function definition for ‘is.ts’
ds: no visible global function definition for ‘frequency’
getds: no visible global function definition for ‘resid’
getds: no visible global function definition for ‘lm.fit’
getds: no visible global function definition for ‘sd’
getds: no visible global function definition for ‘var’
getds: no visible global function definition for ‘fitted’
Undefined global functions or variables:
  fitted frequency is.ts lm.fit resid sd var
Consider adding
  importFrom("stats", "fitted", "frequency", "is.ts", "lm.fit", "resid",
             "sd", "var")
to your NAMESPACE file.
Rd file 'ds.Rd':
  \usage lines wider than 90 characters:
     ds(z, Fm = 6, Fs = 6, type = c("daily", "monthly"), searchQ=TRUE, lag.max=20, ic=c("BIC","AIC"), standardizeQ=TRUE)

These lines will be truncated in the PDF manual.
arrayUpdate : pairUpdate: no visible global function definition for
  ‘runif’
conditionUpdate: no visible global function definition for ‘runif’
designGG: no visible global function definition for ‘runif’
experimentDesignTable: no visible global function definition for
  ‘write.csv’
plotAllScores: no visible global function definition for ‘png’
plotAllScores: no visible global function definition for ‘par’
plotAllScores: no visible global function definition for ‘plot’
plotAllScores: no visible global function definition for ‘text’
plotAllScores: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off par plot png runif text write.csv
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "par", "plot", "text")
  importFrom("stats", "runif")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Packages which this enhances but not available for checking:
  'gurobi', 'Rmosek'
fs.agreement.part: no visible global function definition for ‘as.dist’
fs.agreement.part: no visible global function definition for ‘cor’
fs.leave.k.out.combn: no visible global function definition for ‘sd’
fs.leave.k.out.sample: no visible global function definition for ‘sd’
fs.rd: no visible global function definition for ‘pchisq’
fs.selection: no visible global function definition for ‘p.adjust’
plot.FIT: no visible global function definition for ‘qchisq’
plot.FIT: no visible global function definition for ‘ppoints’
plot.FIT: no visible global function definition for ‘plot’
plot.FIT: no visible global function definition for ‘points’
plot.FIT: no visible global function definition for ‘abline’
plotJn: no visible global function definition for ‘plot’
plotJn: no visible global function definition for ‘points’
robust.distance.signed: no visible global function definition for
  ‘mahalanobis’
snowball: no visible global function definition for ‘is’
snowball: no visible global function definition for ‘median’
weight.sd: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  abline as.dist cor is mahalanobis median p.adjust pchisq plot points
  ppoints qchisq sd
Consider adding
  importFrom("graphics", "abline", "plot", "points")
  importFrom("methods", "is")
  importFrom("stats", "as.dist", "cor", "mahalanobis", "median",
             "p.adjust", "pchisq", "ppoints", "qchisq", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package in Depends field not imported from: ‘dplR’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.get’ ‘InteractiveDetrending’ ‘RemoveTrend’
Rd file 'EPS.value.Rd':
  \examples lines wider than 100 characters:
     co021.subset<-co021.subset[,-c(28,30,31)] ## to remove the following series "645232","646107" and "646118"

These lines will be truncated in the PDF manual.
Package in Depends field not imported from: ‘ash’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘dexter:::get_resp_data’ ‘dexter:::qcolors’
  See the note in ?`:::` about the use of this operator.
Found the following apparent S3 methods exported but not registered:
  plot.mtd plot.sim print.crmsize print.dxcrm print.mtd print.sim
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
simulate_dataframe : generate_dumb_answer: no visible global function
  definition for ‘rbinom’
simulate_dataframe : generate_dumb_answer: no visible global function
  definition for ‘rnorm’
simulate_dataframe : generate_initial: no visible global function
  definition for ‘rbinom’
simulate_dataframe: no visible binding for global variable ‘randu’
simulate_dataframe: no visible global function definition for ‘rbinom’
simulate_dataframe: no visible global function definition for ‘rnorm’
simulate_dataframe: no visible global function definition for ‘rpois’
simulate_dataframe : add_NAs: no visible global function definition for
  ‘rbinom’
Undefined global functions or variables:
  randu rbinom rnorm rpois
Consider adding
  importFrom("datasets", "randu")
  importFrom("stats", "rbinom", "rnorm", "rpois")
to your NAMESPACE file.
makeAdjMatrix: no visible global function definition for ‘combn’
plotPosteriorN: no visible global function definition for ‘plot’
plotPosteriorN: no visible global function definition for ‘title’
plotPosteriorN: no visible global function definition for ‘lines’
plotPosteriorN: no visible global function definition for ‘legend’
venn3: no visible global function definition for ‘plot’
venn3: no visible global function definition for ‘runif’
venn3: no visible global function definition for ‘points’
venn3: no visible global function definition for ‘lines’
venn3: no visible global function definition for ‘text’
venn4: no visible global function definition for ‘plot’
venn4: no visible global function definition for ‘lines’
venn4: no visible global function definition for ‘runif’
venn4: no visible global function definition for ‘points’
Undefined global functions or variables:
  combn legend lines plot points runif text title
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points", "text",
             "title")
  importFrom("stats", "runif")
  importFrom("utils", "combn")
to your NAMESPACE file.
cvm.test : cvm.pval.disc: no visible global function definition for
  ‘integrate’
cvm.test : cvm.pval.disc: no visible global function definition for
  ‘dchisq’
cvm.test : cvm.pval.disc: no visible global function definition for
  ‘nlm’
cvm.test : cvm.stat.disc: no visible global function definition for
  ‘knots’
cvm.test : cvm.pval.disc.sim: no visible global function definition for
  ‘knots’
cvm.test : cvm.pval.disc.sim: no visible global function definition for
  ‘runif’
cvm.test: no visible global function definition for ‘is.stepfun’
cvm.test: no visible global function definition for ‘knots’
ks.test : exact.pval : ts.pval: no visible global function definition
  for ‘ecdf’
ks.test : sim.pval: no visible global function definition for ‘runif’
ks.test : sim.pval : getks: no visible global function definition for
  ‘ecdf’
ks.test: no visible global function definition for ‘is.stepfun’
ks.test: no visible global function definition for ‘knots’
ks.test: no visible global function definition for ‘ecdf’
Undefined global functions or variables:
  dchisq ecdf integrate is.stepfun knots nlm runif
Consider adding
  importFrom("stats", "dchisq", "ecdf", "integrate", "is.stepfun",
             "knots", "nlm", "runif")
to your NAMESPACE file.
dichromat: no visible global function definition for ‘col2rgb’
dichromat: no visible global function definition for ‘predict’
dichromat: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  col2rgb predict rgb
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
  importFrom("stats", "predict")
to your NAMESPACE file.
le.pesquisa: no visible global function definition for ‘txtProgressBar’
le.pesquisa: no visible global function definition for ‘type.convert’
le.pesquisa: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar type.convert
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar",
             "type.convert")
to your NAMESPACE file.
L2eV: no visible binding for global variable ‘constants’
L2w: no visible binding for global variable ‘constants’
dielectric: no visible global function definition for ‘new’
dielectric2plot: no visible global function definition for ‘reshape’
eV2L: no visible binding for global variable ‘constants’
t2eV: no visible binding for global variable ‘constants’
Undefined global functions or variables:
  constants new reshape
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "reshape")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages in Depends field not imported from:
  ‘PropCIs’ ‘gee’ ‘rootSolve’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
diffpci: no visible global function definition for ‘diffpropci.Wald.mp’
diffpci: no visible global function definition for ‘diffpropci.mp’
diffpci: no visible global function definition for ‘scoreci.mp’
exact.cond : exactci: no visible global function definition for ‘qf’
exact.midp : binom.midp : f.low: no visible global function definition
  for ‘dbinom’
exact.midp : binom.midp : f.low: no visible global function definition
  for ‘pbinom’
exact.midp : binom.midp : f.up: no visible global function definition
  for ‘dbinom’
exact.midp : binom.midp : f.up: no visible global function definition
  for ‘pbinom’
exact.midp : binom.midp : one.ci: no visible global function definition
  for ‘uniroot’
np.nv: no visible global function definition for ‘qnorm’
np.t: no visible global function definition for ‘qt’
uncond: no visible global function definition for ‘qnorm’
wald.cc: no visible global function definition for ‘qnorm’
wilson: no visible global function definition for ‘qnorm’
wilson: no visible global function definition for ‘uniroot.all’
wilson.cc: no visible global function definition for ‘qnorm’
wilson.cc: no visible global function definition for ‘uniroot.all’
wilson.phi: no visible global function definition for ‘qnorm’
wilson.phi: no visible global function definition for ‘uniroot.all’
Undefined global functions or variables:
  dbinom diffpropci.Wald.mp diffpropci.mp pbinom qf qnorm qt scoreci.mp
  uniroot uniroot.all
Consider adding
  importFrom("stats", "dbinom", "pbinom", "qf", "qnorm", "qt", "uniroot")
to your NAMESPACE file.
rkMethodPlot: no visible global function definition for ‘par’
rkMethodPlot: no visible global function definition for ‘axis’
rkMethodPlot: no visible global function definition for ‘points’
rkMethodPlot: no visible global function definition for ‘text’
rkMethodPlot: no visible global function definition for ‘segments’
rkimp: no visible global function definition for ‘runif’
stability.bruteforce: no visible global function definition for ‘plot’
stability.bruteforce: no visible global function definition for
  ‘points’
stability.bruteforce: no visible global function definition for
  ‘abline’
stability.multistep: no visible global function definition for ‘plot’
stability.multistep: no visible global function definition for ‘lines’
stability.multistep: no visible global function definition for
  ‘polygon’
stability.multistep: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline axis lines par plot points polygon runif segments text
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "par", "plot",
             "points", "polygon", "segments", "text")
  importFrom("stats", "runif")
to your NAMESPACE file.
Packages required but not available: 'missMethyl', 'methylumi'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘maptools’ ‘spatstat’ ‘spdep’
  Please remove these calls from your code.
fAssocmatrix : fAssocmatrix1: no visible global function definition for
  ‘coordinates<-’
fAssocplot: no visible global function definition for ‘plot’
fAssocplot: no visible global function definition for ‘coordinates’
fAssocplot: no visible global function definition for ‘text’
fAssocplot: no visible global function definition for ‘box’
fDrawfigure: no visible global function definition for ‘slot’
fDrawfigure : <anonymous>: no visible global function definition for
  ‘slot’
fDrawfigure: no visible global function definition for
  ‘SpatialPolygons’
fDrawfigure: no visible global function definition for ‘spsample’
fDrawfigure: no visible global function definition for ‘plot’
fDrawfigure: no visible global function definition for ‘image’
fDrawfigure: no visible global function definition for
  ‘colorRampPalette’
fDrawfigure: no visible global function definition for ‘points’
fRanXY : <anonymous>: no visible global function definition for ‘slot’
fRanXY : <anonymous>: no visible global function definition for
  ‘spsample’
Undefined global functions or variables:
  SpatialPolygons box colorRampPalette coordinates coordinates<- image
  plot points slot spsample text
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "box", "image", "plot", "points", "text")
  importFrom("methods", "slot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Rd file 'fAssocmatrix.Rd':
  \examples lines wider than 100 characters:
     ## Run 20 permutations using individuals accoring to sighting probability (ave no. roos seen on survey  = 6) 

These lines will be truncated in the PDF manual.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘igraph’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
aLine: no visible global function definition for ‘lines’
aLine: no visible global function definition for ‘ecdf’
dip.test: no visible global function definition for ‘complete.cases’
dip.test: no visible global function definition for ‘runif’
dip.test: no visible global function definition for ‘approx’
plot.dip: no visible global function definition for ‘par’
plot.dip: no visible global function definition for ‘ecdf’
plot.dip: no visible global function definition for ‘plot’
plot.dip: no visible global function definition for ‘title’
plot.dip: no visible global function definition for ‘abline’
plot.dip: no visible global function definition for ‘axis’
plot.dip: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline approx axis complete.cases ecdf legend lines par plot runif
  title
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "title")
  importFrom("stats", "approx", "complete.cases", "ecdf", "runif")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘dirmult.pdf’
nullTest: no visible global function definition for ‘rmultinom’
rdirichlet: no visible global function definition for ‘rgamma’
simPop: no visible global function definition for ‘rnorm’
simPop: no visible global function definition for ‘rmultinom’
Undefined global functions or variables:
  rgamma rmultinom rnorm
Consider adding
  importFrom("stats", "rgamma", "rmultinom", "rnorm")
to your NAMESPACE file.
rdisclap: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
p.discrete.adjust : <anonymous>: no visible global function definition
  for ‘stepfun’
Undefined global functions or variables:
  stepfun
Consider adding
  importFrom("stats", "stepfun")
to your NAMESPACE file.
value: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  qchisq
Consider adding
  importFrom("stats", "qchisq")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘RUnit’ ‘grid’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
mix.distlist.facing.gamma : <anonymous>: no visible global function
  definition for ‘dgamma’
mix.distlist.norm: no visible binding for global variable ‘dnorm’
mix.mle: no visible global function definition for ‘sd’
mix.mle: no visible global function definition for ‘quantile’
mix.mle: no visible global function definition for ‘median’
mix.mle: no visible global function definition for ‘optim’
mix.synthetic.facing.gamma: no visible global function definition for
  ‘runif’
mix.synthetic.facing.gamma: no visible global function definition for
  ‘rgamma’
mix.synthetic.normal: no visible global function definition for ‘runif’
mix.synthetic.normal: no visible global function definition for ‘rnorm’
plot.discrimARTs: no visible global function definition for ‘hist’
plot.discrimARTs: no visible global function definition for ‘points’
plot.discrimARTs: no visible global function definition for ‘lines’
plot.discrimARTs: no visible global function definition for ‘grid.text’
plot.discrimARTs: no visible global function definition for ‘gpar’
Undefined global functions or variables:
  dgamma dnorm gpar grid.text hist lines median optim points quantile
  rgamma rnorm runif sd
Consider adding
  importFrom("graphics", "hist", "lines", "points")
  importFrom("stats", "dgamma", "dnorm", "median", "optim", "quantile",
             "rgamma", "rnorm", "runif", "sd")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘INLA’
Rd file 'dualFlashlight.fn.Rd':
  \usage lines wider than 90 characters:
     dualFlashlight.fn(result.df, wellName = "WELL_USAGE", x.name = "mean", y.name = "ssmd", sampleName = "Sample", sampleColor = "black", c ... [TRUNCATED]

Rd file 'imageDesign.fn.Rd':
  \usage lines wider than 90 characters:
     imageDesign.fn(dataOnePlate.df, wellName = NA, rowName, colName, wells = NULL, colors = NULL, title = " ")

Rd file 'imageIntensity.fn.Rd':
  \usage lines wider than 90 characters:
     imageIntensity.fn(data.df, intensityName = NA, plateName = "BARCODE", wellName = "WELL_USAGE", rowName, colName, sampleName = "Sample", ... [TRUNCATED]

Rd file 'plateWellSeries.fn.Rd':
  \usage lines wider than 90 characters:
     plateWellSeries.fn(data.df, intensityName = NA, plateName = "BARCODE", wellName = "WELL_USAGE", rowName, colName, show.wellTypes = NULL ... [TRUNCATED]

These lines will be truncated in the PDF manual.
densest: no visible global function definition for ‘weighted.mean’
diss: no visible global function definition for ‘cov’
neighbors: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov weighted.mean
Consider adding
  importFrom("stats", "cov", "weighted.mean")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘car’ ‘prettyGraphs’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  print.Cmat print.DistatisR print.Splus
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Chi2DistanceFromSort: no visible global function definition for
  ‘model.matrix’
GraphDistatisAll: no visible global function definition for
  ‘createColorVectorsByDesign’
GraphDistatisBoot: no visible global function definition for
  ‘createColorVectorsByDesign’
GraphDistatisBoot: no visible global function definition for
  ‘dataEllipse’
GraphDistatisBoot: no visible global function definition for
  ‘peeledHull’
GraphDistatisCompromise: no visible global function definition for
  ‘createColorVectorsByDesign’
GraphDistatisCompromise: no visible global function definition for
  ‘prettyPlot’
GraphDistatisPartial: no visible global function definition for
  ‘createColorVectorsByDesign’
GraphDistatisPartial: no visible global function definition for
  ‘points’
GraphDistatisPartial: no visible global function definition for
  ‘prettyPlot’
GraphDistatisRv: no visible global function definition for
  ‘createColorVectorsByDesign’
GraphDistatisRv: no visible global function definition for ‘prettyPlot’
Undefined global functions or variables:
  createColorVectorsByDesign dataEllipse model.matrix peeledHull points
  prettyPlot
Consider adding
  importFrom("graphics", "points")
  importFrom("stats", "model.matrix")
to your NAMESPACE file.
dist.multiPhylo: no visible global function definition for ‘as.dist’
gromov.hyperbolicity: no visible global function definition for
  ‘as.dist’
mcmc.target.seq: no visible global function definition for ‘runif’
phylo.diff: no visible global function definition for ‘par’
phylo.diff: no visible global function definition for ‘plot’
Undefined global functions or variables:
  as.dist par plot runif
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.dist", "runif")
to your NAMESPACE file.
Package in Depends field not imported from: ‘RUnit’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
prepare_Rd: extract.val.Rd:25-26: Dropping empty section \note
prepare_Rd: extract.val.Rd:27: Dropping empty section \seealso
Running examples in ‘divest-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: readDicom
> ### Title: Read one or more DICOM directories
> ### Aliases: readDicom sortDicom scanDicom
> 
> ### ** Examples
> 
> path <- system.file("extdata", "raw", package="divest")
> scanDicom(path)
[dcm2niix info] Found 4 DICOM file(s)
[dcm2niix ERROR] You do not have write permissions for the directory /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/divest/extdata/raw
[dcm2niix ERROR] You do not have write permissions for the directory /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/divest/extdata/raw
  label
2  <NA>
1  <NA>
                                                                       rootPath
2 /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/divest/extdata/raw
1 /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/divest/extdata/raw
  files seriesNumber seriesDescription patientName studyDate echoTime
2     2            8        DTIb3000s5        <NA>      <NA>   112.00
1     2            9       fl3D_t1_sag        <NA>      <NA>     4.94
  repetitionTime echoNumber phase diffusion
2           4100         NA FALSE      TRUE
1             11         NA FALSE     FALSE
> readDicom(path, interactive=FALSE)
[dcm2niix info] Found 4 DICOM file(s)
[dcm2niix ERROR] You do not have write permissions for the directory /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/divest/extdata/raw
[dcm2niix info]  Warning: all images appear to be a single slice - please check slice/vector orientation
[dcm2niix ERROR] You do not have write permissions for the directory /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/divest/extdata/raw
Error in .readPath(path.expand(p), flipY, crop, forceStack, verbosity,  : 
  DICOM scan failed
Calls: readDicom -> lapply -> FUN -> .readPath
Execution halted
'library' or 'require' call to ‘glmnet’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘glmnet’ ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: ‘asreml’
'library' or 'require' calls to packages already attached by Depends:
  ‘nlme’ ‘wgaim’
  Please remove these calls from your code.
'library' or 'require' call to ‘asreml’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘ibdreg’ ‘mgcv’ ‘nlme’ ‘qtl’ ‘wgaim’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘qtl:::adjust.rf.ri’
  See the note in ?`:::` about the use of this operator.
Foreign function call to a different package:
  .C(cfunc, ..., PACKAGE = "qtl")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Rd file 'dlcross.Rd':
  \usage lines wider than 90 characters:
     dlcross(format = c("rqtl", "dlmap", "other"), genobj, pheobj, mapobj, idname="ID", genfile, phefile, mapfile, type, step=0, fixpos=0, e ... [TRUNCATED]

Rd file 'dlmap-internal.Rd':
  \usage lines wider than 90 characters:
     dlcross.dlmap(genobj, pheobj, mapobj, idname, genfile, mapfile, phefile, type, step, fixpos, estmap, ...)
     calc.genoprob2(cross, pos, error.prob=1e-04, map.function=c("haldane", "kosambi", "c-f", "morgan"))

Rd file 'dlmap.Rd':
  \usage lines wider than 90 characters:
     plot(x, chr, max.dist, qcol="light blue", mcol="red", pcol="purple", marker.names=FALSE, ...)

These lines will be truncated in the PDF manual.
Warning: no function found corresponding to methods exports from ‘DMwR’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
Packages in Depends field not imported from:
  ‘grid’ ‘lattice’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing object imported by a ':::' call: ‘rpart:::rpconvert’
Unexported objects imported by ':::' calls:
  ‘rpart:::rpart.branch’ ‘rpart:::rpartco’
  ‘rpart:::string.bounding.box’
  See the note in ?`:::` about the use of this operator.
'library' or 'require' call to ‘igraph’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
network.modules: no visible global function definition for
  ‘graph.empty’
network.modules: no visible global function definition for
  ‘add.vertices’
network.modules: no visible global function definition for ‘add.edges’
network.modules: no visible global function definition for ‘tkplot’
network.modules: no visible global function definition for ‘V’
Undefined global functions or variables:
  V add.edges add.vertices graph.empty tkplot
DNMF: no visible global function definition for ‘runif’
NMFpval: no visible global function definition for ‘p.adjust’
ndNMF: no visible global function definition for ‘runif’
rnk: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  p.adjust runif write.table
Consider adding
  importFrom("stats", "p.adjust", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
ppert: no visible global function definition for ‘pbeta’
prepare8pkg: no visible global function definition for ‘glob2rx’
qpert: no visible global function definition for ‘qbeta’
rpert: no visible global function definition for ‘rbeta’
Undefined global functions or variables:
  glob2rx pbeta qbeta rbeta
Consider adding
  importFrom("stats", "pbeta", "qbeta", "rbeta")
  importFrom("utils", "glob2rx")
to your NAMESPACE file.
gimli.31403hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.7111hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.16629hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.24691hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.21546hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.749hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.30765hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.7279hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.13017hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.20754hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.28144hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following calls to attach():
File ‘doParallel/R/doParallel.R’:
  attach(exportEnv)
See section ‘Good practice’ in ‘?attach’.
.info: no visible global function definition for ‘packageDescription’
redisWorker: no visible global function definition for ‘flush.console’
Undefined global functions or variables:
  flush.console packageDescription
Consider adding
  importFrom("utils", "flush.console", "packageDescription")
to your NAMESPACE file.
Found the following calls to attach():
File ‘doSNOW/R/doSNOW.R’:
  attach(exportEnv)
See section ‘Good practice’ in ‘?attach’.
dostats: no visible binding for global variable ‘na.fail’
first: no visible global function definition for ‘head’
last: no visible global function definition for ‘tail’
pval.default: no visible global function definition for ‘.hasSlot’
pval.lm: no visible global function definition for ‘anova’
Undefined global functions or variables:
  .hasSlot anova head na.fail tail
Consider adding
  importFrom("methods", ".hasSlot")
  importFrom("stats", "anova", "na.fail")
  importFrom("utils", "head", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Rd file 'dpa.generate.lag.Rd':
  \usage lines wider than 90 characters:
     dpa.generate.lag(dataframe = NULL, tickColumn = NULL, sourceColumn = NULL, minLag=1,maxLag=1)

Rd file 'dpa.relations.addRelations.Rd':
  \usage lines wider than 90 characters:
     dpa.relations.addRelations(From_column = NULL, To_column = NULL, Lag_in = NULL, minLag = NULL, maxLag = NULL, Direction = NULL)

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/dpglasso.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [22s/24s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dplyr)
  Registered S3 method overwritten by 'dplyr':
    method               from  
    as.data.frame.tbl_df tibble
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > test_check("dplyr")
  ── 1. Failure: funs() gives a clear error message (#3368) (@test-funs.R#28)  ───
  `funs(...)` threw an error with unexpected message.
  Expected match: "`function(si) {\n    mp[si]\n}` must be a function name (quoted or unquoted) or an unquoted call, not `function`"
  Actual message: "`function(si) {\n    mp[si]\n}` must be a function name (quoted or unquoted) or an unquoted call, not ``function``"
  
  ── 2. Failure: funs() gives a clear error message (#3368) (@test-funs.R#36)  ───
  `funs(~mp[.])` threw an error with unexpected message.
  Expected match: "`~mp[.]` must be a function name (quoted or unquoted) or an unquoted call, not `~`"
  Actual message: "`~mp[.]` must be a function name (quoted or unquoted) or an unquoted call, not ``~``"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2947 SKIPPED: 3 FAILED: 2
  1. Failure: funs() gives a clear error message (#3368) (@test-funs.R#28) 
  2. Failure: funs() gives a clear error message (#3368) (@test-funs.R#36) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  call dbDisconnect() when finished working with a connection 
  Execution halted
Error in re-building vignettes:
  ...
`geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
Warning: Removed 1 rows containing non-finite values (stat_smooth).
Warning: Removed 1 rows containing missing values (geom_point).
Quitting from lines 651-653 (programming.Rmd) 
Error: processing vignette ‘programming.Rmd’ failed with diagnostics:
`UQE()` is defunct. Please use `!!get_expr(x)`
Execution halted
File ‘DPpackage/libs/DPpackage.so’:
  Found ‘_gfortran_st_close’, possibly from ‘close’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDBDPdensity.o’, ‘LDDPdensity.o’,
      ‘LDDPsurvival.o’, ‘LDPDdoublyintsba.o’, ‘LDTFPdensity.o’,
      ‘LDTFPglmmpois.o’, ‘LDTFPsurvival.o’, ‘PSgamgam.o’,
      ‘PSgamgauss.o’, ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’,
      ‘ToolsLDTFP.o’
  Found ‘_gfortran_st_open’, possibly from ‘open’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDBDPdensity.o’, ‘LDDPdensity.o’,
      ‘LDDPsurvival.o’, ‘LDPDdoublyintsba.o’, ‘LDTFPdensity.o’,
      ‘LDTFPglmmpois.o’, ‘LDTFPsurvival.o’, ‘PSgamgam.o’,
      ‘PSgamgauss.o’, ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’,
      ‘ToolsLDTFP.o’
  Found ‘_gfortran_st_read’, possibly from ‘read’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDDPdensity.o’, ‘LDDPsurvival.o’,
      ‘LDPDdoublyintsba.o’, ‘PSgamgam.o’, ‘PSgamgauss.o’,
      ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’, ‘ToolsLDTFP.o’
  Found ‘_gfortran_st_rewind’, possibly from ‘rewind’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDDPdensity.o’, ‘LDDPsurvival.o’,
      ‘LDPDdoublyintsba.o’, ‘PSgamgam.o’, ‘PSgamgauss.o’,
      ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’, ‘ToolsLDTFP.o’
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDBDPdensity.o’, ‘LDDPdensity.o’,
      ‘LDDPsurvival.o’, ‘LDPDdoublyintsba.o’, ‘LDTFPdensity.o’,
      ‘LDTFPglmmpois.o’, ‘LDTFPsurvival.o’, ‘PSgamgam.o’,
      ‘PSgamgauss.o’, ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  compnoreggilks.cpp:31:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compnoreggilks.cpp:90:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:32:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:88:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:150:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:207:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:380:8: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/DPWeibull.Rcheck/00install.out’ for details.
Non-standard file/directory found at top level:
  ‘visualRefCard’
The following files look like leftovers:
  ‘drawExpression/visualRefCard/svn-commit.tmp’
Please remove them from your package.
Found the following apparent S3 methods exported but not registered:
  drawDetails.dataframeBox drawDetails.functionText drawDetails.lineBox
  drawDetails.listBox drawDetails.matrixBox drawDetails.vectorBox
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
.drawTree: no visible global function definition for ‘pdf’
.drawTree: no visible global function definition for ‘dev.off’
drawExpression: no visible global function definition for ‘plot.new’
Undefined global functions or variables:
  dev.off pdf plot.new
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "plot.new")
to your NAMESPACE file.
DRaWR: no visible global function definition for ‘write.table’
DRaWR: no visible global function definition for ‘read.table’
DRaWR: no visible global function definition for ‘aggregate’
DRaWR: no visible global function definition for ‘slot’
Undefined global functions or variables:
  aggregate read.table slot write.table
Consider adding
  importFrom("methods", "slot")
  importFrom("stats", "aggregate")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
cdfDRM: no visible global function definition for ‘tail’
densityDRM: no visible binding for global variable ‘density’
drmdel: no visible binding for global variable ‘optim’
drmdel: no visible global function definition for ‘pchisq’
quantEst: no visible global function definition for ‘tail’
quantileCompWald: no visible global function definition for ‘pchisq’
quantileCompWald: no visible global function definition for ‘p.adjust’
quantileDRM: no visible global function definition for ‘tail’
quantileDRM: no visible global function definition for ‘density’
Undefined global functions or variables:
  density optim p.adjust pchisq tail
Consider adding
  importFrom("stats", "density", "optim", "p.adjust", "pchisq")
  importFrom("utils", "tail")
to your NAMESPACE file.
compute_xsq: no visible global function definition for ‘chisq.test’
Undefined global functions or variables:
  chisq.test
Consider adding
  importFrom("stats", "chisq.test")
to your NAMESPACE file.
DSBayes: no visible global function definition for ‘qnorm’
DSBayes: no visible global function definition for ‘coef’
DSBayes: no visible global function definition for ‘vcov’
DSBayes : MLE: no visible global function definition for ‘qnorm’
DSBayes: no visible global function definition for ‘integrate’
DSBayes : qfunc.numer : <anonymous>: no visible global function
  definition for ‘dnorm’
DSBayes : ds.numer: no visible global function definition for
  ‘integrate’
DSBayes : lower: no visible global function definition for ‘qlogis’
DSBayes : lower: no visible global function definition for ‘integrate’
DSBayes : upper: no visible global function definition for ‘qlogis’
DSBayes : upper: no visible global function definition for ‘integrate’
DSBayes: no visible global function definition for ‘optimize’
DSBayes: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  coef dnorm integrate optimize qlogis qnorm uniroot vcov
Consider adding
  importFrom("stats", "coef", "dnorm", "integrate", "optimize", "qlogis",
             "qnorm", "uniroot", "vcov")
to your NAMESPACE file.
AIC.dspat: no visible global function definition for ‘coef’
LTDataFrame: no visible global function definition for ‘as.formula’
coef.dspat: no visible global function definition for ‘coef’
integrate.intensity: no visible global function definition for ‘coef’
integrate.intensity: no visible global function definition for
  ‘predict’
integrate.intensity: no visible global function definition for
  ‘model.matrix’
integrate.intensity: no visible global function definition for ‘vcov’
integrate.intensity: no visible global function definition for ‘fitted’
lgcp.correction: no visible global function definition for ‘predict’
lgcp.correction: no visible global function definition for
  ‘model.matrix’
lgcp.correction: no visible global function definition for ‘fitted’
lgcp.correction: no visible global function definition for ‘var’
lines_to_strips : line_to_strip: no visible global function definition
  for ‘as’
owin.gpc.poly: no visible global function definition for ‘as’
sample.points : sample.points.from.line: no visible global function
  definition for ‘runif’
sample.points: no visible global function definition for ‘model.matrix’
simCovariates: no visible global function definition for ‘quantile’
simPts: no visible global function definition for ‘model.matrix’
transect.intensity: no visible global function definition for ‘predict’
transect.intensity: no visible global function definition for ‘hist’
Undefined global functions or variables:
  as as.formula coef fitted hist model.matrix predict quantile runif
  var vcov
Consider adding
  importFrom("graphics", "hist")
  importFrom("methods", "as")
  importFrom("stats", "as.formula", "coef", "fitted", "model.matrix",
             "predict", "quantile", "runif", "var", "vcov")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
X: no visible global function definition for ‘read.table’
dplot: no visible global function definition for ‘matplot’
dplot: no visible global function definition for ‘legend’
dscor : <anonymous>: no visible global function definition for ‘combn’
dscor : <anonymous> : <anonymous>: no visible global function
  definition for ‘cor.test’
gds: no visible binding for global variable ‘na.omit’
gds : medi: no visible global function definition for ‘median’
gds : quant: no visible global function definition for ‘quantile’
gds: no visible binding for global variable ‘shapiro.test’
tables: no visible binding for global variable ‘chisq.test’
tables: no visible binding for global variable ‘fisher.test’
Undefined global functions or variables:
  chisq.test combn cor.test fisher.test legend matplot median na.omit
  quantile read.table shapiro.test
Consider adding
  importFrom("graphics", "legend", "matplot")
  importFrom("stats", "chisq.test", "cor.test", "fisher.test", "median",
             "na.omit", "quantile", "shapiro.test")
  importFrom("utils", "combn", "read.table")
to your NAMESPACE file.
DStree: no visible global function definition for ‘model.frame’
DStree: no visible global function definition for ‘model.matrix’
DStree: no visible global function definition for ‘model.response’
DStree: no visible global function definition for ‘as.formula’
bag: no visible global function definition for ‘model.frame’
bag: no visible global function definition for ‘model.response’
plot.DStree: no visible global function definition for ‘par’
plot.DStree: no visible global function definition for ‘plot’
plot.DStree: no visible global function definition for ‘rainbow’
plot.DStree: no visible global function definition for ‘lines’
plot.DStree: no visible global function definition for ‘legend’
predict.DStree: no visible global function definition for ‘predict’
print.DStree: no visible global function definition for ‘naprint’
prune.DStree: no visible global function definition for ‘median’
prune.DStree: no visible global function definition for ‘predict’
prune.DStree: no visible binding for global variable ‘var’
summ.MAE: no visible global function definition for ‘predict’
summary.DStree: no visible global function definition for ‘naprint’
Undefined global functions or variables:
  as.formula legend lines median model.frame model.matrix
  model.response naprint par plot predict rainbow var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend", "lines", "par", "plot")
  importFrom("stats", "as.formula", "median", "model.frame",
             "model.matrix", "model.response", "naprint", "predict",
             "var")
to your NAMESPACE file.
DCEA: no visible global function definition for ‘p.adjust’
DS: no visible global function definition for ‘p.adjust’
DS: no visible global function definition for ‘pdf’
DS: no visible global function definition for ‘plot’
DS: no visible global function definition for ‘dev.off’
LFC: no visible global function definition for ‘glm’
LFC: no visible global function definition for ‘predict’
PartialCor: no visible global function definition for ‘na.omit’
comDCGLplot: no visible global function definition for ‘pdf’
comDCGLplot: no visible global function definition for ‘plot’
comDCGLplot: no visible global function definition for ‘dev.off’
percentLinkfilter: no visible global function definition for ‘cor’
qLinkfilter: no visible global function definition for ‘cor’
qLinkfilter: no visible global function definition for ‘pt’
qLinkfilter: no visible global function definition for ‘p.adjust’
rLinkfilter: no visible global function definition for ‘cor’
varianceBasedfilter: no visible binding for global variable ‘var’
varianceBasedfilter: no visible global function definition for ‘median’
varianceBasedfilter: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  cor dev.off glm median na.omit p.adjust pchisq pdf plot predict pt
  var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "plot")
  importFrom("stats", "cor", "glm", "median", "na.omit", "p.adjust",
             "pchisq", "predict", "pt", "var")
to your NAMESPACE file.
DLR: no visible global function definition for ‘formula’
DLR: no visible global function definition for ‘terms’
DLR: no visible global function definition for ‘model.matrix’
DLR: no visible global function definition for ‘as.formula’
DLR: no visible binding for global variable ‘binomial’
DLR: no visible global function definition for ‘coef’
DLR: no visible global function definition for ‘pnorm’
DLR: no visible global function definition for ‘qnorm’
acc.1test: no visible global function definition for ‘qnorm’
pv.gs: no visible global function definition for ‘pchisq’
pv.rpv: no visible global function definition for ‘qnorm’
pv.rpv: no visible global function definition for ‘pnorm’
pv.wgs: no visible global function definition for ‘pchisq’
sesp.diff.ci: no visible global function definition for ‘qnorm’
sesp.mcnemar: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  as.formula binomial coef formula model.matrix pchisq pnorm qnorm
  terms
Consider adding
  importFrom("stats", "as.formula", "binomial", "coef", "formula",
             "model.matrix", "pchisq", "pnorm", "qnorm", "terms")
to your NAMESPACE file.
efron.petrosian: no visible global function definition for ‘dev.new’
efron.petrosian: no visible global function definition for ‘par’
efron.petrosian: no visible global function definition for ‘plot’
efron.petrosian: no visible global function definition for ‘segments’
lynden: no visible global function definition for ‘dev.new’
lynden: no visible global function definition for ‘par’
lynden: no visible global function definition for ‘plot’
lynden: no visible global function definition for ‘segments’
shen: no visible global function definition for ‘image’
shen: no visible global function definition for ‘runif’
shen: no visible global function definition for ‘filled.contour’
shen: no visible binding for global variable ‘rainbow’
shen: no visible binding for global variable ‘topo.colors’
shen: no visible global function definition for ‘topo.colors’
shen: no visible global function definition for ‘persp’
shen: no visible global function definition for ‘dev.new’
shen: no visible global function definition for ‘par’
shen: no visible global function definition for ‘plot’
shen: no visible global function definition for ‘segments’
Undefined global functions or variables:
  dev.new filled.contour image par persp plot rainbow runif segments
  topo.colors
Consider adding
  importFrom("grDevices", "dev.new", "rainbow", "topo.colors")
  importFrom("graphics", "filled.contour", "image", "par", "persp",
             "plot", "segments")
  importFrom("stats", "runif")
to your NAMESPACE file.
DTK.plot: no visible global function definition for ‘plot’
DTK.plot: no visible global function definition for ‘axis’
DTK.plot: no visible global function definition for ‘title’
DTK.plot: no visible global function definition for ‘lines’
DTK.plot: no visible global function definition for ‘points’
DTK.test: no visible binding for global variable ‘sd’
DTK.test: no visible global function definition for ‘qtukey’
TK.test: no visible global function definition for ‘TukeyHSD’
TK.test: no visible global function definition for ‘aov’
Undefined global functions or variables:
  TukeyHSD aov axis lines plot points qtukey sd title
Consider adding
  importFrom("graphics", "axis", "lines", "plot", "points", "title")
  importFrom("stats", "TukeyHSD", "aov", "qtukey", "sd")
to your NAMESPACE file.
DTMC: no visible global function definition for ‘runif’
DTMC: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
to your NAMESPACE file.
dummy: no visible global function definition for ‘model.matrix’
dummy: no visible global function definition for ‘model.frame’
Undefined global functions or variables:
  model.frame model.matrix
Consider adding
  importFrom("stats", "model.frame", "model.matrix")
to your NAMESPACE file.
Rd file 'dummy.Rd':
  \usage lines wider than 90 characters:
     dummy.data.frame(data, names = NULL, omit.constants=TRUE, dummy.classes = getOption("dummy.classes"), all = TRUE, ...)

These lines will be truncated in the PDF manual.
cvSDDT: no visible global function definition for ‘qt’
cvSDDT : Cj_SD.fun: no visible global function definition for ‘combn’
cvSDDT: no visible global function definition for ‘uniroot’
cvSUDT: no visible global function definition for ‘rnorm’
cvSUDT: no visible global function definition for ‘rchisq’
cvSUDT : psi.fun: no visible global function definition for ‘pnorm’
cvSUDT: no visible global function definition for ‘qt’
cvSUDT: no visible global function definition for ‘uniroot’
cvSUDT: no visible global function definition for ‘combn’
nvDT : samplesize: no visible global function definition for ‘rnorm’
nvDT : samplesize: no visible global function definition for ‘rchisq’
nvDT : samplesize: no visible global function definition for ‘pnorm’
nvDT : ssBonf: no visible global function definition for ‘qnorm’
nvDT : ssBonf: no visible global function definition for ‘qt’
nvDT : ssBonf: no visible global function definition for ‘rnorm’
nvDT : ssBonf: no visible global function definition for ‘rchisq’
nvDT : ssBonf: no visible global function definition for ‘pnorm’
nvDT: no visible global function definition for ‘uniroot’
powDT: no visible global function definition for ‘rnorm’
powDT: no visible global function definition for ‘rchisq’
powDT: no visible global function definition for ‘pnorm’
qvSDDT: no visible global function definition for ‘pt’
qvSUDT: no visible global function definition for ‘rnorm’
qvSUDT: no visible global function definition for ‘rchisq’
qvSUDT : psi.fun: no visible global function definition for ‘pnorm’
qvSUDT: no visible global function definition for ‘pt’
qvSUDT : Pj.fun: no visible global function definition for ‘qt’
qvSUDT : Pj.fun: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  combn pnorm pt qnorm qt rchisq rnorm uniroot
Consider adding
  importFrom("stats", "pnorm", "pt", "qnorm", "qt", "rchisq", "rnorm",
             "uniroot")
  importFrom("utils", "combn")
to your NAMESPACE file.
Clough: no visible global function definition for ‘dgamma’
computePosterior,Counts: no visible global function definition for
  ‘dnbinom’
getPosteriorParam,Counts: no visible global function definition for
  ‘qgamma’
getPosteriorParam,Counts: no visible global function definition for
  ‘dgamma’
getPosteriorParam,Counts: no visible global function definition for
  ‘pgamma’
plotPosterior,Counts: no visible global function definition for ‘axis’
plotPosterior,Counts: no visible global function definition for
  ‘abline’
plotPosterior,Counts: no visible global function definition for ‘lines’
plotPosterior,Counts: no visible global function definition for ‘rect’
plotPosterior,Counts: no visible global function definition for ‘curve’
plotPosterior,Counts: no visible global function definition for
  ‘dgamma’
plotPosterior,Counts: no visible global function definition for
  ‘legend’
show,Counts: no visible global function definition for ‘head’
show,Counts: no visible global function definition for ‘tail’
Undefined global functions or variables:
  abline axis curve dgamma dnbinom head legend lines pgamma qgamma rect
  tail
Consider adding
  importFrom("graphics", "abline", "axis", "curve", "legend", "lines",
             "rect")
  importFrom("stats", "dgamma", "dnbinom", "pgamma", "qgamma")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘HISTORY’
'library' or 'require' calls to packages already attached by Depends:
  ‘ggm’ ‘tcltk’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘ggm’ ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
MultiTestH0 : MultiTestOneColumn: no visible global function definition
  for ‘pchisq’
RunClustering : CheckClusterNew: no visible global function definition
  for ‘qchisq’
RunClustering: no visible global function definition for ‘qchisq’
RunDenoising: no visible binding for global variable ‘var’
RunDenoising: no visible global function definition for ‘qchisq’
RunDenoising: no visible binding for global variable ‘median’
RunDenoising: no visible global function definition for ‘var’
RunDenoising : buildEstimate: no visible global function definition for
  ‘qchisq’
Undefined global functions or variables:
  median pchisq qchisq var
Consider adding
  importFrom("stats", "median", "pchisq", "qchisq", "var")
to your NAMESPACE file.
GetIntMod: no visible global function definition for ‘arima’
GetLikeDI: no visible global function definition for ‘arima’
GetLikeDI: no visible global function definition for ‘logLik’
GetPV: no visible global function definition for ‘optimize’
GetPV: no visible global function definition for ‘pchisq’
fitdi: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  arima logLik optimize pchisq
Consider adding
  importFrom("stats", "arima", "logLik", "optimize", "pchisq")
to your NAMESPACE file.
Non-standard files/directories found at top level:
  ‘easy_html_report_tmp_1376284934.59207.tsv’
  ‘easy_html_report_tmp_1376284935.5951.tsv’
  ‘easy_html_report_tmp_1376284936.59848.tsv’
Packages in Depends field not imported from:
  ‘base64enc’ ‘knitr’ ‘markdown’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.file_attachment: no visible global function definition for
  ‘base64encode’
.plot_attachment: no visible global function definition for ‘dev.off’
.update_list: no visible global function definition for ‘modifyList’
easyHtmlReport: no visible global function definition for ‘knit’
easyHtmlReport: no visible global function definition for
  ‘markdownToHTML’
mime_part.data.frame: no visible global function definition for
  ‘write.table’
mime_part.ggplot: no visible binding for global variable ‘pdf’
mime_part.matrix: no visible global function definition for
  ‘write.table’
mime_part.trellis: no visible binding for global variable ‘pdf’
simpleHtmlReport : <anonymous>: no visible global function definition
  for ‘write.table’
Undefined global functions or variables:
  base64encode dev.off knit markdownToHTML modifyList pdf write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "modifyList", "write.table")
to your NAMESPACE file.
MARK.MCMC : Model.Creator: no visible global function definition for
  ‘combn’
MARK.MCMC : formula.Maker: no visible global function definition for
  ‘combn’
Simulate.CH: no visible global function definition for ‘rnorm’
Simulate.CH: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  combn rbinom rnorm
Consider adding
  importFrom("stats", "rbinom", "rnorm")
  importFrom("utils", "combn")
to your NAMESPACE file.
eb: no visible global function definition for ‘optimize’
ebalance: no visible global function definition for ‘var’
Undefined global functions or variables:
  optimize var
Consider adding
  importFrom("stats", "optimize", "var")
to your NAMESPACE file.
ebSNP: no visible global function definition for ‘optim’
Undefined global functions or variables:
  optim
Consider adding
  importFrom("stats", "optim")
to your NAMESPACE file.
ecipex: no visible binding for global variable ‘nistiso’
ecipex : <anonymous>: no visible global function definition for ‘nextn’
ecipex : <anonymous>: no visible global function definition for ‘fft’
ecipex : <anonymous> : <anonymous>: no visible global function
  definition for ‘fft’
Undefined global functions or variables:
  fft nextn nistiso
Consider adding
  importFrom("stats", "fft", "nextn")
to your NAMESPACE file.
dilution: no visible global function definition for ‘grey’
dilution: no visible global function definition for ‘lines’
dilution: no visible global function definition for ‘rect’
dilution: no visible global function definition for ‘segments’
dilution: no visible global function definition for ‘text’
dilution: no visible global function definition for ‘arrows’
pricefit: no visible global function definition for ‘runif’
Undefined global functions or variables:
  arrows grey lines rect runif segments text
Consider adding
  importFrom("grDevices", "grey")
  importFrom("graphics", "arrows", "lines", "rect", "segments", "text")
  importFrom("stats", "runif")
to your NAMESPACE file.
Package in Depends field not imported from: ‘spc’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'ecoCusum.Rd':
  \examples lines wider than 100 characters:
     ## global optimization to h, H and n, when lambda = 0.01, "Nelder-Mead" optimization algorithm doesn't work

Rd file 'ecoEwma.Rd':
  \examples lines wider than 100 characters:
     #yy = ecoEwma(h = seq(.7,1,by=.01), w = seq(0.8,1,by=.01),k = seq(2.9,3.3, by = 0.01), n = 4:5, P0 = 110, P1 = 10, Cf = 50, contour.plo ... [TRUNCATED]

These lines will be truncated in the PDF manual.
UCexactTest: no visible global function definition for ‘is’
UCexactTest: no visible global function definition for ‘new’
pvalue: no visible global function definition for ‘dnbinom’
pvalue: no visible global function definition for ‘pnbinom’
sup.mu: no visible global function definition for ‘predict’
Undefined global functions or variables:
  dnbinom is new pnbinom predict
Consider adding
  importFrom("methods", "is", "new")
  importFrom("stats", "dnbinom", "pnbinom", "predict")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
geteegdata: no visible global function definition for ‘untar’
geteegdata: no visible global function definition for ‘read.table’
geteegdata: no visible global function definition for ‘write.csv’
geteegdata: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  read.table untar write.csv write.table
Consider adding
  importFrom("utils", "read.table", "untar", "write.csv", "write.table")
to your NAMESPACE file.
.gdf : find_loss: no visible global function definition for ‘rnorm’
.p.values : <anonymous>: no visible global function definition for
  ‘pnorm’
.relist.dwt: no visible global function definition for ‘relist’
.relist.dwt: no visible global function definition for ‘as’
.std.wav.coeff : <anonymous>: no visible global function definition for
  ‘mad’
regrid: no visible global function definition for ‘predict’
regrid: no visible global function definition for ‘var’
regrid: no visible global function definition for ‘medpolish’
Undefined global functions or variables:
  as mad medpolish pnorm predict relist rnorm var
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "mad", "medpolish", "pnorm", "predict", "rnorm",
             "var")
  importFrom("utils", "relist")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package suggested but not available for checking: ‘eggCountsExtra’
'library' or 'require' call to ‘sna’ which was already attached by Depends.
  Please remove these calls from your code.
read.egonet: no visible global function definition for ‘read.csv’
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Rd file 'egonet-package.Rd':
  \examples lines wider than 100 characters:
     #Compute the \code{effsize} and \code{constraint} to the restricted network with "EGO" and nodes with "P" in the name (i.e. the relativ ... [TRUNCATED]

Rd file 'index.egonet.Rd':
  \usage lines wider than 90 characters:
     index.egonet(dat, index = list("effsize", "constraint", "outdegree", "indegree", "efficiency", "hierarchy", "centralization", "gden", " ... [TRUNCATED]
  \examples lines wider than 100 characters:
     index.egonet(egomat,index=c("effsize","constraint","outdegree","indegree","efficiency", "centralization", "gden", "ego.gden", my.outdeg ... [TRUNCATED]

These lines will be truncated in the PDF manual.
eiginv: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
boot_pr_comp: no visible global function definition for ‘cov’
boot_pr_comp: no visible global function definition for ‘quantile’
boot_pr_comp: no visible global function definition for ‘segments’
boot_pr_comp: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline cov quantile segments
Consider adding
  importFrom("graphics", "abline", "segments")
  importFrom("stats", "cov", "quantile")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘class’ ‘quantreg’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cluster.segment: no visible global function definition for ‘kmeans’
cluster.segment: no visible global function definition for ‘knn’
comp.anc.dist: no visible global function definition for ‘wilcox.test’
eila: no visible global function definition for ‘hasArg’
get.prob.score: no visible global function definition for ‘glm’
get.prob.score: no visible global function definition for ‘binomial’
get.prob.score: no visible binding for global variable ‘logit’
get.prob.score: no visible global function definition for ‘predict’
quantreg.est: no visible global function definition for ‘rnorm’
quantreg.est: no visible global function definition for ‘rq.fit.fnb’
Undefined global functions or variables:
  binomial glm hasArg kmeans knn logit predict rnorm rq.fit.fnb
  wilcox.test
Consider adding
  importFrom("methods", "hasArg")
  importFrom("stats", "binomial", "glm", "kmeans", "predict", "rnorm",
             "wilcox.test")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages in Depends field not imported from:
  ‘MASS’ ‘coda’ ‘msm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  density.plot
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'density.plot':
  ‘density.plot’

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
comPlot: no visible global function definition for ‘plot’
comPlot: no visible global function definition for ‘lines’
convertEiData: no visible global function definition for ‘model.frame’
plot.eiwild: no visible global function definition for ‘plot’
plot.eiwild: no visible global function definition for ‘par’
plotResult: no visible global function definition for ‘grey’
plotResult: no visible global function definition for
  ‘colorRampPalette’
plotResult: no visible global function definition for ‘plot.new’
plotResult: no visible global function definition for ‘plot.window’
prioriPlot: no visible global function definition for ‘par’
prioriPlot : <anonymous> : <anonymous>: no visible global function
  definition for ‘rgamma’
prioriPlot : <anonymous>: no visible global function definition for
  ‘rbeta’
prioriPlot: no visible global function definition for ‘hist’
prioriPlot : <anonymous>: no visible global function definition for
  ‘rgamma’
prioriPlot : <anonymous> : <anonymous>: no visible global function
  definition for ‘rexp’
prioriPlot : <anonymous>: no visible global function definition for
  ‘rexp’
runMBayes: no visible global function definition for ‘runif’
runMBayes: no visible global function definition for ‘rgamma’
runMBayes: no visible global function definition for ‘rexp’
str0: no visible global function definition for ‘str’
tuneVars: no visible global function definition for ‘sd’
Undefined global functions or variables:
  colorRampPalette grey hist lines model.frame par plot plot.new
  plot.window rbeta rexp rgamma runif sd str
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey")
  importFrom("graphics", "hist", "lines", "par", "plot", "plot.new",
             "plot.window")
  importFrom("stats", "model.frame", "rbeta", "rexp", "rgamma", "runif",
             "sd")
  importFrom("utils", "str")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  print.audit.plan print.audit.plan.KM print.audit.plan.tri
  print.elec.data
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
CAST.calc.opt.cut: no visible global function definition for ‘points’
CAST.calc.opt.cut: no visible global function definition for ‘axis’
CAST.calc.sample: no visible global function definition for ‘uniroot’
KM.audit: no visible global function definition for ‘abline’
KM.audit: no visible global function definition for ‘points’
KM.audit: no visible global function definition for ‘segments’
KM.audit: no visible global function definition for ‘text’
find.stark.SRS.p: no visible global function definition for ‘phyper’
make.opt.packed.bad: no visible global function definition for ‘runif’
make.random.truth: no visible global function definition for ‘runif’
print.elec.data: no visible global function definition for ‘head’
simulateIt: no visible global function definition for ‘abline’
simulateIt: no visible global function definition for ‘points’
simulateIt: no visible global function definition for ‘segments’
simulateIt: no visible global function definition for ‘text’
stark.test.Z: no visible global function definition for ‘pbinom’
tri.audit.sim: no visible global function definition for ‘runif’
trinomial.bound: no visible global function definition for ‘contour’
trinomial.bound: no visible global function definition for ‘segments’
trinomial.bound: no visible global function definition for ‘points’
Undefined global functions or variables:
  abline axis contour head pbinom phyper points runif segments text
  uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "contour", "points",
             "segments", "text")
  importFrom("stats", "pbinom", "phyper", "runif", "uniroot")
  importFrom("utils", "head")
to your NAMESPACE file.
Rd file 'KM.audit.Rd':
  \usage lines wider than 90 characters:
     KM.audit(data, U, Z, alpha = 0.25, plot = FALSE, debug = FALSE, return.Ps = FALSE, truncate.Ps = TRUE)

Rd file 'make.audit.Rd':
  \usage lines wider than 90 characters:
     make.audit(Z = NULL, method = c("tweak", "opt.bad", "opt.bad.WPM", "opt.bad.packed", "opt.bad.packed.WPM", "ok", "no error"), p_d = 0.2 ... [TRUNCATED]

Rd file 'make.opt.packed.bad.Rd':
  \usage lines wider than 90 characters:
     make.opt.packed.bad(Z, max.taint = 1, max.taint.good = max.taint, WPM = FALSE, add.good = 0, add.random = FALSE)

Rd file 'simulateIt.Rd':
  \usage lines wider than 90 characters:
     simulateIt(data, M = 50, alpha = 0.25, plot = FALSE, debug = FALSE, return.Ps = FALSE, truncate.Ps = TRUE)

These lines will be truncated in the PDF manual.
Package in Depends field not imported from: ‘elec’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
BaB: no visible binding for global variable ‘calc.pairwise.e_p’
BaB: no visible global function definition for ‘weight.function’
BaB: no visible global function definition for ‘compute.stark.t’
LKPBound: no visible binding for global variable ‘calc.pairwise.e_p’
LKPBound: no visible global function definition for ‘weight.function’
LKPBound: no visible global function definition for ‘compute.stark.t’
eqValBound: no visible binding for global variable ‘calc.pairwise.e_p’
eqValBound: no visible global function definition for ‘weight.function’
eqValBound: no visible global function definition for ‘compute.stark.t’
getEbsMargin: no visible global function definition for ‘is.elec.data’
getEbsMargin: no visible global function definition for
  ‘maximumMarginBound’
makeStratObj: no visible global function definition for ‘is.elec.data’
makeStratObj: no visible global function definition for
  ‘maximumMarginBound’
strat.elec.data: no visible global function definition for ‘elec.data’
takeOutZeroMMB: no visible global function definition for
  ‘maximumMarginBound’
withReplaceBound: no visible binding for global variable
  ‘calc.pairwise.e_p’
withReplaceBound: no visible global function definition for
  ‘weight.function’
withReplaceBound: no visible global function definition for
  ‘compute.stark.t’
Undefined global functions or variables:
  calc.pairwise.e_p compute.stark.t elec.data is.elec.data
  maximumMarginBound weight.function
Found the following apparent S3 methods exported but not registered:
  print.elo print.seqchecknopres print.sequencecheck scale.elo
  summary.elo
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Likelihood: no visible global function definition for
  ‘makePSOCKcluster’
Likelihood: no visible global function definition for ‘clusterExport’
Likelihood: no visible global function definition for ‘makeForkCluster’
Likelihood.first.run: no visible global function definition for
  ‘clusterApply’
Likelihood.next.runs: no visible global function definition for
  ‘clusterApply’
es.stopCluster: no visible global function definition for ‘stopCluster’
plot.es.pedigree: no visible global function definition for ‘hasArg’
Undefined global functions or variables:
  clusterApply clusterExport hasArg makeForkCluster makePSOCKcluster
  stopCluster
Consider adding
  importFrom("methods", "hasArg")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Non-standard file/directory found at top level:
  ‘etc’
Packages in Depends field not imported from:
  ‘MASS’ ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  image.plot.ts
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘clusterSim’ ‘earth’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘clusterSim’ ‘earth’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
distance: no visible global function definition for
  ‘data.Normalization’
emmatn: no visible global function definition for ‘runif’
estimateModel: no visible global function definition for ‘as.formula’
estimateModel: no visible global function definition for ‘earth’
estimateModel: no visible global function definition for ‘plotmo’
estimateModel: no visible global function definition for ‘predict’
mutation: no visible global function definition for ‘runif’
plot.emma: no visible global function definition for ‘colorRampPalette’
plot.emma: no visible global function definition for ‘par’
plot.emma: no visible global function definition for ‘persp’
plot.emma: no visible global function definition for ‘points’
plot.emma: no visible global function definition for ‘trans3d’
Undefined global functions or variables:
  as.formula colorRampPalette data.Normalization earth par persp plotmo
  points predict runif trans3d
Consider adding
  importFrom("grDevices", "colorRampPalette", "trans3d")
  importFrom("graphics", "par", "persp", "points")
  importFrom("stats", "as.formula", "predict", "runif")
to your NAMESPACE file.
'library' or 'require' call to ‘reshape’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
MFFetch: no visible global function definition for ‘melt’
Undefined global functions or variables:
  melt
Rd file 'emme2.Rd':
  \usage lines wider than 90 characters:
          write.mf(data, numname, bank, file0, mcent, mmat, mat.dir, newname=NULL, newdesc=NULL)
  \examples lines wider than 100 characters:
          x <- matrix(rnorm(mf2), nrow(mf2), ncol(mf2)) #Random generate length(mf) numbers to write dummy data to bank
          write.mf(x, 2, "emme2/emme2ban", file0, file1$global["mcent"], file1$global["mmat"], mat.dir, newname="test", newdesc="test matrix ... [TRUNCATED]
          link.data <- read.link.data("emme2/emme2ban", 1, file0, file1$global["mscen"], file1$global["mlink"], file1$global["mnode"])
          nodes <- read.nodes("emme2/emme2ban", 1, file0, file1$global["mscen"], file1$global["mlink"], file1$global["mnode"])

These lines will be truncated in the PDF manual.
Package which this enhances but not available for checking: ‘glmmADMB’
Found the following apparent S3 methods exported but not registered:
  summary.fmmst summary.fmmt
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
nondominated_ordering: no visible binding for global variable ‘par’
rsbxbeta: no visible global function definition for ‘runif’
Undefined global functions or variables:
  par runif
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "runif")
to your NAMESPACE file.
empiricalFDR: no visible global function definition for ‘axis’
empiricalFDR: no visible global function definition for ‘loess’
empiricalFDR: no visible global function definition for ‘predict’
empiricalFDR: no visible global function definition for ‘lines’
empiricalFDR: no visible global function definition for ‘abline’
fdrBiCurve: no visible global function definition for ‘plot’
fdrBiCurve: no visible global function definition for ‘axis’
fdrBiCurve: no visible global function definition for ‘lines’
fdrBiCurve: no visible global function definition for ‘abline’
fdrBiCurve: no visible global function definition for ‘legend’
simulateCounts: no visible global function definition for
  ‘txtProgressBar’
simulateCounts: no visible global function definition for
  ‘setTxtProgressBar’
simulateCounts: no visible global function definition for ‘rnorm’
simulateCounts: no visible global function definition for ‘hist’
simulateCounts: no visible global function definition for ‘colData’
Undefined global functions or variables:
  abline axis colData hist legend lines loess plot predict rnorm
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "abline", "axis", "hist", "legend", "lines",
             "plot")
  importFrom("stats", "loess", "predict", "rnorm")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
ExactMultinomialTest: no visible global function definition for
  ‘dmultinom’
ExactMultinomialTest : <anonymous>: no visible global function
  definition for ‘dmultinom’
ExactMultinomialTestChisquare : <anonymous>: no visible global function
  definition for ‘dmultinom’
MonteCarloMultinomialTest: no visible global function definition for
  ‘rmultinom’
MonteCarloMultinomialTest: no visible global function definition for
  ‘flush.console’
MonteCarloMultinomialTestChisquare: no visible global function
  definition for ‘rmultinom’
MonteCarloMultinomialTestChisquare: no visible global function
  definition for ‘flush.console’
multinomial.test: no visible global function definition for
  ‘flush.console’
plotMultinom: no visible global function definition for ‘barplot’
plotMultinom: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  barplot dmultinom flush.console mtext rmultinom
Consider adding
  importFrom("graphics", "barplot", "mtext")
  importFrom("stats", "dmultinom", "rmultinom")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Rd file 'EMT-internal.Rd':
  \usage lines wider than 90 characters:
     MonteCarloMultinomialTestChisquare(observed, prob, size, groups, numEvents, ntrial, atOnce)

Rd file 'multinomial.test.Rd':
  \usage lines wider than 90 characters:
     multinomial.test(observed, prob, useChisq = FALSE, MonteCarlo = FALSE, ntrial = 100000, atOnce = 1000000)
  \examples lines wider than 100 characters:
     observed <- c(5,2,1)            # observed data: 5 items in category one, 2 items in category two, 1 item in category three
     prob <- c(0.25, 0.5, 0.25)      # model: hypothetical probability that an item falls into category one, two, or three
     ## Test the hypothesis that all sides of a dice pop up with the same probability (a 6-dimesional problem):
     prob <- c(pdice, pdice, pdice, pdice, pdice, pdice)     # the model, determined by the hypothetical probabilities
     observed <- c(4, 5, 2, 7, 0, 1)                         # the observation consisting of 19 throws ( = sample size)

These lines will be truncated in the PDF manual.
Non-standard file/directory found at top level:
  ‘CHANGES.txt’
'library' or 'require' call to ‘RColorBrewer’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘Rcmdr’ ‘gWidgets’ ‘gWidgetstcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Hmisc’ ‘RColorBrewer’ ‘vcd’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'mosaicPermDialog.Rd':
  \usage lines wider than 90 characters:
                                                             displayPermCommand=TRUE, extendedOptions=TRUE)
     setMosaicPalette(palettename,reverse=FALSE)                                                     

These lines will be truncated in the PDF manual.
Deprecated license: BSD
Checking should be performed on sources prepared by ‘R CMD build’.
matplot_enrichment_curve: no visible global function definition for
  ‘plot’
matplot_enrichment_curve: no visible global function definition for
  ‘lines’
matplot_enrichment_curve: no visible global function definition for
  ‘legend’
plot_enrichment_curve: no visible global function definition for ‘plot’
plot_enrichment_curve: no visible global function definition for
  ‘lines’
plot_enrichment_curve: no visible global function definition for
  ‘plot.xy’
plot_enrichment_curve: no visible global function definition for
  ‘xy.coords’
plot_enrichment_curve: no visible global function definition for
  ‘rainbow’
plot_enrichment_curve: no visible global function definition for
  ‘axTicks’
plot_enrichment_curve: no visible global function definition for ‘rect’
plot_enrichment_curve: no visible global function definition for ‘axis’
plot_enrichment_curve_xlog: no visible global function definition for
  ‘plot’
plot_enrichment_curve_xlog: no visible global function definition for
  ‘lines’
plot_enrichment_curve_xlog: no visible global function definition for
  ‘plot.xy’
plot_enrichment_curve_xlog: no visible global function definition for
  ‘xy.coords’
plot_enrichment_curve_xlog: no visible global function definition for
  ‘rainbow’
plot_enrichment_curve_xlog: no visible global function definition for
  ‘axTicks’
plot_enrichment_curve_xlog: no visible global function definition for
  ‘rect’
plot_enrichment_curve_xlog: no visible global function definition for
  ‘axis’
Undefined global functions or variables:
  axTicks axis legend lines plot plot.xy rainbow rect xy.coords
Consider adding
  importFrom("grDevices", "rainbow", "xy.coords")
  importFrom("graphics", "axTicks", "axis", "legend", "lines", "plot",
             "plot.xy", "rect")
to your NAMESPACE file.
diffcv: no visible global function definition for ‘sd’
diffcvall: no visible global function definition for ‘sd’
diffcvall: no visible global function definition for ‘fligner.test’
diffcvall: no visible global function definition for ‘p.adjust’
diffcvpFK: no visible global function definition for ‘fligner.test’
diffcvpFK: no visible global function definition for ‘p.adjust’
diffexp: no visible global function definition for ‘var’
diffexp: no visible global function definition for ‘t.test’
diffexp: no visible global function definition for ‘p.adjust’
diffexp2: no visible global function definition for ‘var’
diffexp2: no visible global function definition for ‘t.test’
diffexp2: no visible global function definition for ‘p.adjust’
diffnsepperm: no visible global function definition for ‘p.adjust’
diffseall: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  fligner.test p.adjust sd t.test var
Consider adding
  importFrom("stats", "fligner.test", "p.adjust", "sd", "t.test", "var")
to your NAMESPACE file.
Running ‘testthat.R’ [33s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(envnames)
  > 
  > test_check("envnames")
  
  Environments involved:
  Current environment: <environment: R_GlobalEnv>
  Parent environment of env1: <environment: R_GlobalEnv>
  Parent environment of env2: <environment: R_GlobalEnv>
  Parent environment of env11: <environment: 0xd5be08>
  R_GlobalEnv env_of_envs       envir 
       "env2"      "env2"      "env2" 
  correct memory address: <0x72a5e68> 
  observed result: FALSE 
  ── 1. Failure: T21) is_memory_address(): a string obtained as the memory address
  `observed` not equal to `expected`.
  1 element mismatch
  
  Now inside function g 
  Environment name of calling function (using environmentName() function):  ""
  Environment name of calling function as returned by get_fun_calling(): env1$f
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 265 SKIPPED: 14 FAILED: 1
  1. Failure: T21) is_memory_address(): a string obtained as the memory address of an object is identified as a valid memory address (@test-functions.r#109) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Killed
'library' or 'require' call to ‘plotrix’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘Hmisc’ ‘survival’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘plotrix’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘a.alpha.ade’ ‘a.coladd.ade’ ‘a.getcol.ade’ ‘a.glc’
Rd file 'scatter.ade.Rd':
  \examples lines wider than 100 characters:
     scatter.ade(x, y, g, z, vnames=c("blue","red"), alpha=0.25, xlim=c(-5, 5), zticks=c(1, 2, 3, 4, 5), wall=3)

These lines will be truncated in the PDF manual.
Found the following apparent S3 methods exported but not registered:
  print.corXY print.diffDetect print.epi2x2 print.epiKappa
  print.epiTTest print.mcNemar print.n4means print.n4props
  print.sensSpec print.univar summary.corXY summary.diffDetect
  summary.epi2x2 summary.epiKappa summary.epiTTest summary.mcNemar
  summary.n4means summary.n4props summary.sensSpec summary.univar
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
corXY: no visible global function definition for ‘cor’
corXY: no visible global function definition for ‘pnorm’
corXY: no visible global function definition for ‘qnorm’
diffDetect: no visible global function definition for ‘qnorm’
epi2x2: no visible global function definition for ‘pchisq’
epi2x2: no visible global function definition for ‘fisher.test’
epi2x2: no visible global function definition for ‘qnorm’
epiKappa: no visible global function definition for ‘pnorm’
epiKappa: no visible global function definition for ‘qnorm’
epiTTest: no visible global function definition for ‘sd’
epiTTest: no visible global function definition for ‘var’
epiTTest: no visible global function definition for ‘qt’
epiTTest: no visible global function definition for ‘pt’
mcNemar: no visible global function definition for ‘qnorm’
mcNemar: no visible global function definition for ‘pchisq’
n4means: no visible global function definition for ‘qnorm’
n4props: no visible global function definition for ‘qnorm’
sensSpec: no visible global function definition for ‘qnorm’
univar: no visible global function definition for ‘median’
univar: no visible global function definition for ‘sd’
univar: no visible global function definition for ‘var’
univar: no visible global function definition for ‘qt’
univar: no visible global function definition for ‘pt’
univar: no visible global function definition for ‘shapiro.test’
Undefined global functions or variables:
  cor fisher.test median pchisq pnorm pt qnorm qt sd shapiro.test var
Consider adding
  importFrom("stats", "cor", "fisher.test", "median", "pchisq", "pnorm",
             "pt", "qnorm", "qt", "sd", "shapiro.test", "var")
to your NAMESPACE file.
Rd file 'n4props.Rd':
  \examples lines wider than 100 characters:
     ## Not run: Suppose a new drug is thought to reduce heart attack mortality from 0.10 to 0.03. Calculate the required number of subjects ... [TRUNCATED]

These lines will be truncated in the PDF manual.
plot.eb: no visible global function definition for ‘plot’
plot.eb : <anonymous>: no visible global function definition for
  ‘lines’
plot.ebhistorical: no visible global function definition for ‘palette’
plot.ebhistorical: no visible global function definition for ‘dev.new’
plot.ebhistorical: no visible global function definition for ‘par’
plot.ebhistorical: no visible global function definition for
  ‘topo.colors’
plot.ebhistorical: no visible global function definition for ‘plot’
plot.ebhistorical: no visible global function definition for ‘curve’
plot.ebhistorical: no visible global function definition for ‘lines’
plot.ebhistoricalsummary: no visible global function definition for
  ‘topo.colors’
plot.ebhistoricalsummary: no visible global function definition for
  ‘dev.new’
plot.ebhistoricalsummary: no visible global function definition for
  ‘plot’
plot.ebhistoricalsummary: no visible global function definition for
  ‘axis’
plot.ebhistoricalsummary: no visible global function definition for
  ‘lines’
plot.ebhistoricalsummary: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  axis curve dev.new legend lines palette par plot topo.colors
Consider adding
  importFrom("grDevices", "dev.new", "palette", "topo.colors")
  importFrom("graphics", "axis", "curve", "legend", "lines", "par",
             "plot")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘sync.x64.ffs_db’
DiscrSI : CDFGamma: no visible global function definition for ‘pgamma’
EstimateR : SampleFromPosterior : <anonymous>: no visible global
  function definition for ‘rgamma’
EstimateR: no visible global function definition for ‘rnorm’
EstimateR: no visible binding for global variable ‘sd’
EstimateR: no visible binding for global variable ‘quantile’
EstimateR: no visible binding for global variable ‘median’
EstimateR: no visible global function definition for ‘qgamma’
EstimateR: no visible global function definition for ‘par’
EstimateR: no visible global function definition for ‘title’
EstimateR: no visible global function definition for ‘polygon’
EstimateR: no visible global function definition for ‘lines’
EstimateR: no visible global function definition for ‘legend’
EstimateR: no visible global function definition for ‘hist’
WT : DrawOneSetOfAncestries: no visible global function definition for
  ‘rmultinom’
WT: no visible binding for global variable ‘quantile’
WT: no visible binding for global variable ‘sd’
WT: no visible global function definition for ‘par’
WT: no visible global function definition for ‘segments’
WT: no visible global function definition for ‘points’
WT: no visible global function definition for ‘lines’
WT: no visible global function definition for ‘legend’
Undefined global functions or variables:
  hist legend lines median par pgamma points polygon qgamma quantile
  rgamma rmultinom rnorm sd segments title
Consider adding
  importFrom("graphics", "hist", "legend", "lines", "par", "points",
             "polygon", "segments", "title")
  importFrom("stats", "median", "pgamma", "qgamma", "quantile", "rgamma",
             "rmultinom", "rnorm", "sd")
to your NAMESPACE file.
Rd file 'Flu1918.Rd':
  \examples lines wider than 100 characters:
                     # the estimate of the instantaneous reproduction number over the 7-day window finishing on that day.

Rd file 'Flu2009.Rd':
  \examples lines wider than 100 characters:
                     # the estimate of the instantaneous reproduction number over the 7-day window finishing on that day.

Rd file 'Measles1861.Rd':
  \examples lines wider than 100 characters:
                     EstimateR(Measles1861$Incidence, T.Start=17:42, T.End=23:48, method="NonParametricSI", 
                     # the estimate of the instantaneous reproduction number over the 7-day window finishing on that day.

Rd file 'SARS2003.Rd':
  \examples lines wider than 100 characters:
                     EstimateR(SARS2003$Incidence, T.Start=14:101, T.End=20:107, method="NonParametricSI", 
                     # the estimate of the instantaneous reproduction number over the 7-day window finishing on that day.

Rd file 'Smallpox1972.Rd':
  \examples lines wider than 100 characters:
                     EstimateR(Smallpox1972$Incidence, T.Start=27:51, T.End=33:57, method="NonParametricSI", 
                     # the estimate of the instantaneous reproduction number over the 7-day window finishing on that day.

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  motor_param.cpp:257:5: warning: explicitly assigning value of variable of type 'arma::vec' (aka 'Col<double>') to itself [-Wself-assign-overloaded]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/episode.Rcheck/00install.out’ for details.
plot.episplineDensity: no visible global function definition for ‘plot’
plot.episplineDensity: no visible global function definition for
  ‘points’
postproc: no visible global function definition for ‘plot’
postproc: no visible global function definition for ‘points’
preprocess.data: no visible global function definition for ‘sd’
Undefined global functions or variables:
  plot points sd
Consider adding
  importFrom("graphics", "plot", "points")
  importFrom("stats", "sd")
to your NAMESPACE file.
FCIplot: no visible global function definition for ‘na.omit’
FCIplot: no visible global function definition for ‘plot’
FCIplot: no visible global function definition for ‘tail’
FCIplot: no visible global function definition for ‘grid’
FCIplot: no visible global function definition for ‘polygon’
FCIplot: no visible global function definition for ‘rgb’
linpred: no visible global function definition for ‘lm’
mplott: no visible global function definition for ‘par’
mplott: no visible global function definition for ‘plot’
mplott: no visible global function definition for ‘na.omit’
mplott: no visible global function definition for ‘lines’
mplott: no visible global function definition for ‘legend’
mplott: no visible global function definition for ‘grid’
plott: no visible global function definition for ‘lines’
plott: no visible global function definition for ‘par’
plott: no visible global function definition for ‘plot’
plott: no visible global function definition for ‘grid’
tsideplot: no visible global function definition for ‘par’
tsideplot: no visible global function definition for ‘plot’
tsideplot: no visible global function definition for ‘axis’
tsideplot: no visible global function definition for ‘grid’
Undefined global functions or variables:
  axis grid legend lines lm na.omit par plot polygon rgb tail
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "grid", "legend", "lines", "par",
             "plot", "polygon")
  importFrom("stats", "lm", "na.omit")
  importFrom("utils", "tail")
to your NAMESPACE file.
Package suggested but not available for checking: ‘RCytoscape’
Found the following apparent S3 methods exported but not registered:
  plot.bootsize
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
.getFactor: no visible global function definition for ‘integrate’
check.cumulants: no visible global function definition for ‘runif’
edgeworth: no visible global function definition for ‘dnorm’
eql : getEQL: no visible binding for global variable ‘glm’
eql: no visible global function definition for ‘splinefun’
eql: no visible binding for global variable ‘glm’
eql : <anonymous>: no visible global function definition for ‘glm’
plot.approximation: no visible global function definition for ‘mtext’
plot.eql: no visible global function definition for ‘points’
plot.eql: no visible global function definition for ‘par’
plot.eql: no visible global function definition for ‘segments’
plot.eql: no visible global function definition for ‘qchisq’
plot.eql: no visible global function definition for ‘text’
plot.eql: no visible global function definition for ‘abline’
plot.eql : eql.panel: no visible global function definition for
  ‘qchisq’
plot.eql: no visible global function definition for ‘colorRampPalette’
plot.eql: no visible global function definition for ‘heat.colors’
varianceFamily : devf : <anonymous>: no visible global function
  definition for ‘integrate’
varianceFamily: no visible global function definition for ‘make.link’
Undefined global functions or variables:
  abline colorRampPalette dnorm glm heat.colors integrate make.link
  mtext par points qchisq runif segments splinefun text
Consider adding
  importFrom("grDevices", "colorRampPalette", "heat.colors")
  importFrom("graphics", "abline", "mtext", "par", "points", "segments",
             "text")
  importFrom("stats", "dnorm", "glm", "integrate", "make.link", "qchisq",
             "runif", "splinefun")
to your NAMESPACE file.
eqs2lavaan: no visible global function definition for ‘ignore.case’
eqs2lavaan: no visible global function definition for ‘str_join’
eqs2lavaan: no visible binding for global variable ‘r’
eqsCorr: no visible global function definition for ‘cov2cor’
plotCov: no visible global function definition for ‘cov2cor’
plotCov: no visible global function definition for ‘par’
plotCov: no visible global function definition for ‘image’
plotCov: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis cov2cor ignore.case image par r str_join
Consider adding
  importFrom("graphics", "axis", "image", "par")
  importFrom("stats", "cov2cor")
to your NAMESPACE file.
Non-standard files/directories found at top level:
  ‘docs’ ‘license.txt’ ‘status.txt’
'library' or 'require' call to ‘qtl’ which was already attached by Depends.
  Please remove these calls from your code.
Unexported objects imported by ':::' calls:
  ‘qtl:::c.scanone’ ‘qtl:::plot.scanone’
  See the note in ?`:::` about the use of this operator.
Found the following significant warnings:
  utilities.c:175:32: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Equalden.HD.Rcheck/00install.out’ for details.
The following files contain a license that requires
distribution of original sources:
  ‘upgreek.sty’
Please ensure that you have complied with it.
Found the following apparent S3 methods exported but not registered:
  coef.length.model plot.mcmc.list.ergm plot.network.ergm
  summary.statistics
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
ESA: no visible binding for global variable ‘var’
plot.esabcv: no visible global function definition for ‘plot’
plot.esabcv: no visible global function definition for ‘points’
plot.esabcv: no visible global function definition for ‘axis’
plot.esabcv: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis plot points title var
Consider adding
  importFrom("graphics", "axis", "plot", "points", "title")
  importFrom("stats", "var")
to your NAMESPACE file.
ESEA.Main: no visible global function definition for ‘rnorm’
ESEA.Main: no visible global function definition for ‘sd’
ESEA.Main: no visible global function definition for ‘p.adjust’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘plot’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘lines’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘colors’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘points’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘legend’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘text’
PlotPathwayGraph: no visible global function definition for ‘par’
PlotPathwayGraph: no visible global function definition for ‘plot’
PlotRunEnrichment: no visible global function definition for ‘plot’
PlotRunEnrichment: no visible global function definition for ‘lines’
PlotRunEnrichment: no visible global function definition for ‘colors’
PlotRunEnrichment: no visible global function definition for ‘text’
SavePathway2File: no visible global function definition for ‘is’
calEdgeCorScore: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  colors is legend lines na.omit p.adjust par plot points rnorm sd text
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "legend", "lines", "par", "plot", "points",
             "text")
  importFrom("methods", "is")
  importFrom("stats", "na.omit", "p.adjust", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Non-standard file/directory found at top level:
  ‘ESG-Ex.R’
rAllRisksFactors: no visible global function definition for ‘new’
rAssetDistribution: no visible global function definition for ‘new’
rDefaultSpread: no visible global function definition for ‘new’
rLiquiditySpread: no visible global function definition for ‘new’
rRealEstate: no visible global function definition for ‘new’
rShortRate: no visible global function definition for ‘new’
rStock: no visible global function definition for ‘new’
EuroCall_Stock_PriceDistribution,Scenarios: no visible global function
  definition for ‘pnorm’
EuroCall_ZC_PriceDistribution,Scenarios: no visible global function
  definition for ‘pnorm’
EuroPut_Stock_PriceDistribution,Scenarios: no visible global function
  definition for ‘pnorm’
EuroPut_ZC_PriceDistribution,Scenarios: no visible global function
  definition for ‘pnorm’
MartingaleTest,Scenarios: no visible global function definition for
  ‘plot’
MartingaleTest,Scenarios: no visible global function definition for
  ‘lines’
MartingaleTest,Scenarios: no visible global function definition for
  ‘title’
customPathsGeneration,Scenarios: no visible global function definition
  for ‘rnorm’
Undefined global functions or variables:
  lines new plot pnorm rnorm title
Consider adding
  importFrom("graphics", "lines", "plot", "title")
  importFrom("methods", "new")
  importFrom("stats", "pnorm", "rnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
cv.ES: no visible binding for global variable ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘estoutstorage’
descsto: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.Transition: no visible global function definition for ‘rnorm’
.Transition.DC: no visible global function definition for ‘runif’
CondPdf.CC.interval: no visible global function definition for ‘plot’
CondPdf.DC.interval: no visible global function definition for ‘plot’
Simu.Cond.HR: no visible global function definition for ‘rpois’
Simu.Cond.HR: no visible global function definition for ‘runif’
Simu.Cond.HR: no visible global function definition for ‘hist’
Simu.Cond.HR: no visible global function definition for ‘var’
Simu.HR: no visible global function definition for ‘rpois’
Simu.HR: no visible global function definition for ‘runif’
Simu.HR: no visible global function definition for ‘hist’
Simu.HR: no visible global function definition for ‘var’
Simu.PDMP: no visible global function definition for ‘plot’
Simu.PDMP.DC: no visible global function definition for ‘plot’
plotCHR: no visible global function definition for ‘plot’
plotHR: no visible global function definition for ‘plot’
Undefined global functions or variables:
  hist plot rnorm rpois runif var
Consider adding
  importFrom("graphics", "hist", "plot")
  importFrom("stats", "rnorm", "rpois", "runif", "var")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘Hmisc’ ‘xtable’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
corr_p_cell: no visible global function definition for ‘cov.wt’
iqr_cell: no visible global function definition for ‘quantile’
iqr_cell: no visible global function definition for ‘wtd.quantile’
mean_sd_cell: no visible global function definition for ‘wtd.mean’
mean_sd_cell: no visible global function definition for ‘wtd.var’
mode_cell: no visible global function definition for ‘wtd.table’
quantile_cell: no visible global function definition for ‘wtd.quantile’
quantile_cell: no visible global function definition for ‘quantile’
stat_cell: no visible global function definition for ‘quantile’
stat_cell: no visible global function definition for ‘wtd.quantile’
stat_cell: no visible global function definition for ‘wtd.mean’
stat_cell: no visible global function definition for ‘wtd.var’
stat_cell: no visible global function definition for ‘mad’
stat_cell: no visible global function definition for ‘wtd.table’
Undefined global functions or variables:
  cov.wt mad quantile wtd.mean wtd.quantile wtd.table wtd.var
Consider adding
  importFrom("stats", "cov.wt", "mad", "quantile")
to your NAMESPACE file.
etc.diff: no visible global function definition for ‘model.frame’
etc.diff: no visible binding for global variable ‘sd’
etc.diff: no visible global function definition for ‘qt’
etc.diff: no visible global function definition for ‘pt’
etc.diff: no visible global function definition for ‘wilcox.test’
etc.rat: no visible global function definition for ‘model.frame’
etc.rat: no visible binding for global variable ‘sd’
etc.rat: no visible global function definition for ‘qt’
etc.rat: no visible global function definition for ‘pt’
Undefined global functions or variables:
  model.frame pt qt sd wilcox.test
Consider adding
  importFrom("stats", "model.frame", "pt", "qt", "sd", "wilcox.test")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Loading required package: xml2
trying URL ‘https://ec.europa.eu/eurostat/estat-navtree-portlet-prod/BulkDownloadListing?sort=1&file=data%2Ft2020_rk310.tsv.gz’
Content type 'application/octet-stream;charset=UTF-8' length 4490 bytes
==================================================
downloaded 4490 bytes

Table t2020_rk310 cached at /tmp/RtmppqalQX/eurostat/t2020_rk310_num_code_TF.rds

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

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

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

Quitting from lines 435-447 (eurostat_tutorial.Rmd) 
Error: processing vignette ‘eurostat_tutorial.Rmd’ failed with diagnostics:
no applicable method for ‘xmlAttrs’ applied to an object of class "NULL"
Execution halted
powerSet : <anonymous>: no visible global function definition for
  ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
mposterior: no visible global function definition for ‘optim’
rl.pred: no visible global function definition for ‘matplot’
rl.pst: no visible binding for global variable ‘quantile’
rl.pst: no visible global function definition for ‘matplot’
Undefined global functions or variables:
  matplot optim quantile
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "optim", "quantile")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘TODO.md’
make_dyads : ff: no visible global function definition for ‘aggregate’
make_scale: no visible global function definition for ‘read.csv’
plot_dyad: no visible global function definition for ‘is’
read_eventdata : read_ed_file: no visible global function definition
  for ‘read.csv’
Undefined global functions or variables:
  aggregate is read.csv
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "aggregate")
  importFrom("utils", "read.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
evolvabilityBetaMCMC : <anonymous>: no visible binding for global
  variable ‘median’
evolvabilityBetaMCMC: no visible binding for global variable ‘median’
evolvabilityBetaMCMC2: no visible binding for global variable ‘median’
evolvabilityMeans: no visible global function definition for ‘var’
evolvabilityMeansMCMC : <anonymous>: no visible global function
  definition for ‘var’
evolvabilityMeansMCMC: no visible binding for global variable ‘median’
randomBeta: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  median rnorm var
Consider adding
  importFrom("stats", "median", "rnorm", "var")
to your NAMESPACE file.
DPOT: no visible global function definition for ‘optim’
mop.rho: no visible global function definition for ‘median’
Undefined global functions or variables:
  median optim
Consider adding
  importFrom("stats", "median", "optim")
to your NAMESPACE file.
EW : PhiP : Phi: no visible global function definition for ‘pnorm’
EWplot: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot pnorm
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "pnorm")
to your NAMESPACE file.
BinomialCIone: no visible global function definition for ‘na.omit’
PairedCIone: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
build.mcx.obj: no visible global function definition for ‘glm’
build.mcx.obj: no visible binding for global variable ‘poisson’
build.mcx.obj: no visible global function definition for ‘fitted’
cab: no visible global function definition for ‘rbinom’
cab: no visible global function definition for ‘runif’
mcexact: no visible global function definition for ‘update’
rounded.tprob: no visible global function definition for ‘pt’
simtable.cab: no visible global function definition for ‘rbinom’
simtable.cab: no visible global function definition for ‘runif’
Undefined global functions or variables:
  fitted glm poisson pt rbinom runif update
Consider adding
  importFrom("stats", "fitted", "glm", "poisson", "pt", "rbinom",
             "runif", "update")
to your NAMESPACE file.
Found the following assignments to the global environment:
File ‘exams/R/xexams.R’:
  assign(".xweave_svg_grdevice", .xweave_svg_grdevice, envir = .GlobalEnv)
plot.pgrid: no visible global function definition for ‘image’
statistic.cv: no visible global function definition for ‘quantile’
statistic.sim: no visible global function definition for ‘contourLines’
Undefined global functions or variables:
  contourLines image quantile
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "image")
  importFrom("stats", "quantile")
to your NAMESPACE file.
countBamInGRanges.exomeDepth: no visible global function definition for
  ‘as’
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
print.cdf : numform: warning in formatC(x, dig = digits): partial
  argument match of ‘dig’ to ‘digits’
print.cdf: warning in get("x", env = environment(x)): partial argument
  match of ‘env’ to ‘envir’
print.cdf: warning in get("y", env = environment(x)): partial argument
  match of ‘env’ to ‘envir’
print.ogive : numform: warning in formatC(x, dig = digits): partial
  argument match of ‘dig’ to ‘digits’
print.ogive: warning in get("x", env = environment(x)): partial
  argument match of ‘env’ to ‘envir’
print.ogive: warning in get("y", env = environment(x)): partial
  argument match of ‘env’ to ‘envir’
quantile.expert: warning in formatC(paste(100 * probs, "%", sep = ""),
  format = "fg", wid = 1, digits = dig): partial argument match of
  ‘wid’ to ‘width’
MS: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Package in Depends field not imported from: ‘prettyGraphs’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  print.epCA print.epGPCA print.epGraphs print.epMCA print.epMDS
  print.epPCA print.epSVD print.expoOutput
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
computeConstraints: no visible global function definition for
  ‘minmaxHelper’
coreCA: no visible global function definition for ‘repmat’
coreMDS: no visible global function definition for ‘repmat’
corePCA: no visible global function definition for ‘repmat’
epGraphs: no visible global function definition for
  ‘createColorVectorsByDesign’
epGraphs: no visible global function definition for ‘prettyPlot’
epGraphs: no visible global function definition for ‘contributionBars’
expo.scale: no visible binding for global variable ‘sd’
makeDistancesAndWeights: no visible global function definition for
  ‘cor’
makeDistancesAndWeights: no visible global function definition for
  ‘dist’
makeNominalData: no visible global function definition for ‘repmat’
mca.eigen.fix: no visible global function definition for ‘repmat’
pcaSupplementaryColsPreProcessing: no visible global function
  definition for ‘repmat’
pcaSupplementaryRowsPreProcessing: no visible global function
  definition for ‘repmat’
rowNorms: no visible global function definition for ‘repmat’
supplementalProjection: no visible global function definition for
  ‘repmat’
Undefined global functions or variables:
  contributionBars cor createColorVectorsByDesign dist minmaxHelper
  prettyPlot repmat sd
Consider adding
  importFrom("stats", "cor", "dist", "sd")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘ape’ ‘deSolve’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
expoTree.optim: no visible global function definition for ‘optim’
node.age: no visible global function definition for ‘is.binary.tree’
node.age: no visible global function definition for ‘multi2di’
plotLTT: no visible global function definition for ‘rgb’
plotLTT: no visible global function definition for ‘par’
plotLTT: no visible global function definition for ‘lines’
plotLTT: no visible global function definition for ‘axis’
plotLTT: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  axis is.binary.tree lines mtext multi2di optim par rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "lines", "mtext", "par")
  importFrom("stats", "optim")
to your NAMESPACE file.
index.citations: no visible global function definition for
  ‘txtProgressBar’
read.exsic: no visible global function definition for ‘read.csv’
update.pb: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  read.csv setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "read.csv", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Package in Depends field not imported from: ‘rmeta’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
extfunnel: no visible global function definition for ‘qnorm’
extfunnel: no visible global function definition for ‘meta.summaries’
extfunnel: no visible global function definition for ‘flush.console’
extfunnel: no visible global function definition for ‘qt’
extfunnel: no visible global function definition for ‘dev.new’
extfunnel: no visible global function definition for ‘par’
extfunnel: no visible global function definition for ‘plot’
extfunnel: no visible global function definition for ‘polygon’
extfunnel: no visible global function definition for ‘segments’
extfunnel: no visible global function definition for ‘abline’
extfunnel: no visible global function definition for ‘axis’
extfunnel: no visible global function definition for ‘box’
Undefined global functions or variables:
  abline axis box dev.new flush.console meta.summaries par plot polygon
  qnorm qt segments
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axis", "box", "par", "plot",
             "polygon", "segments")
  importFrom("stats", "qnorm", "qt")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
bars: no visible global function definition for ‘segments’
cv.binomial: no visible binding for global variable ‘var’
cv.binomial: no visible global function definition for ‘abline’
cv.normal: no visible binding for global variable ‘var’
cv.normal: no visible global function definition for ‘abline’
cv.poisson: no visible binding for global variable ‘var’
cv.poisson: no visible global function definition for ‘abline’
plot.extlasso: no visible global function definition for ‘matplot’
plot.extlasso: no visible global function definition for ‘axis’
Undefined global functions or variables:
  abline axis matplot segments var
Consider adding
  importFrom("graphics", "abline", "axis", "matplot", "segments")
  importFrom("stats", "var")
to your NAMESPACE file.
exbio: no visible global function definition for ‘as.formula’
exbio: no visible global function definition for ‘glm’
exbio: no visible binding for global variable ‘gaussian’
exbio: no visible global function definition for ‘Gamma’
exbio: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  Gamma as.formula gaussian glm pchisq
Consider adding
  importFrom("stats", "Gamma", "as.formula", "gaussian", "glm", "pchisq")
to your NAMESPACE file.
Rd file 'exbio.Rd':
  \usage lines wider than 90 characters:
     exbio(R, R.alt, cc, n, tol = 0.001, a.start = 1, b.start = 1, max.it = 1000, digits = NULL, model.maf = TRUE)

These lines will be truncated in the PDF manual.
font_install: no visible global function definition for
  ‘installed.packages’
font_install: no visible global function definition for
  ‘install.packages’
fonttable_add: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  install.packages installed.packages write.csv
Consider adding
  importFrom("utils", "install.packages", "installed.packages",
             "write.csv")
to your NAMESPACE file.
toJavaMatrix2D: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
bootstrapCMLE: no visible global function definition for ‘qweibull’
bootstrapCMLE: no visible binding for global variable ‘sd’
bootstrapCMLE: no visible global function definition for ‘quantile’
bootstrapCenWbMix: no visible binding for global variable ‘sd’
bootstrapCenWbMix: no visible global function definition for ‘quantile’
cenWeibullMLE: no visible global function definition for ‘sd’
expmx.p2.censor: no visible global function definition for ‘dweibull’
expmx.p2.censor: no visible global function definition for ‘pweibull’
genWbMixIni: no visible global function definition for ‘runif’
log.llh.p2.censor: no visible global function definition for ‘dweibull’
log.llh.p2.censor: no visible global function definition for ‘pweibull’
quanWbMix : t.fun: no visible global function definition for ‘pweibull’
quanWbMix: no visible global function definition for ‘uniroot’
quanWbMix.int : t.fun: no visible global function definition for
  ‘pweibull’
quanWbMix.int: no visible global function definition for ‘uniroot’
simWbMix: no visible global function definition for ‘rbinom’
simWbMix: no visible global function definition for ‘rweibull’
Undefined global functions or variables:
  dweibull pweibull quantile qweibull rbinom runif rweibull sd uniroot
Consider adding
  importFrom("stats", "dweibull", "pweibull", "quantile", "qweibull",
             "rbinom", "runif", "rweibull", "sd", "uniroot")
to your NAMESPACE file.
Rd file 'distance2point.Rd':
  \usage lines wider than 90 characters:
     distance2point(x, y, viewerDistance, viewerHeight, resolutionX, resolutionY, screenWidth, screenHeight)
  \examples lines wider than 100 characters:
     function( x, y, viewerDistance, viewerHeight, resolutionX, resolutionY, screenWidth, screenHeight ) {

Rd file 'subtendedAngle.Rd':
  \usage lines wider than 90 characters:
     subtendedAngle(x1, y1, x2, y2, viewerDistance = 58.74, viewerHeight = 4.55, resolutionX = 1280, resolutionY = 1024, screenWidth = 33.97 ... [TRUNCATED]
  \examples lines wider than 100 characters:
     function( x1, y1, x2, y2, viewerDistance=58.74, viewerHeight=4.55, resolutionX=1280, resolutionY=1024, screenWidth=33.97, screenHeight= ... [TRUNCATED]
         d1 <- distance2point(x1, y1, viewerDistance, viewerHeight, resolutionX, resolutionY, screenWidth, screenHeight)
         d2 <- distance2point(x2, y2, viewerDistance, viewerHeight, resolutionX, resolutionY, screenWidth, screenHeight)

These lines will be truncated in the PDF manual.
Malformed Description field: should contain one or more complete sentences.
BugReports field is not a suitable URL but contains an email address
  which will be used as from R 3.4.0
createFormula: no visible global function definition for ‘tail’
createFormula: no visible global function definition for ‘head’
createFormula: no visible global function definition for ‘as.formula’
ezsim: no visible global function definition for ‘runif’
plot.ezsim: no visible global function definition for ‘quantile’
plot.ezsim: no visible global function definition for ‘head’
plot.ezsim: no visible global function definition for ‘tail’
plot.ezsim: no visible global function definition for ‘plot’
plot.ezsim: no visible binding for global variable ‘dnorm’
plot.ezsim: no visible binding for global variable ‘pdf’
plot.ezsim: no visible global function definition for ‘dev.off’
plot.ezsim : <anonymous>: no visible global function definition for
  ‘dev.new’
plot.summary.ezsim: no visible global function definition for ‘head’
plot.summary.ezsim: no visible global function definition for ‘tail’
plot.summary.ezsim: no visible binding for global variable ‘pdf’
plot.summary.ezsim: no visible global function definition for ‘dev.off’
plot.summary.ezsim : <anonymous>: no visible global function definition
  for ‘dev.new’
Undefined global functions or variables:
  as.formula dev.new dev.off dnorm head pdf plot quantile runif tail
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("graphics", "plot")
  importFrom("stats", "as.formula", "dnorm", "quantile", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
gibbs2: no visible global function definition for ‘rnorm’
gibbs_sampling: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
fma: no visible global function definition for ‘factanal’
fma: no visible global function definition for ‘runif’
fma: no visible global function definition for ‘kmeans’
fma: no visible global function definition for ‘var’
fma.em.alg: no visible global function definition for ‘var’
misc : q: no visible global function definition for ‘name’
Undefined global functions or variables:
  factanal kmeans name runif var
Consider adding
  importFrom("stats", "factanal", "kmeans", "runif", "var")
to your NAMESPACE file.
Rd file 'fma.Rd':
  \usage lines wider than 90 characters:
     fma(y, k, r, x.z = NULL, x.w = NULL, it = 15, eps = 1e-04, seed = 4, scaling = FALSE, init = NULL)

These lines will be truncated in the PDF manual.
Packages in Depends field not imported from:
  ‘RCurl’ ‘RJSONIO’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
createFactualConnection: no visible global function definition for
  ‘new’
factualGetSchema: no visible global function definition for ‘fromJSON’
factualRead: no visible global function definition for ‘curlEscape’
factualRead: no visible global function definition for ‘fromJSON’
processFactualReadJSON: no visible global function definition for ‘new’
processFactualSchemaJSON: no visible global function definition for
  ‘new’
Undefined global functions or variables:
  curlEscape fromJSON new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Rd file 'factualR.Rd':
  \usage lines wider than 90 characters:
     factualRead(connection , tableID , sort = NULL , limit = NULL , offset = NULL , filters = NULL , subject_key = NULL , reformatNames , v ... [TRUNCATED]

These lines will be truncated in the PDF manual.
faisalconjoint: no visible global function definition for ‘barplot’
faisalconjoint: no visible global function definition for ‘text’
faisalconjoint: no visible global function definition for ‘jpeg’
faisalconjoint: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  barplot dev.off jpeg text
Consider adding
  importFrom("grDevices", "dev.off", "jpeg")
  importFrom("graphics", "barplot", "text")
to your NAMESPACE file.
Found the following significant warnings:

  Warning: 'devtools::create' is deprecated.
  Warning: 'setup' is deprecated.
  Warning: 'create_description' is deprecated.
  Warning: 'use_rstudio' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Error in re-building vignettes:
  ...
Creating package 'fakepack' in '/tmp/Rtmp3couZn'
No DESCRIPTION found. Creating with values:


Prerequisite DESCRIPTION found.
Prerequisite R/throw.R found.
Prerequisite R/throw.R found.
Prerequisite R/throw.R found.
Prerequisite R/throw.R found.
* installing *source* package ‘fakepack’ ...
** R
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  ‘fakepack’ 
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (fakepack)
Prerequisite R/throw.R found.
Prerequisite R/throw.R found.
Prerequisite DESCRIPTION found.
Prerequisite R/throw.R found.
Error: processing vignette ‘An_Introduction_to_fakemake.Rmd’ failed with diagnostics:
there is no package called 'spelling'
Execution halted
File ‘fame/R/windows/zzz.R’:
  .onLoad calls:
    packageStartupMessage("FAME environment variable not set; assuming ",     defaultDir)
    packageStartupMessage("FAME directory ", fameDir, " not found.\n",     "If you have FAME installed, specify it's location ", "via the FAME environment variable.\n",     "Otherwise, this package is pretty useless.\n")

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Aggregation : foo: no visible global function definition for
  ‘weighted.mean’
Aggregation: no visible global function definition for ‘txtProgressBar’
Aggregation: no visible global function definition for
  ‘setTxtProgressBar’
constructSYB: no visible global function definition for ‘str’
fillCountryCode: no visible global function definition for ‘na.omit’
getFAO: no visible global function definition for ‘read.csv’
getWDImetaData: no visible global function definition for ‘write.csv’
getWDItoSYB: no visible global function definition for ‘na.omit’
lsgr: no visible global function definition for ‘na.omit’
lsgr: no visible global function definition for ‘coef’
lsgr: no visible global function definition for ‘lm’
Undefined global functions or variables:
  coef lm na.omit read.csv setTxtProgressBar str txtProgressBar
  weighted.mean write.csv
Consider adding
  importFrom("stats", "coef", "lm", "na.omit", "weighted.mean")
  importFrom("utils", "read.csv", "setTxtProgressBar", "str",
             "txtProgressBar", "write.csv")
to your NAMESPACE file.
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_LIBS but not in PKG_CXXFLAGS
  src/Makevars: it is not portable to include SHLIB_OPENMP_*' macros in PKG_CPPFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
PKG_CPPFLAGS is used for both C and C++ code so it is not portable to
use it for these macros.
basis_hica: no visible global function definition for ‘princomp’
energy_hica: no visible global function definition for ‘dev.new’
energy_hica: no visible global function definition for ‘points’
energy_hica: no visible global function definition for ‘legend’
Undefined global functions or variables:
  dev.new legend points princomp
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "points")
  importFrom("stats", "princomp")
to your NAMESPACE file.
Package suggested but not available for checking: ‘coxKM’
File ‘fastmatch/libs/fastmatch.so’:
  Found non-API call to R: ‘match5’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/FastRWeb.Rcheck/00install.out’ for details.
.run: no visible binding for global variable ‘init’
.run: no visible global function definition for ‘init’
.run: no visible binding for global variable ‘run’
Undefined global functions or variables:
  init run
Note: information on .o files is not available
FBN.histogramMaxima: no visible global function definition for ‘hist’
FBN.kmeans: no visible global function definition for ‘median’
FBN.kmeans: no visible global function definition for ‘kmeans’
FBNormalization: no visible global function definition for ‘read.table’
FBNormalization: no visible global function definition for ‘median’
FBNormalization: no visible global function definition for ‘hist’
FBNormalization: no visible global function definition for ‘par’
FBNormalization: no visible global function definition for ‘dev.print’
FBNormalization: no visible binding for global variable ‘bmp’
FBNormalization: no visible global function definition for ‘sd’
FBNormalization: no visible global function definition for
  ‘write.table’
medianFilter: no visible global function definition for ‘median’
Undefined global functions or variables:
  bmp dev.print hist kmeans median par read.table sd write.table
Consider adding
  importFrom("grDevices", "bmp", "dev.print")
  importFrom("graphics", "hist", "par")
  importFrom("stats", "kmeans", "median", "sd")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Rd file 'FBNormalization.Rd':
  \usage lines wider than 90 characters:
             normDataFileName = NULL, debugFlag = FALSE, plotFlag = FALSE, plotAndSaveFlag = FALSE)

These lines will be truncated in the PDF manual.
'library' or 'require' calls in package code:
  ‘RCurl’ ‘RJSONIO’ ‘XML’ ‘glmnet’ ‘httr’ ‘speedglm’ ‘tcltk’ ‘xtable’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘MASS’ ‘combinat’ ‘glmnet’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fcd.cluster: no visible global function definition for ‘kmeans’
fcd.start: no visible global function definition for ‘ginv’
fcd.start: no visible global function definition for ‘glmnet’
gen.dcbm: no visible global function definition for ‘rbinom’
gen.sbm: no visible global function definition for ‘rbinom’
mis.cluster: no visible global function definition for ‘permn’
spectral.clustering: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  ginv glmnet kmeans permn rbinom
Consider adding
  importFrom("stats", "kmeans", "rbinom")
to your NAMESPACE file.
PTSingleAssetBarrierOption2: no visible global function definition for
  ‘new’
newton: no visible global function definition for ‘plot’
newton: no visible global function definition for ‘abline’
probInRange: no visible global function definition for ‘pnorm’
shortfall_risk: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline new plot pnorm
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("methods", "new")
  importFrom("stats", "pnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
  Warning: 'cBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
      user system elapsed
fcr 10.335  0.566  11.954
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: rainbow
Loading required package: MASS
Loading required package: pcaPP
Loading required package: RCurl
Loading required package: bitops
Killed
asymp.vcov: no visible global function definition for ‘cov’
corFDG: no visible global function definition for ‘cor’
g.exponential: no visible global function definition for ‘integrate’
rho.exponential: no visible global function definition for ‘integrate’
rho.sinus: no visible global function definition for ‘integrate’
tau.exponential: no visible global function definition for ‘integrate’
tau.sinus: no visible global function definition for ‘integrate’
tfun.sinus.rho: no visible global function definition for ‘integrate’
wlsdc: no visible global function definition for ‘optim’
Undefined global functions or variables:
  cor cov integrate optim
Consider adding
  importFrom("stats", "cor", "cov", "integrate", "optim")
to your NAMESPACE file.
FDRreg: no visible global function definition for ‘dnorm’
colnormalize: no visible global function definition for ‘sd’
efron: no visible global function definition for ‘median’
efron: no visible global function definition for ‘hist’
efron: no visible global function definition for ‘glm’
efron: no visible binding for global variable ‘poisson’
efron: no visible global function definition for ‘qchisq’
efron: no visible global function definition for ‘predict’
efron: no visible global function definition for ‘quantile’
efron: no visible global function definition for ‘lm’
efron: no visible global function definition for ‘coef’
make.bspline.matrix: no visible global function definition for
  ‘quantile’
plotFDR: no visible global function definition for ‘hist’
plotFDR: no visible global function definition for ‘par’
plotFDR: no visible global function definition for ‘plot’
plotFDR: no visible global function definition for ‘axis’
plotFDR: no visible global function definition for ‘lines’
plotFDR: no visible global function definition for ‘legend’
plotFDR: no visible global function definition for ‘rug’
plotFDR: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis coef dnorm glm hist legend lines lm median par plot poisson
  predict qchisq quantile rug sd title
Consider adding
  importFrom("graphics", "axis", "hist", "legend", "lines", "par",
             "plot", "rug", "title")
  importFrom("stats", "coef", "dnorm", "glm", "lm", "median", "poisson",
             "predict", "qchisq", "quantile", "sd")
to your NAMESPACE file.
read.hmd: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  print.express.certificate
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
'library' or 'require' calls in package code:
  ‘ggplot2’ ‘gridExtra’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
FFieldPtRepDemo: no visible global function definition for ‘ggplot’
FFieldPtRepDemo: no visible binding for global variable ‘mtcars’
FFieldPtRepDemo: no visible global function definition for ‘aes’
FFieldPtRepDemo: no visible binding for global variable ‘mpg’
FFieldPtRepDemo: no visible global function definition for ‘geom_point’
FFieldPtRepDemo: no visible global function definition for ‘geom_text’
FFieldPtRepDemo: no visible global function definition for ‘ggtitle’
FFieldPtRepDemo: no visible global function definition for
  ‘geom_segment’
FFieldPtRepDemo: no visible global function definition for
  ‘grid.arrange’
Undefined global functions or variables:
  aes geom_point geom_segment geom_text ggplot ggtitle grid.arrange mpg
  mtcars
Consider adding
  importFrom("datasets", "mtcars")
to your NAMESPACE file.
ffmanova: no visible global function definition for ‘model.matrix’
ffmanova: no visible global function definition for ‘model.response’
linregEnd: no visible binding for global variable ‘end’
my_pValueF: no visible global function definition for ‘pf’
print.ffmanova: no visible global function definition for
  ‘printCoefmat’
rotationtest: no visible binding for global variable ‘end’
rotationtest: no visible global function definition for ‘flush.console’
rotationtest: no visible global function definition for ‘rnorm’
stdize: no visible binding for global variable ‘var’
unitest: no visible global function definition for ‘pf’
Undefined global functions or variables:
  end flush.console model.matrix model.response pf printCoefmat rnorm
  var
Consider adding
  importFrom("stats", "end", "model.matrix", "model.response", "pf",
             "printCoefmat", "rnorm", "var")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
ftest: no visible global function definition for ‘wilcox.test’
ftest: no visible global function definition for ‘t.test’
Undefined global functions or variables:
  t.test wilcox.test
Consider adding
  importFrom("stats", "t.test", "wilcox.test")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  .plot.garch.1 .plot.garch.10 .plot.garch.11 .plot.garch.12
  .plot.garch.13 .plot.garch.2 .plot.garch.3 .plot.garch.4
  .plot.garch.5 .plot.garch.6 .plot.garch.7 .plot.garch.8 .plot.garch.9
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Packages in Depends field not imported from:
  ‘mvtnorm’ ‘numDeriv’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dmymvnorm: no visible global function definition for ‘dmvnorm’
dmymvt: no visible global function definition for ‘dmvt’
gof.test: no visible global function definition for ‘quantile’
gof.test : ecdf: no visible global function definition for ‘mecdf’
gof.test: no visible global function definition for ‘jacobian’
gof.test: no visible global function definition for ‘var’
gradCdfT: no visible global function definition for ‘dt’
gradCdfT: no visible global function definition for ‘pt’
gradCdfT: no visible global function definition for ‘pmvt’
influFun: no visible global function definition for ‘jacobian’
mult.sim: no visible global function definition for ‘rnorm’
plackettFormula: no visible global function definition for ‘pt’
plackettFormula: no visible global function definition for ‘pmvt’
pmymvnorm: no visible global function definition for ‘GenzBretz’
pmymvnorm: no visible global function definition for ‘TVPACK’
pmymvnorm : <anonymous>: no visible global function definition for
  ‘pmvnorm’
pmymvt: no visible global function definition for ‘GenzBretz’
pmymvt: no visible global function definition for ‘TVPACK’
pmymvt : <anonymous>: no visible global function definition for ‘pmvt’
rmymvnorm: no visible global function definition for ‘rmvnorm’
rmymvt: no visible global function definition for ‘rmvt’
Undefined global functions or variables:
  GenzBretz TVPACK dmvnorm dmvt dt jacobian mecdf pmvnorm pmvt pt
  quantile rmvnorm rmvt rnorm var
Consider adding
  importFrom("stats", "dt", "pt", "quantile", "rnorm", "var")
to your NAMESPACE file.
fgeasy: no visible global function definition for ‘dist’
fgeasy : cor.est: no visible global function definition for ‘cor.test’
fgeasy: no visible binding for global variable ‘var’
fgperm : runrand: no visible global function definition for ‘runif’
fgperm : runrand: no visible global function definition for ‘ave’
fgploc : runrand: no visible global function definition for ‘runif’
fgploc : runrand: no visible global function definition for ‘ave’
fyshuffle: no visible global function definition for ‘runif’
plot.fg: no visible global function definition for ‘par’
plot.fg: no visible global function definition for ‘plot’
plot.fg: no visible global function definition for ‘segments’
plot.fg: no visible binding for global variable ‘quantile’
plot.fg: no visible global function definition for ‘abline’
plot.fg: no visible global function definition for ‘axis’
summary.fg: no visible binding for global variable ‘quantile’
Undefined global functions or variables:
  abline ave axis cor.test dist par plot quantile runif segments var
Consider adding
  importFrom("graphics", "abline", "axis", "par", "plot", "segments")
  importFrom("stats", "ave", "cor.test", "dist", "quantile", "runif",
             "var")
to your NAMESPACE file.
fieldsim: no visible global function definition for ‘rnorm’
midpoint: no visible global function definition for ‘rnorm’
setAtlas_under: no visible global function definition for ‘runif’
setCovf_under : Ibeta: no visible global function definition for
  ‘pbeta’
visualize: no visible global function definition for ‘colorRampPalette’
Undefined global functions or variables:
  colorRampPalette pbeta rnorm runif
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "pbeta", "rnorm", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘filehash’ ‘DBI’
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  ‘RSQLite’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
createSQLite: no visible global function definition for ‘dbDriver’
createSQLite: no visible global function definition for ‘dbConnect’
createSQLite: no visible global function definition for
  ‘dbUnloadDriver’
createSQLite: no visible global function definition for ‘dbGetQuery’
initializeSQLite: no visible global function definition for ‘dbDriver’
initializeSQLite: no visible global function definition for ‘dbConnect’
initializeSQLite: no visible global function definition for ‘new’
dbDelete,filehashSQLite-character: no visible global function
  definition for ‘dbGetQuery’
dbDisconnect,filehashSQLite: no visible global function definition for
  ‘dbUnloadDriver’
dbFetch,filehashSQLite-character: no visible global function definition
  for ‘dbGetQuery’
dbInsert,filehashSQLite-character: no visible global function
  definition for ‘dbGetQuery’
dbList,filehashSQLite: no visible global function definition for
  ‘dbGetQuery’
dbMultiFetch,filehashSQLite-character: no visible global function
  definition for ‘dbGetQuery’
Undefined global functions or variables:
  dbConnect dbDriver dbGetQuery dbUnloadDriver new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' call to ‘tkrplot’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘methods’ ‘tkrplot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'POICalc.Rd':
  \examples lines wider than 100 characters:
        irisPOI@wordsInQuery <- c('high.Sepal.Length', 'high.Sepal.Width', 'high.Petal.Length', 'high.Petal.Width',
                                  'low.Sepal.Length', 'low.Sepal.Width', 'low.Petal.Length', 'low.Petal.Width')

Rd file 'POIcoords_-.Rd':
  \examples lines wider than 100 characters:
        irisPOI@wordsInQuery <- c('high.Sepal.Length', 'high.Sepal.Width', 'high.Petal.Length', 'high.Petal.Width',
                                  'low.Sepal.Length', 'low.Sepal.Width', 'low.Petal.Length', 'low.Petal.Width')

Rd file 'plotPOI.Rd':
  \examples lines wider than 100 characters:
          graphPOI@docs <- matrix(c(seq(1:nrow(graphPOI@objeto)), seq(1:nrow(graphPOI@objeto))), ncol = 2)
        graphPOI@objeto <- graphPOI@objeto <- rbind(c(0,.05), c(.05,0), c(0,-.05), c(-.05,0) ,round(circulo(0,0,.3,PLOT = FALSE),2))
         1 - (max(USArrests[,4]) - USArrests[,4]) / (max(max(USArrests[,4]) - USArrests[,4])),                                               ... [TRUNCATED]
        usaPOI@wordsInQuery <- c(paste('High', names(USArrests[,c(1,2,4)])), paste('Low', names(USArrests[,c(1,2,4)])))

These lines will be truncated in the PDF manual.
lsmacof: no visible global function definition for ‘cmdscale’
plotInc: no visible global function definition for ‘rainbow’
plotInc: no visible global function definition for ‘plot’
prepareCalib: no visible global function definition for ‘lm’
Undefined global functions or variables:
  cmdscale lm plot rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "plot")
  importFrom("stats", "cmdscale", "lm")
to your NAMESPACE file.
fishmove : coefs: no visible global function definition for ‘coef’
fishmove : coefs: no visible global function definition for ‘pf’
fishmove: no visible global function definition for ‘lm’
fishmove: no visible global function definition for ‘predict.lm’
fishmove.estimate: no visible global function definition for ‘quantile’
fishmove.estimate : ddoublenorm: no visible global function definition
  for ‘dnorm’
fishmove.query: no visible global function definition for ‘hasArg’
fishmove.query : f: no visible global function definition for ‘pnorm’
fishmove.query: no visible global function definition for ‘uniroot’
pdk: no visible global function definition for ‘hasArg’
pdk : eq: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  coef dnorm hasArg lm pf pnorm predict.lm quantile uniroot
Consider adding
  importFrom("methods", "hasArg")
  importFrom("stats", "coef", "dnorm", "lm", "pf", "pnorm", "predict.lm",
             "quantile", "uniroot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Depends: includes the non-default packages:
  'gWidgets', 'tcltk', 'tkrplot', 'RGtk2', 'gWidgetsRGtk2',
  'cairoDevice'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Non-standard file/directory found at top level:
  ‘NAMESPACE.txt’
'library' or 'require' calls to packages already attached by Depends:
  ‘RGtk2’ ‘cairoDevice’ ‘gWidgets’ ‘gWidgetsRGtk2’ ‘tcltk’ ‘tkrplot’
  Please remove these calls from your code.
Package in Depends field not imported from: ‘FitAR’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  fitted.FitARMA
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
FitARMA: no visible global function definition for ‘PacfDL’
FitARMA: no visible global function definition for ‘GetARMeanMLE’
FitARMA: no visible global function definition for
  ‘BackcastResidualsAR’
FitARMA: no visible global function definition for ‘acf’
FitARMA: no visible global function definition for ‘LjungBoxTest’
FitARMA: no visible global function definition for ‘tsp’
GetFitARMA: no visible global function definition for ‘LoglikelihoodAR’
GetFitARMA: no visible global function definition for ‘ChampernowneD’
GetFitARMA : EntropyARMA: no visible global function definition for
  ‘PacfToAR’
GetFitARMA : EntropyARMA: no visible global function definition for
  ‘PacfDL’
GetFitARMA : EntropyARMA: no visible global function definition for
  ‘FastLoglikelihoodAR’
GetFitARMA: no visible global function definition for ‘optim’
GetFitARMA: no visible global function definition for ‘PacfToAR’
InformationMatrixARMA: no visible global function definition for
  ‘InvertibleQ’
InformationMatrixARMA: no visible global function definition for
  ‘toeplitz’
SimulateGaussianARMA: no visible global function definition for ‘rnorm’
SimulateGaussianARMA: no visible global function definition for
  ‘toeplitz’
TacvfARMA: no visible global function definition for ‘InvertibleQ’
Undefined global functions or variables:
  BackcastResidualsAR ChampernowneD FastLoglikelihoodAR GetARMeanMLE
  InvertibleQ LjungBoxTest LoglikelihoodAR PacfDL PacfToAR acf optim
  rnorm toeplitz tsp
Consider adding
  importFrom("stats", "acf", "optim", "rnorm", "toeplitz", "tsp")
to your NAMESPACE file.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’ ‘leaps’ ‘ltsa’
A package should be listed in only one of these fields.
Package in Depends field not imported from: ‘bestglm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'GetLeapsAR.Rd':
  \usage lines wider than 90 characters:
     GetLeapsAR(z, lag.max = 15, Criterion = "UBIC", Best = 3, Candidates=5, t="default", ExactQ=FALSE)

Rd file 'PlotARSdf.Rd':
  \usage lines wider than 90 characters:
     PlotARSdf(phi = NULL, theta = NULL, units = "radial", logSdf = FALSE, InnovationVariance = 1, main = NULL, sub = NULL, lwd=3, col="blue ... [TRUNCATED]

Rd file 'SelectModel.Rd':
  \usage lines wider than 90 characters:
     SelectModel(z, lag.max = 15, ARModel = c("AR", "ARz", "ARp"), Criterion = "default", Best = 3, Candidates = 5, t="default")

Rd file 'UnitRootTest.Rd':
  \usage lines wider than 90 characters:
     UnitRootTest(z, method = c("MLE", "ExactMLE", "LS", "All"), statistic = c("Z", "T"), NumBoot = 1000, PValueMethod = c("DH", "ET"))

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: ‘ExtDist’
'library' or 'require' calls in package code:
  ‘devEMF’ ‘doMC’ ‘foreach’ ‘grDevices’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: ‘ActuDistns’
Missing or unexported object: ‘ggmap::has_goog_key’
src/Makevars.win: SHLIB_OPENMP_FCFLAGS is included in PKG_FCFLAGS but not in PKG_LIBS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
RIind: no visible global function definition for ‘aggregate’
RIind: no visible binding for global variable ‘sd’
RIpop: no visible global function definition for ‘aggregate’
RIpop: no visible binding for global variable ‘sd’
SI: no visible global function definition for ‘sd’
SI2: no visible global function definition for ‘sd’
SI3: no visible global function definition for ‘aggregate’
SI3: no visible global function definition for ‘pairs’
SI3: no visible global function definition for ‘cor’
SI4: no visible global function definition for ‘aggregate’
SI4: no visible global function definition for ‘sd’
fCV: no visible global function definition for ‘sd’
Undefined global functions or variables:
  aggregate cor pairs sd
Consider adding
  importFrom("graphics", "pairs")
  importFrom("stats", "aggregate", "cor", "sd")
to your NAMESPACE file.
GCV: no visible global function definition for ‘lm’
GCV: no visible global function definition for ‘resid’
ffplot: no visible global function definition for ‘par’
ffplot: no visible global function definition for ‘plot’
ffplot: no visible global function definition for ‘points’
ffplot: no visible global function definition for ‘legend’
flowfield: no visible global function definition for ‘write.table’
gpr: no visible global function definition for ‘quantile’
gpr: no visible global function definition for ‘var’
smoothp: no visible global function definition for ‘lm’
smoothp: no visible global function definition for ‘predict’
smoothp: no visible global function definition for ‘resid’
smoothp: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  legend lm optimize par plot points predict quantile resid var
  write.table
Consider adding
  importFrom("graphics", "legend", "par", "plot", "points")
  importFrom("stats", "lm", "optimize", "predict", "quantile", "resid",
             "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Rd file 'flsa.Rd':
  \usage lines wider than 90 characters:
     flsa(y, lambda1=0, lambda2=NULL, connListObj = NULL, splitCheckSize=1e+09, verbose=FALSE, thr = 1e-09, maxGrpNum=4*length(y))
  \examples lines wider than 100 characters:
     ### therefore, res2Dim does not give out the solution as a 2 dimensional matrix (unlike the direct version above)

These lines will be truncated in the PDF manual.
prepare_Rd: Flury-package.Rd:37-39: Dropping empty section \examples
prepare_Rd: apples.Rd:19-21: Dropping empty section \details
prepare_Rd: basketball.Rd:28-29: Dropping empty section \references
prepare_Rd: challenger.Rd:18-20: Dropping empty section \details
prepare_Rd: computers.Rd:16-18: Dropping empty section \details
prepare_Rd: cork.Rd:19-20: Dropping empty section \details
prepare_Rd: dead.beetles.Rd:17-19: Dropping empty section \details
prepare_Rd: deer.Rd:14-16: Dropping empty section \details
prepare_Rd: dogwood.Rd:22-24: Dropping empty section \details
prepare_Rd: f.twins.Rd:23-25: Dropping empty section \details
prepare_Rd: flea.beetles.Rd:22-24: Dropping empty section \details
prepare_Rd: ghq.Rd:25-27: Dropping empty section \details
prepare_Rd: lookup.Rd:15-17: Dropping empty section \details
prepare_Rd: lookup.Rd:18-20: Dropping empty section \source
prepare_Rd: m.twins.Rd:24-26: Dropping empty section \details
prepare_Rd: mumps.Rd:14-16: Dropping empty section \details
prepare_Rd: pipits.Rd:17-19: Dropping empty section \details
prepare_Rd: pipits2.Rd:18-19: Dropping empty section \details
prepare_Rd: robustus.Rd:17-19: Dropping empty section \details
prepare_Rd: sibling.heads.Rd:18-20: Dropping empty section \details
prepare_Rd: snailsf.Rd:25-27: Dropping empty section \details
prepare_Rd: steve.Rd:19-20: Dropping empty section \details
prepare_Rd: steve.Rd:26-27: Dropping empty section \references
prepare_Rd: turtles.Rd:19: Dropping empty section \details
prepare_Rd: vasoc.Rd:18-20: Dropping empty section \details
prepare_Rd: wine.sugar.Rd:22-24: Dropping empty section \details
export: no visible global function definition for ‘write.table’
flux.odae : <anonymous>: no visible global function definition for
  ‘combn’
mf.flux: no visible global function definition for ‘runsd’
plot.fluss: no visible global function definition for ‘dev.new’
plot.fluss: no visible global function definition for ‘pdf’
plot.fluss: no visible global function definition for ‘dev.off’
plot.fluxes: no visible global function definition for ‘dev.new’
plot.fluxes: no visible global function definition for ‘devAskNewPage’
plot.fluxes: no visible global function definition for ‘pdf’
plot.fluxes: no visible global function definition for ‘dev.off’
plot.fluxxes: no visible global function definition for ‘dev.new’
plot.fluxxes: no visible global function definition for ‘devAskNewPage’
plot.fluxxes: no visible global function definition for ‘pdf’
plot.fluxxes: no visible global function definition for ‘dev.off’
reco.bulk : get.out: no visible global function definition for
  ‘boxplot.stats’
Undefined global functions or variables:
  boxplot.stats combn dev.new dev.off devAskNewPage pdf runsd
  write.table
Consider adding
  importFrom("grDevices", "boxplot.stats", "dev.new", "dev.off",
             "devAskNewPage", "pdf")
  importFrom("utils", "combn", "write.table")
to your NAMESPACE file.
BSOptionValue: no visible global function definition for ‘pnorm’
ImpliedVol: no visible global function definition for ‘uniroot’
callFMstable: no visible global function definition for ‘integrate’
fitGivenQuantile: no visible global function definition for ‘uniroot’
matchQuartiles: no visible global function definition for ‘optim’
putFMstable: no visible global function definition for ‘integrate’
standardStableQuantile: no visible global function definition for
  ‘qnorm’
tailsGstable: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate optim pnorm qnorm uniroot
Consider adding
  importFrom("stats", "integrate", "optim", "pnorm", "qnorm", "uniroot")
to your NAMESPACE file.
'library' or 'require' call to ‘limma’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  fmt.default plot.fmt
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
fmt.default: no visible global function definition for ‘loessFit’
fmt.default: no visible global function definition for
  ‘trigammaInverse’
plot.fmt: no visible global function definition for ‘par’
plot.fmt: no visible global function definition for ‘plot’
plot.fmt: no visible global function definition for ‘points’
Undefined global functions or variables:
  loessFit par plot points trigammaInverse
Consider adding
  importFrom("graphics", "par", "plot", "points")
to your NAMESPACE file.
Rd file 'foba.Rd':
  \usage lines wider than 90 characters:
     foba(x,y, type=c("foba","foba.aggressive", "foba.conservative", "forward","backward"), steps=0, intercept=TRUE, nu=0.5,lambda=1e-10) 

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

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'library' or 'require' call to ‘rgl’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls to packages already attached by Depends:
  ‘combinat’ ‘genetics’
  Please remove these calls from your code.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘forensic/R/zzz.R’:
  .First.lib calls:
    cat("## Statistical Methods in Forensic Genetics \n")
    cat("## The work was supported by the project 1M06014 of the Ministry of \n        Education, Youth and Sports of the Czech Republic. \n")
    require(genetics, quietly = TRUE)
    require(combinat, quietly = TRUE)

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

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

Probably some imports need to be declared in the NAMESPACE file.
&,fseries-numeric: no visible global function definition for ‘new’
*,fseries-fseries: no visible global function definition for ‘new’
*,fseries-numeric: no visible global function definition for ‘new’
*,numeric-fseries: no visible global function definition for ‘new’
+,fseries-fseries: no visible global function definition for ‘new’
+,fseries-numeric: no visible global function definition for ‘new’
+,numeric-fseries: no visible global function definition for ‘new’
-,fseries-ANY: no visible global function definition for ‘new’
-,fseries-numeric: no visible global function definition for ‘new’
-,numeric-fseries: no visible global function definition for ‘new’
/,fseries-numeric: no visible global function definition for ‘new’
[<-,fseries-matrix-missing-matrix: no visible global function
  definition for ‘new’
[<-,fseries-numeric-missing-numeric: no visible global function
  definition for ‘new’
initialize,fseries: no visible global function definition for
  ‘validObject’
rfseries,numeric-numeric-numeric: no visible global function definition
  for ‘runif’
rfseries,numeric-numeric-numeric: no visible global function definition
  for ‘rbinom’
rfseries,numeric-numeric-numeric: no visible global function definition
  for ‘new’
Undefined global functions or variables:
  new rbinom runif validObject
Consider adding
  importFrom("methods", "new", "validObject")
  importFrom("stats", "rbinom", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
ForwardSearch.fit: no visible global function definition for ‘glm.fit’
ForwardSearch.plot: no visible global function definition for ‘lines’
ForwardSearch.pointwise.asymptotics: no visible global function
  definition for ‘qnorm’
ForwardSearch.pointwise.asymptotics: no visible global function
  definition for ‘dnorm’
Undefined global functions or variables:
  dnorm glm.fit lines qnorm
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "dnorm", "glm.fit", "qnorm")
to your NAMESPACE file.
'library' or 'require' call to ‘shapefiles’ which was already attached by Depends.
  Please remove these calls from your code.
dino.dist: no visible global function definition for ‘as.dist’
earth.dist: no visible global function definition for ‘as.dist’
ecol.dist: no visible global function definition for ‘as.dist’
loc.map: no visible global function definition for ‘points’
msn.map: no visible global function definition for ‘points’
msn.map: no visible global function definition for ‘lines’
mstlines: no visible global function definition for ‘lines’
nmds.mst: no visible global function definition for ‘lines’
rclust.null: no visible global function definition for ‘sd’
sim.occ: no visible global function definition for ‘rlnorm’
spp.est: no visible global function definition for ‘sd’
Undefined global functions or variables:
  as.dist lines points rlnorm sd
Consider adding
  importFrom("graphics", "lines", "points")
  importFrom("stats", "as.dist", "rlnorm", "sd")
to your NAMESPACE file.
Rd file 'create.matrix.Rd':
  \usage lines wider than 90 characters:
       create.matrix(x,tax.name="genus",locality="locality",time.col=NULL,time=NULL,abund=FALSE,abund.col="abundance")

Rd file 'new.lat.long.Rd':
  \examples lines wider than 100 characters:
     #Travel from 0,0 to a new location at a bearing of 45 degrees from North (clockwise) and 1000 km away

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  fourierin_1d.cpp:55:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  fourierin_1d.cpp:77:17: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  fourierin_2d.cpp:107:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  fourierin_2d.cpp:146:12: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  fourierin_cx_1d.cpp:55:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  fourierin_cx_1d.cpp:77:17: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  fourierin_cx_2d.cpp:104:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  fourierin_cx_2d.cpp:143:12: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/fourierin.Rcheck/00install.out’ for details.
GenObs: no visible global function definition for ‘rnorm’
GenObs.T: no visible global function definition for ‘rt’
MeasL: no visible global function definition for ‘rbeta’
OutDet: no visible global function definition for ‘median’
RanCur: no visible global function definition for ‘rnorm’
init: no visible global function definition for ‘prcomp’
Undefined global functions or variables:
  median prcomp rbeta rnorm rt
Consider adding
  importFrom("stats", "median", "prcomp", "rbeta", "rnorm", "rt")
to your NAMESPACE file.
Rd file 'fpca.mle.Rd':
  \usage lines wider than 90 characters:
     fpca.mle(data.m, M.set,r.set, ini.method="EM", basis.method="bs", sl.v=rep(0.5,10), max.step=50,
  \examples lines wider than 100 characters:
      ##model selection result: the true model M=5, r=3 is selected with the smallest CV score among all converged models
      ##look at the CV scores and convergence for each model: note that model (M=5, r=4) does not converge. 
     #get predicted trajectories on a fine grid: the same grid for which mean and eigenfunctions are evaluated
     plot(t.c,y.c,ylim=range(pred[,id]),xlab="time",ylab="obs", main=paste("predicted trajectory of curve", id))
      ##model selection result: the true model M=5, r=3 is selected with the smallest CV score among all converged models
      plot(grids.new,result$eigenfunctions[i,],ylim=range(result$eigenfunctions),xlab="time",ylab=paste("eigenfunction",i))
      ##look at the CV scores and convergence for each model: note that model (M=5, r=4) does not converge. 

These lines will be truncated in the PDF manual.
Packages suggested but not available for checking:
  'Rsocp', 'Rnlminb2', 'Rdonlp2'
Non-standard files/directories found at top level:
  ‘Calling’ ‘Done’ ‘filters.R’
confint.fracdiff: no visible global function definition for ‘coef’
confint.fracdiff: no visible global function definition for ‘qnorm’
fdGPH: no visible global function definition for ‘na.fail’
fdGPH: no visible global function definition for ‘as.ts’
fdGPH: no visible global function definition for ‘lm’
fdGPH: no visible global function definition for ‘coef’
fdGPH: no visible global function definition for ‘resid’
fdSperio: no visible global function definition for ‘na.fail’
fdSperio: no visible global function definition for ‘as.ts’
fdSperio: no visible global function definition for ‘lm’
fdSperio: no visible global function definition for ‘coef’
fdSperio: no visible global function definition for ‘resid’
fracdiff.sim: no visible binding for global variable ‘rnorm’
logLik.fracdiff: no visible global function definition for ‘coef’
print.fracdiff: no visible global function definition for ‘coef’
print.summary.fracdiff: no visible global function definition for
  ‘printCoefmat’
print.summary.fracdiff: no visible global function definition for
  ‘symnum’
summary.fracdiff: no visible global function definition for ‘coef’
summary.fracdiff: no visible global function definition for ‘pnorm’
summary.fracdiff: no visible global function definition for ‘logLik’
summary.fracdiff: no visible global function definition for ‘AIC’
Undefined global functions or variables:
  AIC as.ts coef lm logLik na.fail pnorm printCoefmat qnorm resid rnorm
  symnum
Consider adding
  importFrom("stats", "AIC", "as.ts", "coef", "lm", "logLik", "na.fail",
             "pnorm", "printCoefmat", "qnorm", "resid", "rnorm",
             "symnum")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘pcaPP’ ‘snowFT’ ‘wavelets’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
ComputeDCT2FFT: no visible global function definition for ‘fft’
ComputeSemipgramFFT: no visible global function definition for ‘fft’
WaveVarFD: no visible global function definition for ‘modwt’
do.fd.estimate: no visible global function definition for
  ‘performParallel’
do.fd.estimate2d.simple: no visible global function definition for
  ‘median’
fd.Genton: no visible global function definition for ‘qn’
fd.estimate.matrix: no visible global function definition for
  ‘performParallel’
fd.plot.legend: no visible global function definition for ‘legend’
fd.plot.loglog: no visible global function definition for ‘plot’
fd.plot.loglog: no visible global function definition for ‘points’
fd.plot.loglog: no visible global function definition for ‘abline’
summary.FractalDim: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  abline fft legend median modwt performParallel plot points qn sd
Consider adding
  importFrom("graphics", "abline", "legend", "plot", "points")
  importFrom("stats", "fft", "median", "sd")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘futile.any’ ‘futile.logger’ ‘quantmod’ ‘timeDate’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'fractal.Rd':
  \usage lines wider than 90 characters:
     fractal.uniform(seed, patterns, count = NULL, epochs = NULL, origin = '1970-01-01', date.fun = as.Date, only = NULL)
     fractal.random(seed, patterns, count = NULL, epochs = NULL, origin = '1970-01-01', date.fun = as.Date, only = NULL)

Rd file 'getPortfolioPrices.Rd':
  \usage lines wider than 90 characters:
     getPortfolioPrices(symbols, obs = NULL, end = Sys.Date(), start = NULL, calendar = holidayNYSE, seeds = NULL, patterns = NULL, ..., typ ... [TRUNCATED]

Rd file 'process.Rd':
  \usage lines wider than 90 characters:
     ou.process(theta, mu = 0, sigma = 1, initial=mu, end = Sys.Date(), start = NULL, obs = NULL)

These lines will be truncated in the PDF manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘CCP’ ‘MASS’ ‘calibrate’ ‘corpcor’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘CCP’ ‘MASS’ ‘calibrate’ ‘corpcor’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
custom.draw.circle: no visible global function definition for ‘lines’
frcc: no visible binding for global variable ‘sd’
frcc: no visible global function definition for ‘cor.shrink’
frcc: no visible global function definition for ‘cor’
frcc: no visible global function definition for ‘p.asym’
generate_multivariate_normal_sample: no visible global function
  definition for ‘mvrnorm’
plot_units: no visible binding for global variable ‘sd’
plot_units: no visible global function definition for ‘plot’
plot_units: no visible global function definition for ‘points’
plot_units: no visible global function definition for ‘textxy’
plot_variables: no visible global function definition for ‘plot’
plot_variables: no visible global function definition for ‘points’
plot_variables: no visible global function definition for ‘textxy’
plot_variables: no visible global function definition for ‘segments’
Undefined global functions or variables:
  cor cor.shrink lines mvrnorm p.asym plot points sd segments textxy
Consider adding
  importFrom("graphics", "lines", "plot", "points", "segments")
  importFrom("stats", "cor", "sd")
to your NAMESPACE file.
cv.work: no visible global function definition for ‘predict’
fakedata: no visible global function definition for ‘runif’
Undefined global functions or variables:
  predict runif
Consider adding
  importFrom("stats", "predict", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: ‘GenABEL’
src/Makevars: it is not portable to include SHLIB_OPENMP_*' macros in PKG_CPPFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
PKG_CPPFLAGS is used for both C and C++ code so it is not portable to
use it for these macros.
Non-standard file/directory found at top level:
  ‘FrF2.catlg128-Ex.R’
Package in Depends field not imported from: ‘FrF2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages suggested but not available for checking: 'dggrids', 'INLA'
Packages in Depends field not imported from:
  ‘Rmpfr’ ‘partitions’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Bell : nways: no visible global function definition for ‘setparts’
Bell: no visible global function definition for ‘restrictedparts’
CalIncLapInt : Deriv: no visible global function definition for ‘D’
CalIncLapInt: no visible global function definition for ‘is.whole’
CalIncLapInt: no visible global function definition for ‘mpfr’
CalIncLapInt: no visible global function definition for ‘chooseMpfr’
derivErfc : Deriv: no visible global function definition for ‘D’
derivErfc : Erfc: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  D chooseMpfr is.whole mpfr pnorm restrictedparts setparts
Consider adding
  importFrom("stats", "D", "pnorm")
to your NAMESPACE file.
ROCscore: no visible global function definition for ‘par’
ROCscore: no visible global function definition for ‘axis’
ROCscore: no visible global function definition for ‘mtext’
ROCscore: no visible global function definition for ‘legend’
alphafrontier.2d: no visible global function definition for ‘par’
alphafrontier.2d: no visible global function definition for ‘polygon’
alphafrontier.2d: no visible global function definition for ‘lines’
alphafrontier.2d: no visible global function definition for ‘points’
alphafrontier.3d: no visible global function definition for ‘layout’
alphafrontier.3d: no visible global function definition for ‘barplot’
alphafrontier.3d: no visible global function definition for ‘axis’
alphafrontier.3d: no visible global function definition for ‘lines’
alphafrontier.3d: no visible global function definition for ‘na.omit’
ordermfrontier.2d: no visible global function definition for ‘par’
ordermfrontier.2d: no visible global function definition for ‘polygon’
ordermfrontier.2d: no visible global function definition for ‘lines’
ordermfrontier.2d: no visible global function definition for ‘points’
ordermscore.boot: no visible global function definition for ‘sd’
Undefined global functions or variables:
  axis barplot layout legend lines mtext na.omit par points polygon sd
Consider adding
  importFrom("graphics", "axis", "barplot", "layout", "legend", "lines",
             "mtext", "par", "points", "polygon")
  importFrom("stats", "na.omit", "sd")
to your NAMESPACE file.
prepare_Rd: frt.Rd:21: Dropping empty section \note
prepare_Rd: frt.paired.Rd:23: Dropping empty section \note
prepare_Rd: shoes.Rd:19: Dropping empty section \details
prepare_Rd: shoes.Rd:21-22: Dropping empty section \references
prepare_Rd: tomatoes.Rd:16: Dropping empty section \details
prepare_Rd: tomatoes.Rd:18: Dropping empty section \references
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_LIBS but not in PKG_CXXFLAGS
  src/Makevars: it is not portable to include SHLIB_OPENMP_*' macros in PKG_CPPFLAGS
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but not in PKG_CFLAGS
  src/Makevars.win: it is not portable to include SHLIB_OPENMP_*' macros in PKG_CPPFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
PKG_CPPFLAGS is used for both C and C++ code so it is not portable to
use it for these macros.
'library' or 'require' calls to packages already attached by Depends:
  ‘Matrix’ ‘splines’
  Please remove these calls from your code.
prepare_Rd: baseline.Rd:123: Dropping empty section \examples
prepare_Rd: display.tests.Rd:43: Dropping empty section \references
prepare_Rd: display.tests.Rd:57: Dropping empty section \examples
prepare_Rd: extract.pars.Rd:114: Dropping empty section \examples
prepare_Rd: locate.peaks.Rd:72: Dropping empty section \examples
prepare_Rd: make.par.file.Rd:117: Dropping empty section \examples
prepare_Rd: run.all.Rd:76: Dropping empty section \examples
prepare_Rd: run.analysis.Rd:153: Dropping empty section \examples
prepare_Rd: run.baselines.Rd:91: Dropping empty section \examples
prepare_Rd: run.cluster.matrix.Rd:171: Dropping empty section \examples
prepare_Rd: run.lrg.peaks.Rd:95: Dropping empty section \examples
prepare_Rd: run.peaks.Rd:99: Dropping empty section \examples
prepare_Rd: run.strong.peaks.Rd:115: Dropping empty section \examples
Non-standard files/directories found at top level:
  ‘COPYRIGHT’ ‘pmden.R’
Copyright information should be in file inst/COPYRIGHTS
Rd file 'ftnonpar-internal.Rd':
  \usage lines wider than 90 characters:
     genmrcheck(y,yhat,thresh=-1,sigma=1,DYADIC=FALSE,beta=0.5,method=1,thr.const=2,schwelle = 1e+09)

Rd file 'genpmreg.Rd':
  \usage lines wider than 90 characters:
     genpmreg(y, beta = 0.5, squeezing.factor = 0.5, verbose = FALSE, localsqueezing = TRUE, DYADIC = TRUE, thr.const = 2, extrema.nr = -1,  ... [TRUNCATED]

Rd file 'l1pmreg.Rd':
  \usage lines wider than 90 characters:
     quantpmreg(y, beta = 0.5, squeezing.factor = 0.5, verbose = FALSE, localsqueezing = TRUE, DYADIC = TRUE, thr.const = 2, extrema.nr = -1 ... [TRUNCATED]
     l1pmreg(y, beta=0.5, squeezing.factor = 0.5, verbose = FALSE, localsqueezing = TRUE, DYADIC = TRUE, thr.const = 2, extrema.nr = -1, ban ... [TRUNCATED]

Rd file 'mintvmon.Rd':
  \usage lines wider than 90 characters:
     mintvmon(y, sigma = -1, DYADIC = TRUE, thresh = -1, method = 2, MONCONST = TRUE, CONVCONST = FALSE)

Rd file 'pmden.Rd':
  \usage lines wider than 90 characters:
     pmden(x, DISCR=FALSE,verbose = FALSE, bandwidth=-1, extrema.nr = -1, accuracy = mad(x)/1000,  extrema.mean = TRUE,maxkuipnr=19,asympbou ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘snowfall’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fugeR.evo: no visible global function definition for ‘runif’
fugeR.sfRun: no visible global function definition for ‘sfInit’
fugeR.sfRun: no visible global function definition for ‘sfLibrary’
fugeR.sfRun: no visible global function definition for ‘sfExport’
fugeR.sfRun: no visible global function definition for ‘sfLapply’
fugeR.sfRun: no visible global function definition for ‘sfStop’
Undefined global functions or variables:
  runif sfExport sfInit sfLapply sfLibrary sfStop
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
mfpcaPlot: no visible global function definition for ‘dev.new’
mfpcaPlot: no visible global function definition for ‘par’
plotOC: no visible global function definition for ‘dev.new’
plotfd: no visible global function definition for ‘dev.new’
plotfd: no visible global function definition for ‘plot’
Undefined global functions or variables:
  dev.new par plot
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "par", "plot")
to your NAMESPACE file.
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_LIBS but not in PKG_CXXFLAGS
  src/Makevars: it is not portable to include SHLIB_OPENMP_*' macros in PKG_CPPFLAGS
  src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_LIBS but not in PKG_CXXFLAGS
  src/Makevars.win: it is not portable to include SHLIB_OPENMP_*' macros in PKG_CPPFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
PKG_CPPFLAGS is used for both C and C++ code so it is not portable to
use it for these macros.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Funclustering/makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Non-standard file/directory found at top level:
  ‘copying’
bic.generation: no visible global function definition for ‘lm’
bic.generation: no visible global function definition for ‘BIC’
bic.generation : <anonymous>: no visible global function definition for
  ‘lm’
bic.generation : <anonymous>: no visible global function definition for
  ‘BIC’
data.generation : <anonymous> : <anonymous>: no visible global function
  definition for ‘sd’
Undefined global functions or variables:
  BIC lm sd
Consider adding
  importFrom("stats", "BIC", "lm", "sd")
to your NAMESPACE file.
.FunFEM.main: no visible global function definition for ‘kmeans’
.FunFEM.main: no visible global function definition for ‘rmultinom’
.FunFEM.main: no visible global function definition for ‘cutree’
.FunFEM.main: no visible global function definition for ‘hclust’
.FunFEM.main: no visible global function definition for ‘dist’
.FunFEM.main: no visible global function definition for ‘par’
.FunFEM.main: no visible global function definition for ‘plot’
.mstep: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov cutree dist hclust kmeans par plot rmultinom
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "cov", "cutree", "dist", "hclust", "kmeans",
             "rmultinom")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘RUnit’ ‘futile.options’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.validateGuardExpression: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
fuzzyBHexact: warning in round(pvals, d = dp): partial argument match
  of ‘d’ to ‘digits’
fuzzyBHexact: warning in round(pprev, d = dp): partial argument match
  of ‘d’ to ‘digits’
fuzzyBHexact: warning in round(p.minus, d = 4): partial argument match
  of ‘d’ to ‘digits’
fuzzyBHexact: warning in round(p.plus, d = 4): partial argument match
  of ‘d’ to ‘digits’
fuzzyBHexact: warning in round(a.minus, d = 4): partial argument match
  of ‘d’ to ‘digits’
fuzzyBHexact: warning in round(a.plus, d = 4): partial argument match
  of ‘d’ to ‘digits’
fuzzyBHexact: warning in round(new.p.minus, d = 4): partial argument
  match of ‘d’ to ‘digits’
fuzzyBHexact: warning in round(new.p.plus, d = 4): partial argument
  match of ‘d’ to ‘digits’
fuzzyBHexact: warning in round(pvals, d = 4): partial argument match of
  ‘d’ to ‘digits’
fuzzyBHexact: warning in round(pprev, d = 4): partial argument match of
  ‘d’ to ‘digits’
fuzzyBHexact: warning in round(tau, d = 4): partial argument match of
  ‘d’ to ‘digits’
probRejTies: no visible binding for global variable ‘nn’
Undefined global functions or variables:
  nn
NeedsCompilation field must take value ‘yes’ or ‘no’
'library' or 'require' call to ‘splines’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gensurf: no visible global function definition for ‘persp’
gensurf: no visible global function definition for ‘rainbow’
plotMF: no visible global function definition for ‘plot.new’
plotMF: no visible global function definition for ‘plot.window’
plotMF: no visible global function definition for ‘runif’
plotMF: no visible global function definition for ‘predict’
plotMF: no visible global function definition for ‘interpSpline’
plotMF: no visible global function definition for ‘lines’
plotMF: no visible global function definition for ‘text’
plotMF: no visible global function definition for ‘title’
plotMF: no visible global function definition for ‘axis’
plotMF: no visible global function definition for ‘box’
Undefined global functions or variables:
  axis box interpSpline lines persp plot.new plot.window predict
  rainbow runif text title
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "persp", "plot.new",
             "plot.window", "text", "title")
  importFrom("stats", "predict", "runif")
to your NAMESPACE file.
Rd file 'newFIS.Rd':
  \usage lines wider than 90 characters:
     newFIS(FISName, FISType = "mamdani", version = "1.0", andMethod = "min", orMethod = "max", impMethod = "min", aggMethod = "max", defuzz ... [TRUNCATED]

These lines will be truncated in the PDF manual.
alpha: no visible global function definition for ‘var’
coefH: no visible global function definition for ‘var’
coefZ: no visible global function definition for ‘var’
coefZ: no visible binding for global variable ‘var’
fs.MSA: no visible global function definition for ‘runif’
fs.MSA: no visible global function definition for ‘boxplot’
plot.fs.class: no visible global function definition for ‘lines’
plot.fs.class: no visible global function definition for ‘text’
plot.fs.class: no visible global function definition for ‘axis’
plot.fs.class: no visible global function definition for ‘segments’
plot.fs.class: no visible global function definition for ‘title’
plot.fs.class: no visible global function definition for
  ‘devAskNewPage’
plot.fs.class : <anonymous>: no visible global function definition for
  ‘quantile’
plot.fs.n1.class: no visible global function definition for ‘segments’
plot.fs.n1.class: no visible global function definition for ‘axis’
plot.fs.n1.class: no visible global function definition for ‘lines’
plot.fs.n1.class: no visible global function definition for ‘legend’
search.normal: no visible global function definition for ‘var’
search.normal: no visible binding for global variable ‘var’
search.normal: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  axis boxplot devAskNewPage legend lines qnorm quantile runif segments
  text title var
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "axis", "boxplot", "legend", "lines",
             "segments", "text", "title")
  importFrom("stats", "qnorm", "quantile", "runif", "var")
to your NAMESPACE file.
Rd file 'fwdmsa-package.Rd':
  \examples lines wider than 100 characters:
        plot(fs1.1, type="objective", observations=1:618, col="gray70", n0=TRUE, n1=fs.res.cont.n1$n1, xlim=c(0,650))

These lines will be truncated in the PDF manual.
'library' or 'require' call to ‘foreach’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
fxreturns: no visible binding for global variable ‘FXRatesCHF’
fxreturns : <anonymous>: no visible global function definition for
  ‘tail’
gbreakpoints: no visible global function definition for ‘%dopar%’
gbreakpoints: no visible global function definition for ‘foreach’
Undefined global functions or variables:
  %dopar% FXRatesCHF foreach tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘MASS’ ‘igraph’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
DBNScoreStep1: no visible global function definition for ‘lm’
DBNScoreStep1: no visible global function definition for ‘rlm’
DBNScoreStep1: no visible global function definition for ‘pt’
DBNScoreStep2: no visible global function definition for ‘lm’
DBNScoreStep2: no visible global function definition for ‘rlm’
DBNScoreStep2: no visible global function definition for ‘pt’
SimulGeneExpressionAR1: no visible global function definition for
  ‘rnorm’
SimulGeneExpressionAR1: no visible global function definition for ‘ts’
SimulNetworkAdjMatrix: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  lm pt rlm rnorm runif ts
Consider adding
  importFrom("stats", "lm", "pt", "rnorm", "runif", "ts")
to your NAMESPACE file.
crossover: no visible global function definition for ‘runif’
exchangeSols: no visible global function definition for ‘runif’
fps: no visible global function definition for ‘runif’
mutation: no visible global function definition for ‘runif’
plotBicluster: no visible global function definition for ‘gray’
plotBicluster: no visible global function definition for ‘heatmap’
reproduction: no visible global function definition for ‘runif’
Undefined global functions or variables:
  gray heatmap runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("stats", "heatmap", "runif")
to your NAMESPACE file.
FPTsimul: no visible global function definition for ‘runif’
histplot: no visible global function definition for ‘dev.new’
histplot: no visible global function definition for ‘hist’
histplot: no visible global function definition for ‘par’
histplot: no visible global function definition for ‘plot’
histplot: no visible global function definition for ‘legend’
mdt: no visible binding for global variable ‘deltat’
plot.FPTdensity: no visible global function definition for ‘dev.new’
plot.FPTdensity: no visible global function definition for ‘plot’
res_summary: no visible global function definition for ‘write.table’
res_summary: no visible global function definition for ‘sd’
res_summary: no visible global function definition for ‘median’
vdt: no visible binding for global variable ‘deltat’
Undefined global functions or variables:
  deltat dev.new hist legend median par plot runif sd write.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "hist", "legend", "par", "plot")
  importFrom("stats", "deltat", "median", "runif", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
CI.RMSEA: no visible global function definition for ‘qchisq’
CI.RMSEA: no visible global function definition for ‘pchisq’
GAIPE.RMSEA: no visible global function definition for ‘par’
GAIPE.RMSEA: no visible global function definition for ‘plot’
GAIPE.RMSEA: no visible global function definition for ‘abline’
GAIPE.RMSEA: no visible global function definition for ‘colors’
GAIPE.RMSEA: no visible global function definition for ‘text’
GAIPE.RMSEA: no visible global function definition for ‘arrows’
GAIPE.RMSEA: no visible global function definition for ‘points’
GAIPE.RMSEA: no visible global function definition for ‘axis’
GAIPE.RMSEA: no visible global function definition for ‘lines’
GAIPE.RMSEA: no visible global function definition for ‘legend’
GAIPE.RMSEA: no visible global function definition for ‘pchisq’
GAIPE.RMSEA: no visible global function definition for ‘qchisq’
GAIPE.RMSEA: no visible global function definition for ‘mtext’
GAIPE.RMSEA: no visible global function definition for ‘title’
PA.RMSEA: no visible global function definition for ‘pchisq’
PA.RMSEA: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  abline arrows axis colors legend lines mtext par pchisq plot points
  qchisq text title
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "abline", "arrows", "axis", "legend", "lines",
             "mtext", "par", "plot", "points", "text", "title")
  importFrom("stats", "pchisq", "qchisq")
to your NAMESPACE file.
cvriskMSM: no visible global function definition for ‘predict’
plotcvriskMSM: no visible global function definition for ‘plot’
plotcvriskMSM: no visible binding for global variable ‘lines’
plotcvriskMSM: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines plot predict
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "predict")
to your NAMESPACE file.
Non-standard files/directories found at top level:
  ‘changeLog’ ‘gnugpl2.txt’
'library' or 'require' calls in package code:
  ‘parallel’ ‘snowfall’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘Matrix’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GAMBoost: no visible global function definition for ‘binomial’
GAMBoost: no visible global function definition for ‘gaussian’
GAMBoost: no visible global function definition for ‘poisson’
GAMBoost: no visible binding for global variable ‘sd’
GAMBoost: no visible global function definition for ‘Matrix’
calc.confidence.bands: no visible global function definition for
  ‘predict’
cv.GAMBoost: no visible global function definition for ‘binomial’
cv.GAMBoost : eval.fold: no visible global function definition for
  ‘predict’
cv.GAMBoost: no visible global function definition for ‘mclapply’
cv.GAMBoost: no visible binding for global variable ‘var’
estimPVal: no visible global function definition for ‘mclapply’
plot.GAMBoost: no visible global function definition for ‘plot’
plot.GAMBoost: no visible global function definition for ‘lines’
Undefined global functions or variables:
  Matrix binomial gaussian lines mclapply plot poisson predict sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "binomial", "gaussian", "poisson", "predict", "sd",
             "var")
to your NAMESPACE file.
Package in Depends field not imported from: ‘gamlss’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘gamlss:::.gamlss.bi.list’
  See the note in ?`:::` about the use of this operator.
finterp.data.frame: no visible global function definition for
  ‘as.formula’
finterp.data.frame: no visible global function definition for ‘terms’
finterp.data.frame: no visible global function definition for
  ‘model.matrix’
finterp.data.frame: no visible global function definition for
  ‘model.frame’
finterp.default: no visible global function definition for ‘terms’
finterp.default: no visible global function definition for
  ‘model.matrix’
finterp.default: no visible global function definition for
  ‘model.frame’
gamlss.nl: no visible global function definition for ‘nlm’
nl: no visible global function definition for ‘is’
nlgamlss: no visible global function definition for ‘NO’
nlgamlss: no visible global function definition for ‘as.gamlss.family’
nlgamlss: no visible global function definition for ‘nlm’
nlgamlss: no visible global function definition for ‘cov2cor’
summary.nlgamlss: no visible global function definition for ‘coef’
summary.nlgamlss: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  NO as.formula as.gamlss.family coef cov2cor is model.frame
  model.matrix nlm pnorm terms
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "as.formula", "coef", "cov2cor", "model.frame",
             "model.matrix", "nlm", "pnorm", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').

Found the following calls to attach():
File ‘gamlss.nl/R/nlgamlss.R’:
  attach(data)
See section ‘Good practice’ in ‘?attach’.
Found the following apparent S3 methods exported but not registered:
  print.Gammareg print.summary.Gammareg summary.Gammareg
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
gammahetero1: no visible global function definition for ‘terms’
gammahetero1: no visible global function definition for ‘model.matrix’
gammahetero1: no visible global function definition for ‘glm.fit’
gammahetero1: no visible global function definition for ‘Gamma’
gammahetero1: no visible global function definition for ‘qt’
gammahetero2: no visible global function definition for ‘terms’
gammahetero2: no visible global function definition for ‘model.matrix’
gammahetero2: no visible global function definition for ‘glm.fit’
gammahetero2: no visible global function definition for ‘Gamma’
gammahetero2: no visible global function definition for ‘qt’
print.summary.Gammareg: no visible global function definition for
  ‘printCoefmat’
summary.Gammareg: no visible global function definition for ‘coef’
Undefined global functions or variables:
  Gamma coef glm.fit model.matrix printCoefmat qt terms
Consider adding
  importFrom("stats", "Gamma", "coef", "glm.fit", "model.matrix",
             "printCoefmat", "qt", "terms")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘Read-and-delete-me’
Package in Depends field not imported from: ‘GANPAdata’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
prepare_Rd: GANPA-package.Rd:30: Dropping empty section \seealso
prepare_Rd: GANPA-package.Rd:31: Dropping empty section \examples
prepare_Rd: GSE.Test.Main.Rd:24: Dropping empty section \details
prepare_Rd: GSE.Test.Main.Rd:32: Dropping empty section \note
prepare_Rd: GSE.Test.Main.Rd:33: Dropping empty section \seealso
prepare_Rd: weight.gsets.test.Rd:14: Dropping empty section \details
prepare_Rd: weight.gsets.test.Rd:25: Dropping empty section \note
prepare_Rd: weight.gsets.with.msprot.Rd:17: Dropping empty section \details
prepare_Rd: weight.gsets.with.msprot.Rd:27: Dropping empty section \note
prepare_Rd: weight.gsets.with.msprot.Rd:31: Dropping empty section \examples
Rd file 'GSE.Test.Main.Rd':
  \usage lines wider than 90 characters:
     GSE.Test.Main(gExprs.obj, gsets, gNET, check.exprs = TRUE, msp.groups, size.min = 15, size.max = 500, permN = 1000, randN = 30, permFDR ... [TRUNCATED]
  \examples lines wider than 100 characters:
     # GSE.Test.Main(gExprs.obj=gExprs.p53, gsets=gsets.msigdb.pnas, gNET=gNET, check.exprs=TRUE, msp.groups=msp.groups, size.min=15, size.m ... [TRUNCATED]

These lines will be truncated in the PDF manual.
'library' or 'require' call to ‘orthopolynom’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘orthopolynom’ ‘polynom’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
contindic.gb2: no visible global function definition for ‘contour’
contindic.gb2: no visible global function definition for ‘box’
contindic.gb2: no visible global function definition for ‘mtext’
contprof.gb2: no visible global function definition for ‘image’
contprof.gb2: no visible global function definition for ‘heat.colors’
contprof.gb2: no visible global function definition for ‘contour’
contprof.gb2: no visible global function definition for ‘text’
contprof.gb2: no visible global function definition for ‘box’
dplot.cavgb2: no visible global function definition for ‘par’
dplot.cavgb2: no visible global function definition for ‘curve’
dplot.cavgb2: no visible global function definition for ‘legend’
dplot.cavgb2: no visible global function definition for ‘plot’
dplot.cavgb2: no visible global function definition for ‘lines’
dplot.cgb2: no visible global function definition for ‘curve’
dplot.cgb2: no visible global function definition for ‘lines’
dplot.cgb2: no visible global function definition for ‘legend’
plotsML.gb2: no visible global function definition for ‘par’
plotsML.gb2: no visible global function definition for ‘plot’
plotsML.gb2: no visible global function definition for ‘abline’
plotsML.gb2: no visible global function definition for ‘curve’
plotsML.gb2: no visible global function definition for ‘legend’
saveplot : <local>: no visible global function definition for ‘dev.set’
saveplot : <local>: no visible global function definition for
  ‘dev.print’
saveplot : <local>: no visible binding for global variable ‘pdf’
Undefined global functions or variables:
  abline box contour curve dev.print dev.set heat.colors image legend
  lines mtext par pdf plot text
Consider adding
  importFrom("grDevices", "dev.print", "dev.set", "heat.colors", "pdf")
  importFrom("graphics", "abline", "box", "contour", "curve", "image",
             "legend", "lines", "mtext", "par", "plot", "text")
to your NAMESPACE file.
Package in Depends field not imported from: ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘tools:::.Rd_get_argument_names’ ‘tools:::RdTags’ ‘tools:::fetchRdDB’
  See the note in ?`:::` about the use of this operator.
coeplot: no visible global function definition for ‘plot’
coeplot: no visible global function definition for ‘axis’
coeplot: no visible global function definition for ‘lines’
coeplot: no visible global function definition for ‘title’
coeplot: no visible global function definition for ‘legend’
corplot: no visible global function definition for ‘par’
corplot: no visible global function definition for ‘pairs’
corplot: no visible global function definition for ‘strwidth’
lm.estimate: no visible global function definition for ‘as.formula’
lm.estimate: no visible global function definition for ‘glm’
panel.cor: no visible global function definition for ‘par’
panel.cor: no visible global function definition for ‘cor’
panel.cor: no visible global function definition for ‘strwidth’
panel.cor: no visible global function definition for ‘text’
panel.smooth.r: no visible global function definition for ‘par’
panel.smooth.r: no visible global function definition for ‘points’
panel.smooth.r: no visible global function definition for ‘lines’
posplot: no visible global function definition for ‘par’
posplot: no visible global function definition for ‘barplot’
posplot: no visible global function definition for ‘plot’
posplot: no visible global function definition for ‘points’
Undefined global functions or variables:
  as.formula axis barplot cor glm legend lines pairs par plot points
  strwidth text title
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines", "pairs",
             "par", "plot", "points", "strwidth", "text", "title")
  importFrom("stats", "as.formula", "cor", "glm")
to your NAMESPACE file.
gcat.test: no visible global function definition for ‘pnorm’
generate_sub: no visible global function definition for ‘runif’
pfcn: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm runif
Consider adding
  importFrom("stats", "pnorm", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: ‘gputools’
Found the following apparent S3 methods exported but not registered:
  reorder.hclust
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'cpairs.Rd':
  \usage lines wider than 90 characters:
     cpairs(data, order = NULL, panel.colors = NULL, border.color = "grey70", show.points = TRUE, ...)

Rd file 'cparcoord.Rd':
  \usage lines wider than 90 characters:
     cparcoord(data, order = NULL, panel.colors = NULL, col = 1, lty = 1, horizontal = FALSE, mar = NULL, ...)

These lines will be truncated in the PDF manual.
Found the following calls to attach():
File ‘g.data/R/g.data.attach.R’:
  attach(NULL, pos, basename(dir))
See section ‘Good practice’ in ‘?attach’.
Package in Depends field not imported from: ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
DownloadGdelt: no visible global function definition for
  ‘packageVersion’
DownloadGdelt: no visible global function definition for
  ‘download.file’
GdeltZipToDataframe: no visible global function definition for
  ‘read.delim’
GdeltZipToDataframe: no visible global function definition for ‘unzip’
GetSizeOfGDELT: no visible global function definition for ‘read.delim’
IsValidGDELT: no visible global function definition for ‘read.delim’
IsValidGDELT: no visible global function definition for ‘md5sum’
NormEventCounts: no visible global function definition for
  ‘download.file’
NormEventCounts: no visible global function definition for ‘read.csv’
Undefined global functions or variables:
  download.file md5sum packageVersion read.csv read.delim unzip
Consider adding
  importFrom("utils", "download.file", "packageVersion", "read.csv",
             "read.delim", "unzip")
to your NAMESPACE file.
Found the following significant warnings:
  cGetHCS.c:9:33: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  cIdentical.c:9:34: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/gdmp.Rcheck/00install.out’ for details.
Non-standard files/directories found at top level:
  ‘README.too’ ‘blurb’
plot.rbga: no visible global function definition for ‘par’
plot.rbga: no visible global function definition for ‘hist’
plot.rbga: no visible global function definition for ‘plot’
plot.rbga: no visible global function definition for ‘lines’
rbga: no visible global function definition for ‘runif’
rbga: no visible global function definition for ‘dnorm’
rbga.bin: no visible global function definition for ‘dnorm’
rbga.bin: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dnorm hist lines par plot runif
Consider adding
  importFrom("graphics", "hist", "lines", "par", "plot")
  importFrom("stats", "dnorm", "runif")
to your NAMESPACE file.
clopper.pearson.ci: no visible global function definition for ‘qbeta’
cm.clopper.pearson.ci: no visible global function definition for
  ‘uniroot’
cm.clopper.pearson.ci : <anonymous>: no visible global function
  definition for ‘pbeta’
cm.n.clopper.pearson: no visible global function definition for
  ‘uniroot’
cm.n.clopper.pearson : <anonymous>: no visible global function
  definition for ‘pbeta’
n.clopper.pearson: no visible global function definition for ‘uniroot’
n.clopper.pearson : <anonymous>: no visible global function definition
  for ‘pbeta’
rgbinom: no visible global function definition for ‘runif’
Undefined global functions or variables:
  pbeta qbeta runif uniroot
Consider adding
  importFrom("stats", "pbeta", "qbeta", "runif", "uniroot")
to your NAMESPACE file.
genmvnorm: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Package suggested but not available for checking: ‘genderdata’
gPopCreate: no visible global function definition for ‘rnorm’
periodogram.freq: no visible global function definition for ‘spectrum’
periodogram.freq: no visible global function definition for ‘frequency’
periodogram.spec.single: no visible global function definition for
  ‘spectrum’
periodogram.spec.single: no visible global function definition for
  ‘fft’
robust.g.test: no visible global function definition for ‘read.table’
robust.g.test: no visible global function definition for ‘density’
robust.spectrum: no visible global function definition for ‘density’
robust.spectrum.single: no visible global function definition for ‘fft’
spearman: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor density fft frequency read.table rnorm spectrum
Consider adding
  importFrom("stats", "cor", "density", "fft", "frequency", "rnorm",
             "spectrum")
  importFrom("utils", "read.table")
to your NAMESPACE file.
t1p1: no visible global function definition for ‘var’
t1p1: no visible global function definition for ‘pt’
t1p2: no visible global function definition for ‘pt’
Undefined global functions or variables:
  pt var
Consider adding
  importFrom("stats", "pt", "var")
to your NAMESPACE file.
Rd file 'flexorhtest.Rd':
  \examples lines wider than 100 characters:
          plot(x,y, main="Location and Strong Order Restrictions",cex.axis=1.5, cex.lab=1.5, cex.main=1.5, cex=1.5)

These lines will be truncated in the PDF manual.
load.genelist: no visible global function definition for ‘read.delim’
Undefined global functions or variables:
  read.delim
Consider adding
  importFrom("utils", "read.delim")
to your NAMESPACE file.
Rd file 'geneListPie-package.Rd':
  \examples lines wider than 100 characters:
     glist<-c("ABCB7","ABCF1","ABHD2","ACAD9","ACIN1","AMOTL1","ANLN","ANXA4","APBA2","APBA3","BAI3","BCLAF1","BEST1")

Rd file 'geneListProfile.Rd':
  \examples lines wider than 100 characters:
     glist<-c("ABCB7","ABCF1","ABHD2","ACAD9","ACIN1","AMOTL1","ANLN","ANXA4","APBA2","APBA3","BAI3","BCLAF1","BEST1")

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: ‘RHugin’
fit.dbn: no visible global function definition for ‘as’
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' calls to packages already attached by Depends:
  ‘igraph’ ‘splines’
  Please remove these calls from your code.
Found the following apparent S3 methods exported but not registered:
  plot.GeneReg
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Found an obsolete/platform-specific call in the following function:
  ‘timedelay.lm’
Found the platform-specific device:
  ‘x11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
timedelay.lm: no visible global function definition for ‘lm’
timedelay.lm: no visible global function definition for ‘AIC’
timedelay.lm: no visible global function definition for ‘pdf’
timedelay.lm: no visible global function definition for ‘x11’
timedelay.lm: no visible global function definition for ‘rainbow’
timedelay.lm: no visible global function definition for ‘title’
timedelay.lm: no visible global function definition for ‘lines’
timedelay.lm: no visible global function definition for ‘predict’
timedelay.lm: no visible global function definition for ‘points’
timedelay.lm: no visible global function definition for ‘legend’
timedelay.lm: no visible global function definition for ‘dev.off’
timedelay.univariate.lm: no visible global function definition for ‘lm’
timedelay.univariate.lm: no visible global function definition for
  ‘AIC’
ts.bspline: no visible global function definition for ‘lm’
ts.bspline: no visible global function definition for ‘predict’
Undefined global functions or variables:
  AIC dev.off legend lines lm pdf points predict rainbow title x11
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "rainbow", "x11")
  importFrom("graphics", "legend", "lines", "points", "title")
  importFrom("stats", "AIC", "lm", "predict")
to your NAMESPACE file.
prepare_Rd: GeneReg-package.Rd:12-13: Dropping empty section \usage
prepare_Rd: GeneReg-package.Rd:14-15: Dropping empty section \arguments
Found the following apparent S3 methods exported but not registered:
  diseq.ci summary.LD.data.frame
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Package unavailable to check Rd xrefs: ‘GeneticsDesign’
S3 methods shown with full name in documentation object 'diseq':
  ‘diseq.ci’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
ForImp.Mahala: no visible global function definition for ‘combn’
ForImp.Mahala: no visible global function definition for ‘var’
ForImp.Mahala: no visible global function definition for ‘quantile’
ForImp.Mahala : <anonymous>: no visible global function definition for
  ‘var’
ForImp.Mahala : <anonymous> : <anonymous>: no visible global function
  definition for ‘var’
ForImp.Mahala : <anonymous> : <anonymous>: no visible global function
  definition for ‘quantile’
ForImp.PCA: no visible global function definition for ‘cov’
ForImp.PCA: no visible global function definition for ‘princomp’
ForImp.PCA: no visible global function definition for ‘combn’
ForImp.PCA: no visible global function definition for ‘quantile’
ForImp.PCA : <anonymous> : <anonymous>: no visible global function
  definition for ‘quantile’
Undefined global functions or variables:
  combn cov princomp quantile var
Consider adding
  importFrom("stats", "cov", "princomp", "quantile", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
Package in Depends field not imported from: ‘KernSmooth’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
KernSec: no visible global function definition for ‘na.omit’
KernSur: no visible global function definition for ‘na.fail’
KernSur: no visible global function definition for ‘na.omit’
bandwidthselect: no visible global function definition for ‘na.omit’
bandwidthselect: no visible global function definition for ‘dpik’
correlationselect: no visible global function definition for ‘cor’
nearest: no visible global function definition for ‘na.fail’
nearest: no visible global function definition for ‘na.omit’
per: no visible global function definition for ‘na.fail’
Undefined global functions or variables:
  cor dpik na.fail na.omit
Consider adding
  importFrom("stats", "cor", "na.fail", "na.omit")
to your NAMESPACE file.
MOSS_GWAS: no visible global function definition for ‘complete.cases’
MOSS_GWAS_main: no visible global function definition for ‘rbinom’
MOSS_GWAS_main: no visible global function definition for ‘na.omit’
MOSS_GWAS_main: no visible global function definition for ‘glm’
MOSS_GWAS_main: no visible global function definition for ‘poisson’
MOSS_Hierarchical: no visible global function definition for
  ‘as.formula’
MOSS_Hierarchical: no visible global function definition for ‘rbinom’
cvFunc: no visible global function definition for ‘na.omit’
findDualGenerators: no visible global function definition for ‘na.omit’
findGenerators: no visible global function definition for ‘na.omit’
findLogMargLik: no visible global function definition for ‘na.omit’
findModel: no visible global function definition for ‘as.formula’
findNeighbours: no visible global function definition for ‘na.omit’
fitInteractionModels: no visible global function definition for
  ‘na.omit’
fitInteractionModels: no visible global function definition for ‘glm’
fitInteractionModels: no visible global function definition for
  ‘poisson’
getSubsets: no visible global function definition for ‘na.omit’
logLaplace: no visible global function definition for ‘as.formula’
logLaplace: no visible global function definition for ‘model.matrix’
logLaplace: no visible global function definition for ‘glm’
logLaplace: no visible global function definition for ‘poisson’
mWindow: no visible global function definition for ‘complete.cases’
prettyFormula: no visible global function definition for ‘na.omit’
randomHierModel: no visible global function definition for ‘rbinom’
recode_data: no visible global function definition for ‘complete.cases’
Undefined global functions or variables:
  as.formula complete.cases glm model.matrix na.omit poisson rbinom
Consider adding
  importFrom("stats", "as.formula", "complete.cases", "glm",
             "model.matrix", "na.omit", "poisson", "rbinom")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  predict.gensemble print.gensemble
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
ab.create: no visible global function definition for ‘new’
ab.predict: no visible binding for global variable ‘predict’
gensemble: no visible global function definition for ‘new’
perturb: no visible global function definition for ‘rnorm’
pred_error: no visible global function definition for ‘na.omit’
reg_iter_summary: no visible global function definition for ‘var’
reg_iter_summary: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor na.omit new predict rnorm var
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "cor", "na.omit", "predict", "rnorm", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Rd file 'AbstractModel-class.Rd':
  \examples lines wider than 100 characters:
     abm <- ab.create(model.call="ksvm", model.args=ksvm_model_args, predict.args=list(type="probabilities"), xtrans=as.matrix)
     abm <- ab.create(model.call="rpart", model.args=list(control=rpart.control(minsplit=0)), predict.args=list(type='prob'))
     abm <- ab.create(model.call="nnet", model.args=list(size=3, linout=TRUE, maxit=400, rang=0.001, decay=0.0001), xtrans=as.matrix)
     abm <- ab.create(model.call="rpart", model.args=list(method='anova', control=rpart.control(minsplit=2, cp=1e-03)))

Rd file 'predict.gensemble.Rd':
  \usage lines wider than 90 characters:
     predict(object, X, type = c("prob", "class"), method = c("prob", "vote"), return.all = F, ...)

These lines will be truncated in the PDF manual.
splineAnalyze: no visible global function definition for ‘var’
splineAnalyze: no visible global function definition for ‘par’
splineAnalyze: no visible global function definition for ‘plot’
splineAnalyze: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines par plot var
Consider adding
  importFrom("graphics", "lines", "par", "plot")
  importFrom("stats", "var")
to your NAMESPACE file.
PAEA : <anonymous>: no visible global function definition for
  ‘integrate’
PAEAAnalysis: no visible global function definition for
  ‘txtProgressBar’
PAEAAnalysis : <anonymous>: no visible global function definition for
  ‘setTxtProgressBar’
PAEAAnalysis: no visible global function definition for ‘par’
PAEAAnalysis: no visible global function definition for ‘barplot’
chdirSig: no visible global function definition for ‘prcomp’
chdirSig: no visible global function definition for ‘rchisq’
chdirSig: no visible global function definition for ‘txtProgressBar’
chdirSig : <anonymous> : <anonymous>: no visible global function
  definition for ‘setTxtProgressBar’
chdirplots : <anonymous>: no visible global function definition for
  ‘par’
chdirplots : <anonymous>: no visible global function definition for
  ‘plot’
chdirplots : <anonymous>: no visible global function definition for
  ‘arrows’
chdirplots : <anonymous>: no visible global function definition for
  ‘barplot’
multigmtPAEAAnalysis: no visible global function definition for
  ‘txtProgressBar’
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for ‘setTxtProgressBar’
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for ‘data’
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for ‘write.table’
Undefined global functions or variables:
  arrows barplot data integrate par plot prcomp rchisq
  setTxtProgressBar txtProgressBar write.table
Consider adding
  importFrom("graphics", "arrows", "barplot", "par", "plot")
  importFrom("stats", "integrate", "prcomp", "rchisq")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar",
             "write.table")
to your NAMESPACE file.
SimTangleData: no visible global function definition for ‘runif’
SimTangleData: no visible global function definition for ‘dist’
SimTangleData: no visible global function definition for ‘rnorm’
SimTangleData: no visible global function definition for ‘qgamma’
SimTangleData: no visible global function definition for ‘pnorm’
SimTangleData: no visible global function definition for ‘rmultinom’
TangleInference: no visible global function definition for ‘rnorm’
TangleInferenceGauss : thetaOpt: no visible global function definition
  for ‘dist’
TangleInferenceGauss : thetaOpt: no visible global function definition
  for ‘optim’
TangleInferenceGauss : predError: no visible global function definition
  for ‘dist’
Undefined global functions or variables:
  dist optim pnorm qgamma rmultinom rnorm runif
Consider adding
  importFrom("stats", "dist", "optim", "pnorm", "qgamma", "rmultinom",
             "rnorm", "runif")
to your NAMESPACE file.
Rd file 'fujitopo.Rd':
  \examples lines wider than 100 characters:
     PLOC=list(LON=range(fujitopo$lon), x=range(fujitopo$lon), LAT=range(fujitopo$lat), y=range(fujitopo$lat))

These lines will be truncated in the PDF manual.
getJson: no visible global function definition for ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
geoscaleBox: no visible global function definition for ‘boxplot’
geoscaleBox: no visible global function definition for ‘par’
geoscaleBox: no visible global function definition for ‘plot’
geoscaleBox: no visible global function definition for ‘text’
geoscaleBox: no visible global function definition for ‘segments’
geoscaleBox: no visible global function definition for ‘rect’
geoscaleBox: no visible global function definition for ‘rgb’
geoscaleBox: no visible global function definition for ‘polygon’
geoscaleBox: no visible global function definition for ‘points’
geoscaleBox: no visible global function definition for ‘axis’
geoscalePlot: no visible global function definition for ‘par’
geoscalePlot: no visible global function definition for ‘plot’
geoscalePlot: no visible global function definition for ‘text’
geoscalePlot: no visible global function definition for ‘segments’
geoscalePlot: no visible global function definition for ‘rect’
geoscalePlot: no visible global function definition for ‘rgb’
geoscalePlot: no visible global function definition for ‘points’
geoscalePlot: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis boxplot par plot points polygon rect rgb segments text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "boxplot", "par", "plot", "points",
             "polygon", "rect", "segments", "text")
to your NAMESPACE file.
ImagePoly: no visible global function definition for ‘plot’
performSinglePlot: no visible global function definition for
  ‘heat.colors’
Undefined global functions or variables:
  heat.colors plot
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "plot")
to your NAMESPACE file.
Found the following calls to data() loading into the global environment:
File ‘geotools/R/zzz.R’:
  data(fr_geo_rad)
See section ‘Good practice’ in ‘?data’.
GESTr: no visible global function definition for ‘rnorm’
GESTr: no visible global function definition for ‘sd’
GESTr : <anonymous>: no visible global function definition for ‘pnorm’
TranSAM : magChange: no visible global function definition for ‘median’
TranSAM : dstat: no visible global function definition for ‘sd’
TranSAM: no visible binding for global variable ‘sd’
TranSAM: no visible global function definition for ‘quantile’
findReplicateGroups: no visible global function definition for ‘qnorm’
findReplicateGroups: no visible global function definition for ‘sd’
fitGMM : simulateData: no visible global function definition for
  ‘rnorm’
fitGMM : simulateData: no visible global function definition for ‘sd’
fitGMM: no visible global function definition for ‘median’
fitGMM: no visible global function definition for ‘ks.test’
fitRockeDurbin: no visible global function definition for ‘dist’
fitRockeDurbin : findLowGenes: no visible global function definition
  for ‘median’
fitRockeDurbin : findLowGenes: no visible global function definition
  for ‘mad’
fitRockeDurbin: no visible binding for global variable ‘sd’
getMonotonicConfidences_multiclass: no visible global function
  definition for ‘pnorm’
getMonotonicConfidences_multiclass: no visible global function
  definition for ‘sd’
Undefined global functions or variables:
  dist ks.test mad median pnorm qnorm quantile rnorm sd
Consider adding
  importFrom("stats", "dist", "ks.test", "mad", "median", "pnorm",
             "qnorm", "quantile", "rnorm", "sd")
to your NAMESPACE file.
Rd file 'TranSAM.Rd':
  \usage lines wider than 90 characters:
     TranSAM(x,samples1,samples2,minChange=0.2,var_filter=0.01,maxFDR=1,changeStep=0.1,scoreFun="magChange")
  \examples lines wider than 100 characters:
     selected.columns <- sort(c(sample(1:ncol(ABIdata),30),which(colnames(ABIdata) %in% c("GSM194513","GSM194514","GSM194515","GSM194516","G ... [TRUNCATED]

These lines will be truncated in the PDF manual.
'library' or 'require' call to ‘party’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘party’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gTree: no visible global function definition for ‘ctree’
gTree: no visible global function definition for ‘ctree_control’
guttmanErrors: no visible global function definition for ‘runif’
Undefined global functions or variables:
  ctree ctree_control runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Running ‘testthat.R’ [28s/39s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(getTBinR)
  > 
  > test_check("getTBinR")
  trying URL 'https://extranet.who.int/tme/generateCSV.asp?ds=estimates'
  downloaded 711 KB
  
  trying URL 'https://extranet.who.int/tme/generateCSV.asp?ds=dictionary'
  downloaded 63 KB
  
  trying URL 'https://extranet.who.int/tme/generateCSV.asp?ds=estimates'
  downloaded 711 KB
  
  trying URL 'https://extranet.who.int/tme/generateCSV.asp?ds=mdr_rr_estimates'
  downloaded 30 KB
  
  ── 1. Failure: map_tb_burden can have a custom legend specified. (@test-map_tb_b
  plot$labels$fill not equal to `test_label`.
  1/1 mismatches
  x[1]: "`test (test - test)`"
  y[1]: "test (test - test)"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 83 SKIPPED: 29 FAILED: 1
  1. Failure: map_tb_burden can have a custom legend specified. (@test-map_tb_burden.R#62) 
  
  Error: testthat unit tests failed
  Execution halted
Missing or unexported object: ‘stable::dstable.quick’
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
'library' or 'require' call to ‘multtest’ which was already attached by Depends.
  Please remove these calls from your code.
Rd file 'gexmap.Rd':
  \usage lines wider than 90 characters:
     gexmap(genome = "homosapiens", scale = "", source = "", res = "", isGO = FALSE, isMAP = TRUE, lim_chi = 5, global_test_choice = 4, pcor ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  FORCE_certify.c:116:15: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/GFORCE.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_41_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/gglasso.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.

Attaching package: 'gglogo'

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

    fortify

Killed
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘ggplot2’
A package should be listed in only one of these fields.
Package in Depends field not imported from: ‘ggplot2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ggroc: no visible global function definition for ‘ggplot’
ggroc: no visible global function definition for ‘aes’
ggroc: no visible global function definition for ‘geom_point’
ggroc: no visible global function definition for ‘geom_line’
ggroc: no visible global function definition for ‘theme’
ggroc: no visible global function definition for ‘element_text’
ggroc: no visible global function definition for ‘labs’
ggroc: no visible global function definition for ‘ggsave’
Undefined global functions or variables:
  aes element_text geom_line geom_point ggplot ggsave labs theme
Running examples in ‘ggspatial-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: layer_spatial
> ### Title: Turn a spatial object into a ggplot2 layer
> ### Aliases: layer_spatial annotation_spatial layer_spatial.default
> ###   annotation_spatial.default
> 
> ### ** Examples
> 
> load_longlake_data()
> 
> ggplot() +
+ 
+   # annotation_spatial() layers don't train the scales, so data stays central
+   annotation_spatial(longlake_roadsdf, size = 2, col = "black") +
+   annotation_spatial(longlake_roadsdf, size = 1.6, col = "white") +
+ 
+   # raster layers train scales and get projected automatically
+   layer_spatial(longlake_depth_raster, aes(alpha = stat(band1)), fill = "darkblue") +
+   scale_alpha_continuous(na.value = 0) +
+ 
+   # layer_spatial() layers train the scales
+   layer_spatial(longlake_depthdf, aes(col = DEPTH.M)) +
+ 
+   # spatial-aware automagic scale bar
+   annotation_scale(location = "tl") +
+ 
+   # spatial-aware automagic north arrow
+   annotation_north_arrow(location = "br", which_north = "true")
Error in FUN(X[[i]], ...) : object 'DEPTH.M' not found
Calls: <Anonymous> ... <Anonymous> -> f -> scales_add_defaults -> lapply -> FUN
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 36-39 (ggspatial.Rmd) 
Error: processing vignette ‘ggspatial.Rmd’ failed with diagnostics:
object ‘DEPTH.M’ not found
Execution halted
checkRd: (7) coord_tern.Rd:32: Tag \strong is invalid in a \code block
checkRd: (7) geom_Xisoprop.Rd:65: Tag \strong is invalid in a \code block
checkRd: (7) geom_confidence_tern.Rd:94: Tag \strong is invalid in a \code block
checkRd: (7) geom_crosshair_tern.Rd:89: Tag \strong is invalid in a \code block
checkRd: (7) geom_density_tern.Rd:102: Tag \strong is invalid in a \code block
checkRd: (7) geom_errorbarX.Rd:82: Tag \strong is invalid in a \code block
checkRd: (7) geom_errorbarX.Rd:87: Tag \strong is invalid in a \code block
checkRd: (7) geom_errorbarX.Rd:92: Tag \strong is invalid in a \code block
checkRd: (7) geom_interpolate_tern.Rd:105: Tag \strong is invalid in a \code block
checkRd: (7) geom_label_viewport.Rd:81: Tag \strong is invalid in a \code block
checkRd: (7) geom_mean_ellipse.Rd:84: Tag \strong is invalid in a \code block
checkRd: (7) geom_text_viewport.Rd:77: Tag \strong is invalid in a \code block
Namespace with empty importFrom: ‘statmod’
acovamcmc: no visible global function definition for ‘rnorm’
acovamcmc: no visible global function definition for ‘rgamma’
acovamcmc: no visible binding for global variable ‘quantile’
acovamcmc: no visible global function definition for ‘quantile’
acovamcmc: no visible global function definition for ‘var’
plot.acovamcmc: no visible global function definition for ‘dev.new’
plot.acovamcmc: no visible global function definition for ‘par’
plot.acovamcmc: no visible global function definition for ‘plot’
plot.acovamcmc: no visible global function definition for ‘density’
plot.acovamcmc: no visible global function definition for ‘acf’
plot.acovamcmc: no visible global function definition for ‘contour’
plot.acovamcmc: no visible global function definition for ‘image’
plot.acovamcmc: no visible global function definition for ‘persp’
Undefined global functions or variables:
  acf contour density dev.new image par persp plot quantile rgamma
  rnorm var
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "contour", "image", "par", "persp", "plot")
  importFrom("stats", "acf", "density", "quantile", "rgamma", "rnorm",
             "var")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘gibbs.met/R/firstlib.R’:
  .First.lib calls:
    cat("Naive Gibbs Sampling with Metropolis steps(gibbs.met) loaded\n",     "COPYRIGHT 2008 (c) Longhai Li (http://math.usask.ca/~longhai)\n",     "Type ?begin.gibbs.met for help to this package\n", sep = "")

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

met_gaussian : one_transition: no visible global function definition
  for ‘rnorm’
met_gaussian : one_transition: no visible global function definition
  for ‘runif’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
ssa.btl: no visible global function definition for ‘rbinom’
ssa.btl: no visible global function definition for ‘rpois’
ssa.btl.diag: no visible global function definition for ‘rbinom’
ssa.btl.diag: no visible global function definition for ‘rpois’
ssa.d: no visible global function definition for ‘runif’
ssa.d.diag: no visible global function definition for ‘runif’
ssa.etl: no visible global function definition for ‘rpois’
ssa.etl.diag: no visible global function definition for ‘rpois’
ssa.otl: no visible global function definition for ‘runif’
ssa.otl: no visible global function definition for ‘rpois’
ssa.otl.diag: no visible global function definition for ‘runif’
ssa.otl.diag: no visible global function definition for ‘rpois’
ssa.plot: no visible global function definition for ‘rainbow’
ssa.plot: no visible global function definition for ‘matplot’
ssa.plot: no visible global function definition for ‘title’
ssa.plot: no visible global function definition for ‘legend’
ssa.plot: no visible global function definition for ‘mtext’
ssa.run: no visible global function definition for ‘flush.console’
ssa.terminate: no visible global function definition for ‘sd’
Undefined global functions or variables:
  flush.console legend matplot mtext rainbow rbinom rpois runif sd
  title
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend", "matplot", "mtext", "title")
  importFrom("stats", "rbinom", "rpois", "runif", "sd")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Running examples in ‘giphyr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gif_search
> ### Title: Search GIFs by key words throught giphy API
> ### Aliases: gif_search
> 
> ### ** Examples
> 
> gif_search("cat")
Error in bind_rows_(x, .id) : Argument 19 must be length 1, not 3
Calls: gif_search ... content_exporter -> map_df -> <Anonymous> -> bind_rows_
Execution halted
choro.legend: no visible global function definition for ‘strwidth’
choro.legend: no visible global function definition for ‘legend’
choro.legend: no visible global function definition for ‘text’
jitter.points: no visible global function definition for ‘rnorm’
level.plot: no visible global function definition for ‘.filled.contour’
map.scale: no visible global function definition for ‘par’
map.scale: no visible global function definition for ‘rect’
map.scale: no visible global function definition for ‘lines’
map.scale: no visible global function definition for ‘text’
map.scale: no visible global function definition for ‘strheight’
north.arrow: no visible global function definition for ‘polygon’
north.arrow: no visible global function definition for ‘text’
north.arrow: no visible global function definition for ‘strheight’
poly.labels: no visible global function definition for ‘slot’
poly.labels : <anonymous>: no visible global function definition for
  ‘slot’
quantileCuts: no visible global function definition for ‘quantile’
sdCuts: no visible global function definition for ‘sd’
Undefined global functions or variables:
  .filled.contour legend lines par polygon quantile rect rnorm sd slot
  strheight strwidth text
Consider adding
  importFrom("graphics", ".filled.contour", "legend", "lines", "par",
             "polygon", "rect", "strheight", "strwidth", "text")
  importFrom("methods", "slot")
  importFrom("stats", "quantile", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘lattice’
A package should be listed in only one of these fields.
Package in Depends field not imported from: ‘lattice’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘lattice:::latticeParseFormula’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘lattice:::compute.packet’ ‘lattice:::cond.orders’
  ‘lattice:::construct.scales’ ‘lattice:::cupdate’
  ‘lattice:::limits.and.aspect’ ‘lattice:::logLimits’
  ‘lattice:::needAutoKey’ ‘lattice:::prepanel.null’
  ‘lattice:::scale.limits’ ‘lattice:::trellis.skeleton’
  ‘lattice:::updateList’
  See the note in ?`:::` about the use of this operator.
Found the following apparent S3 methods exported but not registered:
  pyramid2.formula
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
panel.pyramid: no visible global function definition for
  ‘trellis.par.get’
panel.pyramid: no visible global function definition for
  ‘current.panel.limits’
panel.pyramid: no visible global function definition for ‘panel.abline’
panel.pyramid: no visible global function definition for ‘panel.rect’
pyramid2.formula: no visible global function definition for
  ‘lattice.getOption’
pyramid2.formula: no visible global function definition for
  ‘is.shingle’
pyramid2.formula: no visible global function definition for
  ‘as.factorOrShingle’
pyramidlattice: no visible global function definition for ‘update’
useOuterStrips2: no visible global function definition for ‘modifyList’
useOuterStrips2 : new.strip: no visible global function definition for
  ‘strip.default’
useOuterStrips2 : new.strip.left: no visible global function definition
  for ‘strip.default’
useOuterStrips2: no visible global function definition for ‘update’
Undefined global functions or variables:
  as.factorOrShingle current.panel.limits is.shingle lattice.getOption
  modifyList panel.abline panel.rect strip.default trellis.par.get
  update
Consider adding
  importFrom("stats", "update")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
fptcdf: no visible global function definition for ‘dnorm’
fptcdf: no visible global function definition for ‘pnorm’
fptpdf: no visible global function definition for ‘pnorm’
fptpdf: no visible global function definition for ‘dnorm’
lba: no visible global function definition for ‘as.formula’
lba: no visible global function definition for ‘model.frame’
lba : logl: no visible global function definition for ‘head’
lba: no visible global function definition for ‘optim’
pmod: no visible global function definition for ‘model.frame’
pmod: no visible global function definition for ‘model.matrix’
rlba: no visible global function definition for ‘pnorm’
rlba: no visible global function definition for ‘rnorm’
rlba: no visible global function definition for ‘runif’
tablba: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as.formula dnorm head model.frame model.matrix optim pnorm rnorm
  runif
Consider adding
  importFrom("stats", "as.formula", "dnorm", "model.frame",
             "model.matrix", "optim", "pnorm", "rnorm", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  anova.gllm summary.gllm
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
anova.gllm: no visible global function definition for ‘pchisq’
emgllm: no visible global function definition for ‘model.matrix’
print.ld2: no visible global function definition for ‘anova’
scoregllm: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  anova model.matrix pchisq
Consider adding
  importFrom("stats", "anova", "model.matrix", "pchisq")
to your NAMESPACE file.
Authors@R field gives persons with no role:
  Mark S.
        Handcock Developer <handcock@stat.ucla.edu>
  Michael S.
        Rendall Developer <mrendall@rand.org>
Package in Depends field not imported from: ‘emplik’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  coef.glmc deviance.glmc effects.glmc family.glmc fitted.glmc
  print.summary.glmc residuals.glmc summary.glmc
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Calls with DUP:
   .C("gaulep", as.double(x), as.double(y), as.double(ls[i]), as.double(kappa), 
       as.double(tol), as.integer(max.ite), as.integer(n), as.integer(p), 
       as.double(beta0), DUP = FALSE)
   .C("binlep", as.double(x), as.double(y), as.double(ls[i]), as.double(kappa), 
       as.double(tol), as.integer(max.ite), as.integer(n), as.integer(p), 
       as.double(beta0), DUP = FALSE)
   .C("gaulep", as.double(train.x), as.double(train.y), as.double(ls[i]), 
       as.double(kappa), as.double(tol), as.integer(max.ite), as.integer(nj), 
       as.integer(p), as.double(beta0), DUP = FALSE)
   .C("binlep", as.double(train.x), as.double(train.y), as.double(ls[i]), 
       as.double(kappa), as.double(tol), as.integer(max.ite), as.integer(nj), 
       as.integer(p), as.double(beta0), DUP = FALSE)
   .C("gaulep", as.double(x), as.double(y), as.double(ls[i]), as.double(kappa), 
       as.double(tol), as.integer(max.ite), as.integer(n), as.integer(p), 
       as.double(beta0), DUP = FALSE)
   .C("binlep", as.double(x), as.double(y), as.double(ls[i]), as.double(kappa), 
       as.double(tol), as.integer(max.ite), as.integer(n), as.integer(p), 
       as.double(beta0), DUP = FALSE)
DUP is no longer supported and will be ignored.
SetLambda: no visible global function definition for ‘lm’
Undefined global functions or variables:
  lm
Consider adding
  importFrom("stats", "lm")
to your NAMESPACE file.
Found the following significant warnings:
  glmmTMB.cpp:845:10: warning: explicitly assigning value of variable of type 'vector<Type>' to itself [-Wself-assign-overloaded]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/glmmTMB.Rcheck/00install.out’ for details.
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.
globalboosttest: no visible global function definition for ‘predict’
globalboosttest: no visible global function definition for ‘lm’
globalboosttest: no visible global function definition for ‘glm’
globalboosttest: no visible binding for global variable ‘binomial’
globalboosttest: no visible global function definition for ‘points’
globalboosttest: no visible global function definition for ‘AIC’
Undefined global functions or variables:
  AIC binomial glm lm points predict
Consider adding
  importFrom("graphics", "points")
  importFrom("stats", "AIC", "binomial", "glm", "lm", "predict")
to your NAMESPACE file.
prepare_Rd: globalboosttest.Rd:56: Dropping empty section \seealso
Rd file 'globalboosttest.Rd':
  \usage lines wider than 90 characters:
     globalboosttest(X,Y,Z=NULL,nperm=1000,mstop=1000,mstopAIC=FALSE,pvalueonly=TRUE,plot=FALSE,...)

These lines will be truncated in the PDF manual.
.nPerms: no visible global function definition for ‘terms’
expr.dev.test: no visible global function definition for ‘terms’
expr.dev.test: no visible global function definition for ‘model.matrix’
expr.dev.test: no visible global function definition for ‘pchisq’
lancaster: no visible global function definition for ‘pgamma’
liptak: no visible global function definition for ‘pnorm’
summary.dev.test : ci: no visible global function definition for
  ‘qnorm’
varwiselogLik : <anonymous>: no visible global function definition for
  ‘deviance’
varwiselogLik.regression: no visible global function definition for
  ‘glm.fit’
Undefined global functions or variables:
  deviance glm.fit model.matrix pchisq pgamma pnorm qnorm terms
Consider adding
  importFrom("stats", "deviance", "glm.fit", "model.matrix", "pchisq",
             "pgamma", "pnorm", "qnorm", "terms")
to your NAMESPACE file.
CreateFormula: no visible global function definition for ‘as.formula’
GeneratePvalues: no visible binding for global variable ‘binomial’
globalARTP: no visible binding for global variable ‘binomial’
globalFisher: no visible binding for global variable ‘binomial’
globalFisher: no visible global function definition for ‘pchisq’
globalSimes: no visible binding for global variable ‘binomial’
pvalFmla: no visible binding for global variable ‘binomial’
pvalFmla: no visible global function definition for ‘glm’
pvalFmla: no visible global function definition for ‘anova’
runPermut: no visible binding for global variable ‘binomial’
runPvalues: no visible binding for global variable ‘binomial’
Undefined global functions or variables:
  anova as.formula binomial glm pchisq
Consider adding
  importFrom("stats", "anova", "as.formula", "binomial", "glm", "pchisq")
to your NAMESPACE file.
ScoreTest: no visible global function definition for ‘pchisq’
Var1: no visible global function definition for ‘runif’
gLRT1: no visible global function definition for ‘pchisq’
gLRT2: no visible global function definition for ‘pchisq’
gLRT3: no visible global function definition for ‘pchisq’
gLRT4: no visible global function definition for ‘pf’
Undefined global functions or variables:
  pchisq pf runif
Consider adding
  importFrom("stats", "pchisq", "pf", "runif")
to your NAMESPACE file.
plot.bGAMM: no visible global function definition for ‘par’
plot.bGAMM: no visible global function definition for ‘plot’
plot.bGAMM: no visible global function definition for ‘lines’
plot.bGAMM: no visible global function definition for ‘rug’
Undefined global functions or variables:
  lines par plot rug
Consider adding
  importFrom("graphics", "lines", "par", "plot", "rug")
to your NAMESPACE file.
Running examples in ‘gmnl-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getSummary.gmnl
> ### Title: Get Model Summaries for Use with "mtable"
> ### Aliases: getSummary.gmnl
> 
> ### ** Examples
> 
> ## Estimate MNL models
> data("TravelMode", package = "AER")
> library(mlogit)
> TM <- mlogit.data(TravelMode, choice = "choice", shape = "long", 
+                  alt.levels = c("air", "train", "bus", "car"), chid.var = "individual")
>                  
> mnl.1 <- gmnl(choice ~ wait + vcost + travel + gcost | 0, data = TM)
> mnl.2 <- gmnl(choice ~ wait + vcost                  | 0, data = TM) 
> 
> ## Table
> library(memisc)
Loading required package: lattice
Loading required package: MASS

Attaching package: ‘memisc’

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

    contr.sum, contr.treatment, contrasts

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

    as.array

> mtable("MNL 1"= mnl.1, "MNL 2" = mnl.2, 
+        summary.stats = c("N", "Log-likelihood", "BIC", "AIC"))
Error in UseMethod("getSummary") : 
  no applicable method for 'getSummary' applied to an object of class "gmnl"
Calls: mtable -> lapply -> FUN
Execution halted
Found the following significant warnings:
  Evaluation.cpp:173:9: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to true [-Wtautological-undefined-compare]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/gnmf.Rcheck/00install.out’ for details.
File ‘gnmf/libs/gnmf.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘FactorMatrix.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘FactorMatrix.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package in Depends field not imported from: ‘lpSolve’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  print.llgpcptab print.llgpout print.llgptab
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
prepare_Rd: llgpcp.Rd:45-46: Dropping empty section \examples
Rd file 'llgpcp.Rd':
  \usage lines wider than 90 characters:
     llgpcp(coefficients, targets, achievements, variable.classes, maxiter = 1000, verbose = FALSE)

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

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

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'library' or 'require' calls in package code:
  ‘lava’ ‘numDeriv’ ‘survival’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
cumres.lvmfit : myres: no visible global function definition for ‘vars’
cumres.lvmfit: no visible global function definition for ‘iid’
plot.cumres : sampleproc: no visible global function definition for
  ‘lines’
plot.cumres : predband : <anonymous>: no visible binding for global
  variable ‘rgb’
plot.cumres : predband : <anonymous>: no visible global function
  definition for ‘col2rgb’
plot.cumres : predband: no visible global function definition for
  ‘lines’
plot.cumres : predband: no visible global function definition for
  ‘polygon’
Undefined global functions or variables:
  col2rgb iid lines polygon rgb vars
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
  importFrom("graphics", "lines", "polygon")
to your NAMESPACE file.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘GANPA’ ‘WGCNA’
A package should be listed in only one of these fields.
'library' or 'require' calls to packages already attached by Depends:
  ‘GANPA’ ‘WGCNA’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘GANPA’ ‘WGCNA’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GOGANPA: no visible global function definition for ‘GSE.Test.Main’
selectRho: no visible global function definition for
  ‘scaleFreeFitIndex’
Undefined global functions or variables:
  GSE.Test.Main scaleFreeFitIndex
Packages in Depends field not imported from:
  ‘fGarch’ ‘fastICA’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
UprodR: no visible global function definition for ‘combn’
goinit: no visible global function definition for ‘as.formula’
ccor,GoGARCH : <anonymous>: no visible global function definition for
  ‘cov2cor’
ccor,Gopredict : <anonymous>: no visible global function definition for
  ‘cov2cor’
goest,Goestica: no visible global function definition for ‘fastICA’
goest,Goestml: no visible global function definition for ‘nlminb’
goest,Goestmm : <anonymous>: no visible global function definition for
  ‘combn’
goest,Goestnls: no visible global function definition for ‘optim’
show,Goinit: no visible global function definition for ‘head’
show,Gopredict: no visible global function definition for ‘head’
update,GoGARCH: no visible global function definition for
  ‘update.formula’
update,Goestica: no visible global function definition for
  ‘update.formula’
update,Goestml: no visible global function definition for
  ‘update.formula’
update,Goestmm: no visible global function definition for
  ‘update.formula’
update,Goestnls: no visible global function definition for
  ‘update.formula’
Undefined global functions or variables:
  as.formula combn cov2cor fastICA head nlminb optim update.formula
Consider adding
  importFrom("stats", "as.formula", "cov2cor", "nlminb", "optim",
             "update.formula")
  importFrom("utils", "combn", "head")
to your NAMESPACE file.
gpairs: no visible global function definition for ‘hclust’
gpairs: no visible global function definition for ‘dist’
gpairs : scatterplot.panel: no visible global function definition for
  ‘lm’
gpairs : scatterplot.panel: no visible global function definition for
  ‘predict’
gpairs : scatterplot.panel: no visible global function definition for
  ‘prcomp’
gpairs : scatterplot.panel: no visible global function definition for
  ‘cor’
gpairs : scatterplot.panel: no visible global function definition for
  ‘cor.test’
gpairs : scatterplot.panel: no visible global function definition for
  ‘hsv’
gpairs : scatterplot.panel: no visible global function definition for
  ‘na.omit’
gpairs : scatterplot.panel: no visible global function definition for
  ‘pf’
gpairs : scatterplot.panel: no visible global function definition for
  ‘grey’
Undefined global functions or variables:
  cor cor.test dist grey hclust hsv lm na.omit pf prcomp predict
Consider adding
  importFrom("grDevices", "grey", "hsv")
  importFrom("stats", "cor", "cor.test", "dist", "hclust", "lm",
             "na.omit", "pf", "prcomp", "predict")
to your NAMESPACE file.
Random.Start: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
CumulativeVarPlot: no visible global function definition for ‘plot’
CumulativeVarPlot: no visible global function definition for ‘axis’
PCplot: no visible global function definition for ‘par’
PCplot: no visible global function definition for ‘plot’
PCplot: no visible global function definition for ‘rainbow’
PCplot: no visible global function definition for ‘density’
gDist: no visible global function definition for ‘plot’
gDist: no visible global function definition for ‘density’
gDist: no visible global function definition for ‘abline’
gPCA.batchdetect: no visible global function definition for ‘var’
Undefined global functions or variables:
  abline axis density par plot rainbow var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "axis", "par", "plot")
  importFrom("stats", "density", "var")
to your NAMESPACE file.
The following files are already in R: ‘Sweave.sty’
Please remove them from your package.
Warning: no function found corresponding to methods exports from ‘gpclib’ for: ‘coerce’, ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
read.polyfile: no visible global function definition for ‘as’
write.polyfile: no visible global function definition for ‘is’
write.polyfile: no visible global function definition for ‘as’
[,gpc.poly: no visible global function definition for ‘new’
append.poly,gpc.poly-gpc.poly: no visible global function definition
  for ‘new’
coerce,data.frame-gpc.poly: no visible global function definition for
  ‘as’
coerce,list-gpc.poly: no visible global function definition for ‘as’
coerce,matrix-gpc.poly: no visible global function definition for ‘new’
coerce,numeric-gpc.poly: no visible global function definition for
  ‘new’
coerce,numeric-gpc.poly.nohole: no visible global function definition
  for ‘new’
intersect,gpc.poly-gpc.poly: no visible global function definition for
  ‘as’
intersect,gpc.poly-gpc.poly: no visible global function definition for
  ‘new’
setdiff,gpc.poly-gpc.poly: no visible global function definition for
  ‘as’
setdiff,gpc.poly-gpc.poly: no visible global function definition for
  ‘new’
tristrip,gpc.poly: no visible global function definition for ‘as’
union,gpc.poly-gpc.poly: no visible global function definition for ‘as’
union,gpc.poly-gpc.poly: no visible global function definition for
  ‘new’
Undefined global functions or variables:
  as is new
Consider adding
  importFrom("methods", "as", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Namespaces with empty importFrom:
  ‘scatterplot3d’ ‘sqldf’
Resdata : prepdata: no visible global function definition for ‘sqldf’
gpca : Build3d: no visible global function definition for ‘dev.new’
gpca : Build3d: no visible global function definition for
  ‘scatterplot3d’
gpca : Build3d: no visible global function definition for ‘text’
gpca : Build3d: no visible global function definition for ‘plot’
gpca : Build3d: no visible global function definition for ‘abline’
gpca : Build3d: no visible global function definition for ‘rect’
gpca: no visible global function definition for ‘cor’
gpca: no visible global function definition for ‘dev.new’
gpca: no visible global function definition for ‘plot’
gpca: no visible global function definition for ‘text’
gpca: no visible global function definition for ‘abline’
gpca: no visible global function definition for ‘rect’
gpca: no visible global function definition for ‘scatterplot3d’
gpca: no visible global function definition for ‘segments’
gpca: no visible global function definition for ‘points’
gpca: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  abline cor dev.new plot points rect scatterplot3d segments sqldf text
  write.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "plot", "points", "rect", "segments",
             "text")
  importFrom("stats", "cor")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Missing or unexported object: ‘TSA::tsdiag.Arima’
.r1: no visible global function definition for ‘cor’
.r2: no visible global function definition for ‘cor’
rgp: no visible global function definition for ‘runif’
rgp: no visible global function definition for ‘rexp’
Undefined global functions or variables:
  cor rexp runif
Consider adding
  importFrom("stats", "cor", "rexp", "runif")
to your NAMESPACE file.
gpfr: no visible global function definition for ‘rnorm’
gpfr: no visible global function definition for ‘runif’
gpfrpred : <anonymous>: no visible global function definition for
  ‘predict’
gpfrtrain: no visible global function definition for ‘nlminb’
gppredict: no visible global function definition for ‘predict’
gpr: no visible global function definition for ‘rnorm’
gpr: no visible global function definition for ‘runif’
gpr: no visible global function definition for ‘lm’
gpr: no visible global function definition for ‘resid’
gpr: no visible global function definition for ‘nlminb’
main1: no visible global function definition for ‘lm’
main1: no visible global function definition for ‘resid’
main2 : <anonymous>: no visible global function definition for
  ‘predict’
main2: no visible global function definition for ‘predict’
main3: no visible global function definition for ‘lm’
main3: no visible global function definition for ‘resid’
plot.gpfr: no visible global function definition for ‘polygon’
plot.gpfr: no visible global function definition for ‘rgb’
plot.gpfr: no visible global function definition for ‘matpoints’
plot.gpfr: no visible global function definition for ‘matlines’
plot.gpfr: no visible global function definition for ‘lines’
plot.gpr: no visible global function definition for ‘plot’
plot.gpr: no visible global function definition for ‘polygon’
plot.gpr: no visible global function definition for ‘rgb’
plot.gpr: no visible global function definition for ‘points’
plot.gpr: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines lm matlines matpoints nlminb plot points polygon predict resid
  rgb rnorm runif
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "matlines", "matpoints", "plot",
             "points", "polygon")
  importFrom("stats", "lm", "nlminb", "predict", "resid", "rnorm",
             "runif")
to your NAMESPACE file.
GP_fit: no visible global function definition for ‘kmeans’
GP_fit: no visible global function definition for ‘optim’
plot.GP: no visible global function definition for ‘matplot’
plot.GP: no visible global function definition for ‘lines’
plot.GP: no visible global function definition for ‘legend’
Undefined global functions or variables:
  kmeans legend lines matplot optim
Consider adding
  importFrom("graphics", "legend", "lines", "matplot")
  importFrom("stats", "kmeans", "optim")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  boxplot.n plot.lm2
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Checking should be performed on sources prepared by ‘R CMD build’.
Packages in Depends field not imported from:
  ‘foreach’ ‘ggplot2’ ‘isotone’ ‘plyr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls in package code:
  ‘mgcv’ ‘rgl’ ‘tcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
KL: no visible global function definition for ‘complete.cases’
MergeNodes: no visible global function definition for ‘colors’
cross.validate: no visible global function definition for ‘runif’
fit.APFA: no visible global function definition for ‘complete.cases’
fit.APFA: no visible global function definition for ‘aggregate’
select.beagle: no visible global function definition for ‘write.table’
select.beagle: no visible global function definition for ‘aggregate’
select.beagle: no visible global function definition for ‘colors’
simulateAPFA: no visible global function definition for ‘runif’
st: no visible global function definition for ‘colors’
Undefined global functions or variables:
  aggregate colors complete.cases runif write.table
Consider adding
  importFrom("grDevices", "colors")
  importFrom("stats", "aggregate", "complete.cases", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Package in Depends field not imported from: ‘Matrix’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GrassmannOptim: no visible global function definition for ‘rnorm’
GrassmannOptim: no visible global function definition for ‘runif’
GrassmannOptim : <anonymous>: no visible global function definition for
  ‘expm’
GrassmannOptim : <anonymous>: no visible global function definition for
  ‘Matrix’
Undefined global functions or variables:
  Matrix expm rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'taxstats', 'taxstats1516'
accrualReport: multiple local function definitions for ‘gg’ with
  different formal arguments
bestcut2: no visible global function definition for ‘pchisq’
cov.func: no visible global function definition for ‘rbinom’
cov.func: no visible global function definition for ‘cov’
cov.func: no visible global function definition for ‘pnorm’
cox.summary: no visible global function definition for ‘predict’
em.func: no visible global function definition for ‘quantile’
genSurvData: no visible global function definition for ‘rweibull’
greyzone.func: no visible global function definition for ‘points’
greyzone.func: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline cov pchisq pnorm points predict quantile rbinom rweibull
Consider adding
  importFrom("graphics", "abline", "points")
  importFrom("stats", "cov", "pchisq", "pnorm", "predict", "quantile",
             "rbinom", "rweibull")
to your NAMESPACE file.
grid.graph: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Non-standard file/directory found at top level:
  ‘R.css’
Package in Depends field not imported from: ‘spatstat’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GriegSmith: no visible global function definition for ‘is.ppp’
envelopes: no visible binding for global variable ‘quantile’
plot.GriegSmith: no visible global function definition for ‘plot’
plot.GriegSmith: no visible global function definition for ‘lines’
plot.GriegSmith: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis is.ppp lines plot quantile
Consider adding
  importFrom("graphics", "axis", "lines", "plot")
  importFrom("stats", "quantile")
to your NAMESPACE file.
Rd file 'GriegSmith.Rd':
  \examples lines wider than 100 characters:
                     if (max(datapoints[,1]) != max(datapoints[,2])) stop("Your count data must have equal dimensions")

Rd file 'belongtoint.Rd':
  \examples lines wider than 100 characters:
             sum(vect[,1] >= xval & vect[,1] < (xval+int.x) & vect[,2] >= yval & vect[,2] < (yval+int.y));

Rd file 'envelopes.Rd':
  \examples lines wider than 100 characters:
                     perm<-matrix(sample(as.vector(countdata),size=2^(dimention*2),replace=FALSE),nrow=2^dimention,byrow=TRUE);
             ret.val<-cbind(apply(GSpermprev[,-1],1,quantile,probs=c(.05)),apply(GSpermprev[,-1],1,quantile,probs=c(.95)))

Rd file 'sumofsquares.Rd':
  \examples lines wider than 100 characters:
             squaredsums<-sum(apply(submatricies,1,addem,data=singlecounts,xmatlen=xsublength,ymatlen=ysublength));

Rd file 'sums.Rd':
  \usage lines wider than 90 characters:
     sums(coords, dim, xmin = min(coords[, 1]), xmax = max(coords[, 1]), ymin = min(coords[, 2]), ymax = max(coords[, 2]))
  \examples lines wider than 100 characters:
     function (coords,dim,xmin=min(coords[,1]),xmax=max(coords[,1]),ymin=min(coords[,2]),ymax=max(coords[,2])){
             cnts<-matrix(apply(bins,1,belongtoint,vect=coords,int.x=xints,int.y=yints),nrow=dim,byrow=TRUE);

These lines will be truncated in the PDF manual.
PCgamma : <anonymous>: no visible global function definition for
  ‘prcomp’
PCgamma : <anonymous> : <anonymous>: no visible global function
  definition for ‘glm’
PCgamma : <anonymous> : <anonymous>: no visible global function
  definition for ‘update’
PCgamma : <anonymous> : <anonymous>: no visible global function
  definition for ‘pchisq’
PCgamma : <anonymous> : <anonymous>: no visible global function
  definition for ‘lm’
PCgamma : <anonymous> : <anonymous>: no visible global function
  definition for ‘anova’
PCgamma: no visible global function definition for ‘qgamma’
PCgamma: no visible global function definition for ‘pgamma’
RNAgamma : rnafunc: no visible global function definition for
  ‘model.matrix’
RNAgamma : rnafunc: no visible global function definition for
  ‘as.formula’
RNAgamma: no visible global function definition for ‘qgamma’
RNAgamma: no visible global function definition for ‘pgamma’
STTtoShapeParameter : f: no visible global function definition for
  ‘qgamma’
STTtoShapeParameter: no visible global function definition for
  ‘optimize’
Undefined global functions or variables:
  anova as.formula glm lm model.matrix optimize pchisq pgamma prcomp
  qgamma update
Consider adding
  importFrom("stats", "anova", "as.formula", "glm", "lm", "model.matrix",
             "optimize", "pchisq", "pgamma", "prcomp", "qgamma",
             "update")
to your NAMESPACE file.
.gsa.assignGATKTableToEnvironment: no visible global function
  definition for ‘type.convert’
Undefined global functions or variables:
  type.convert
Consider adding
  importFrom("utils", "type.convert")
to your NAMESPACE file.
'library' or 'require' call to ‘impute’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  print.GSA print.GSA.func summary.GSA.genesets
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
GSA: no visible global function definition for ‘impute.knn’
GSA.correlate: no visible global function definition for ‘quantile’
GSA.func: no visible global function definition for ‘quantile’
GSA.func: no visible global function definition for ‘var’
GSA.func: no visible global function definition for ‘qnorm’
GSA.func: no visible global function definition for ‘pt’
GSA.plot: no visible global function definition for ‘plot’
GSA.plot: no visible global function definition for ‘points’
GSA.plot: no visible global function definition for ‘legend’
GSA.xl.correlate: no visible global function definition for ‘quantile’
GSA.xl.plot: no visible global function definition for ‘runif’
GSA.xl.summary.genesets: no visible global function definition for
  ‘quantile’
est.s0: no visible global function definition for ‘quantile’
est.s0: no visible global function definition for ‘mad’
est.s0: no visible global function definition for ‘var’
paired.perm: no visible global function definition for ‘runif’
paired.ttest.func: no visible global function definition for ‘var’
tCorr.func: no visible global function definition for ‘cor’
taCorr.func: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor impute.knn legend mad plot points pt qnorm quantile runif var
Consider adding
  importFrom("graphics", "legend", "plot", "points")
  importFrom("stats", "cor", "mad", "pt", "qnorm", "quantile", "runif",
             "var")
to your NAMESPACE file.
Rd file 'GSA.Rd':
  \usage lines wider than 90 characters:
     method=c("maxmean","mean","absmean"), resp.type=c("Quantitative","Two class unpaired","Survival","Multiclass", "Two class paired", "tCo ... [TRUNCATED]
  \examples lines wider than 100 characters:
     GSA.obj<-GSA(x,y, genenames=genenames, genesets=genesets,  resp.type="Two class unpaired", nperms=100)
     #   GSA.obj<-GSA(x,y, genenames=genenames, genesets=geneset.obj$genesets,  resp.type="Two class unpaired", nperms=100)

Rd file 'GSA.func.Rd':
  \usage lines wider than 90 characters:
     s0 = NULL, s0.perc = NULL, minsize = 15, maxsize= 500, restand = TRUE, restand.basis=c("catalog","data")) 
  \examples lines wider than 100 characters:
     #   GSA.func.obj<-GSA.func(x,y, genenames=genenames, genesets=geneset.obj$genesets,  resp.type="Two class unpaired")

Rd file 'GSA.genescores.Rd':
  \examples lines wider than 100 characters:
     GSA.obj<-GSA(x,y, genenames=genenames, genesets=genesets,  resp.type="Two class unpaired", nperms=100)

Rd file 'GSA.listsets.Rd':
  \examples lines wider than 100 characters:
     GSA.obj<-GSA(x,y, genenames=genenames, genesets=genesets,  resp.type="Two class unpaired", nperms=100)

Rd file 'GSA.plot.Rd':
  \examples lines wider than 100 characters:
     GSA.obj<-GSA(x,y, genenames=genenames, genesets=genesets,  resp.type="Two class unpaired", nperms=100)

These lines will be truncated in the PDF manual.
S3 methods shown with full name in documentation object 'GSA-internal':
  ‘print.GSA.func’ ‘print.GSA’ ‘summary.GSA.genesets’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
garsim: no visible global function definition for ‘rnorm’
garsim: no visible global function definition for ‘rpois’
Undefined global functions or variables:
  rnorm rpois
Consider adding
  importFrom("stats", "rnorm", "rpois")
to your NAMESPACE file.
plotgsCP: no visible global function definition for ‘opts’
plotgsPower: no visible global function definition for ‘opts’
qplotit: no visible global function definition for ‘opts’
Undefined global functions or variables:
  opts
binding: no visible global function definition for ‘rnorm’
binding: no visible binding for global variable ‘var’
binding: no visible global function definition for ‘uniroot’
equivonly: no visible global function definition for ‘rnorm’
equivonly: no visible binding for global variable ‘var’
equivonly: no visible global function definition for ‘uniroot’
figureE: no visible global function definition for ‘rgb’
figureEF: no visible global function definition for ‘rgb’
nfix : f: no visible global function definition for ‘pnorm’
nfix : f: no visible global function definition for ‘qnorm’
nfix: no visible global function definition for ‘uniroot’
nonbinding: no visible global function definition for ‘rnorm’
nonbinding: no visible binding for global variable ‘var’
nonbinding: no visible global function definition for ‘uniroot’
oc: no visible global function definition for ‘rnorm’
oc: no visible global function definition for ‘var’
Undefined global functions or variables:
  pnorm qnorm rgb rnorm uniroot var
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "pnorm", "qnorm", "rnorm", "uniroot", "var")
to your NAMESPACE file.
Namespaces with empty importFrom:
  ‘gee’ ‘geepack’
Rd file 'gtcorr.matrix.Rd':
  \usage lines wider than 90 characters:
     gtcorr.matrix(r, c, m = 1, p, sigma = 0, se = 1, sp = 1, r.prime, c.prime, arrangement = c("rectangular", "diagonal", "random"), model  ... [TRUNCATED]

Rd file 'gtcorr.matrix.user.Rd':
  \usage lines wider than 90 characters:
     gtcorr.matrix.user(clusters, p, sigma=0, se=1, sp=1, model = c("beta-binomial", "Madsen", "Morel-Neerchal"))

These lines will be truncated in the PDF manual.
gte: no visible global function definition for ‘model.extract’
gte: no visible global function definition for ‘model.matrix’
gte: no visible binding for global variable ‘sd’
gte: no visible global function definition for ‘dnorm’
plot.gte: no visible global function definition for ‘plot’
plot.gte: no visible global function definition for ‘par’
plot.gte: no visible global function definition for ‘polygon’
plot.gte: no visible global function definition for ‘gray’
plot.gte: no visible global function definition for ‘lines’
plot.gte: no visible global function definition for ‘legend’
Undefined global functions or variables:
  dnorm gray legend lines model.extract model.matrix par plot polygon
  sd
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "legend", "lines", "par", "plot", "polygon")
  importFrom("stats", "dnorm", "model.extract", "model.matrix", "sd")
to your NAMESPACE file.
Found the following possibly unsafe calls:
File ‘gtools/R/unByteCode.R’:
  unlockBinding(name, env = env)
Found the following apparent S3 methods exported but not registered:
  plot.gvlma plot.gvlmaDel print.gvlma print.gvlmaDel summary.gvlma
  summary.gvlmaDel update.gvlma
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Non-standard file/directory found at top level:
  ‘TITEL’
calculate.threshold: no visible global function definition for ‘pchisq’
gwerAM: no visible global function definition for ‘rnorm’
gwerAM: no visible binding for global variable ‘quantile’
Undefined global functions or variables:
  pchisq quantile rnorm
Consider adding
  importFrom("stats", "pchisq", "quantile", "rnorm")
to your NAMESPACE file.
normalweight: no visible binding for global variable ‘NW_above’
normalweight: no visible binding for global variable ‘NW_below’
obese: no visible global function definition for ‘data’
obese: no visible binding for global variable ‘OB_above’
obese: no visible binding for global variable ‘OB_below’
overweight: no visible global function definition for ‘data’
overweight: no visible binding for global variable ‘OW_above’
overweight: no visible binding for global variable ‘OW_below’
Undefined global functions or variables:
  NW_above NW_below OB_above OB_below OW_above OW_below data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘GWG/R/obese.R’:
  data(OB_above)
  data(OB_below)
File ‘GWG/R/overweight.R’:
  data(OW_above)
  data(OW_below)
See section ‘Good practice’ in ‘?data’.
Found the following apparent S3 methods exported but not registered:
  $.guiWidget [[.guiWidget [[<-.guiWidget
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
browseDataAsCSV: no visible global function definition for ‘write.csv’
browseDataAsCSV: no visible global function definition for ‘browseURL’
tcltkDialog: no visible global function definition for ‘runif’
tl_get_column_name: no visible global function definition for ‘tail’
.add,gTexttcltk-guiWidgetsToolkittcltk-character: no visible global
  function definition for ‘rnorm’
.font<-,gTexttcltk-guiWidgetsToolkittcltk: no visible global function
  definition for ‘rnorm’
.font<-,tcltkObject-guiWidgetsToolkittcltk: no visible global function
  definition for ‘rnorm’
.gdf,guiWidgetsToolkittcltk: no visible global function definition for
  ‘head’
.visible<-,gGraphicstcltk-guiWidgetsToolkittcltk-ANY: no visible global
  function definition for ‘dev.set’
Undefined global functions or variables:
  browseURL dev.set head rnorm runif tail write.csv
Consider adding
  importFrom("grDevices", "dev.set")
  importFrom("stats", "rnorm", "runif")
  importFrom("utils", "browseURL", "head", "tail", "write.csv")
to your NAMESPACE file.
Non-standard files/directories found at top level:
  ‘Summary_results.html’ ‘Weights_table.html’
'library' or 'require' calls to packages already attached by Depends:
  ‘fields’ ‘lars’
  Please remove these calls from your code.
Package in Depends field not imported from: ‘lars’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gwl.beta: no visible global function definition for ‘lars’
gwl.cv.err: no visible global function definition for ‘lars’
gwl.est: no visible global function definition for ‘lm’
gwr.bw.est: no visible global function definition for ‘lm’
gwr.est: no visible global function definition for ‘lm’
gwr.rsquare: no visible global function definition for ‘cor’
gwrr.est: no visible global function definition for ‘lm’
Undefined global functions or variables:
  cor lars lm
Consider adding
  importFrom("stats", "cor", "lm")
to your NAMESPACE file.
GxMestimator: no visible global function definition for ‘na.omit’
initialization_chol: no visible global function definition for ‘cov’
initialization_corr: no visible global function definition for ‘cov’
initialization_nlmain: no visible global function definition for
  ‘lm.fit’
print.summaryGxMclass: no visible global function definition for
  ‘pnorm’
print.summaryGxMclass: no visible global function definition for
  ‘printCoefmat’
Undefined global functions or variables:
  cov lm.fit na.omit pnorm printCoefmat
Consider adding
  importFrom("stats", "cov", "lm.fit", "na.omit", "pnorm",
             "printCoefmat")
to your NAMESPACE file.
hf.bt: no visible global function definition for ‘median’
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
hsTableReader: no visible global function definition for ‘object.size’
hsWriteTable: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  object.size write.table
Consider adding
  importFrom("utils", "object.size", "write.table")
to your NAMESPACE file.
Rd file 'hsKeyValReader.Rd':
  \usage lines wider than 90 characters:
     hsKeyValReader(file = "", chunkSize = -1, skip = 0, sep = "\t",FUN = function(k, v) cat(paste(k, v, sep = ": "), sep = "\n"))

Rd file 'hsLineReader.Rd':
  \examples lines wider than 100 characters:
       str <- "Hello here are some\nlines of text\nto read in, chunkSize\nlines at a time.\nHow interesting.\nhuh?"

Rd file 'hsTableReader.Rd':
  \examples lines wider than 100 characters:
       str <- "key1\t3.9\nkey1\t8.9\nkey1\t1.2\nkey1\t3.9\nkey1\t8.9\nkey1\t1.2\nkey2\t9.9\nkey2\t10.1\nkey3\t1.0\nkey3\t3.4\nkey4\t9.4\n"
       hsTableReader(con,cols,chunkSize=5,FUN=reducerFullKeys,ignoreKey=FALSE,singleKey=FALSE,PFUN=reducerPartialKey)
       hsTableReader(con,cols,chunkSize=6,FUN=reducerKeyAtOnce,ignoreKey=FALSE,singleKey=TRUE,PFUN=reducerPartialKey)
       hsTableReader(con,cols,chunkSize=6,FUN=reducerManyCompleteKeys,ignoreKey=FALSE,singleKey=FALSE,PFUN=reducerPartialKey)

These lines will be truncated in the PDF manual.
Found the following apparent S3 methods exported but not registered:
  print.hankeltest
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
.hankel.critValExp: no visible global function definition for
  ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
EMvar: no visible global function definition for ‘model.matrix’
RecodeHaplos: no visible global function definition for ‘na.omit’
RecodeHaplos: no visible global function definition for ‘tail’
anova.hapassoc: no visible global function definition for ‘pchisq’
handleMissings: no visible global function definition for ‘na.omit’
hapassoc: no visible global function definition for ‘binomial’
hapassoc: no visible global function definition for ‘formula’
hapassoc: no visible global function definition for ‘glm’
hapassoc : <anonymous>: no visible global function definition for ‘glm’
hapassoc: no visible global function definition for ‘model.frame’
hapassoc: no visible global function definition for ‘model.matrix’
hapassoc: no visible binding for global variable ‘contrasts’
hapassoc: no visible global function definition for ‘glm.control’
hapassoc : <anonymous>: no visible global function definition for
  ‘glm.control’
probY: no visible global function definition for ‘dbinom’
probY: no visible global function definition for ‘dpois’
probY: no visible global function definition for ‘dnorm’
probY: no visible global function definition for ‘dgamma’
summary.hapassoc: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  binomial contrasts dbinom dgamma dnorm dpois formula glm glm.control
  model.frame model.matrix na.omit pchisq tail
Consider adding
  importFrom("stats", "binomial", "contrasts", "dbinom", "dgamma",
             "dnorm", "dpois", "formula", "glm", "glm.control",
             "model.frame", "model.matrix", "na.omit", "pchisq")
  importFrom("utils", "tail")
to your NAMESPACE file.
allele.marq: no visible global function definition for ‘na.omit’
depart.LDL: no visible global function definition for ‘aov’
freq.all: no visible global function definition for ‘na.omit’
hapim.LD.add: no visible global function definition for ‘optim’
hapim.LDL.add: no visible global function definition for ‘optim’
obj.haplomax.HS.add: no visible global function definition for ‘aov’
obj.haplomax.add: no visible global function definition for ‘aov’
vrais.LD.add: no visible global function definition for ‘dnorm’
vrais.LDL.add.pere: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  aov dnorm na.omit optim
Consider adding
  importFrom("stats", "aov", "dnorm", "na.omit", "optim")
to your NAMESPACE file.
gimli.6821hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
AssignQTL : <anonymous>: no visible global function definition for
  ‘rgamma’
AssignSingleQTL: no visible global function definition for ‘rgamma’
ListQTL : <anonymous>: no visible global function definition for
  ‘rgamma’
SampleBaseHaplotype: no visible global function definition for ‘runif’
SampleHaplotype: no visible global function definition for ‘rpois’
SampleHaplotype: no visible global function definition for ‘runif’
SampleHaplotype: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  rbinom rgamma rpois runif
Consider adding
  importFrom("stats", "rbinom", "rgamma", "rpois", "runif")
to your NAMESPACE file.
clustersG: no visible global function definition for ‘combn’
pairneidist: no visible global function definition for ‘as.dist’
pairneidist: no visible global function definition for ‘combn’
steplimit : .TempletonProb: no visible global function definition for
  ‘integrate’
distance,Dna: no visible global function definition for ‘dist’
distance,Dna: no visible global function definition for ‘combn’
distance,Dna: no visible global function definition for ‘as.dist’
pairnei,matrix: no visible global function definition for ‘as.dist’
show,Dna: no visible global function definition for ‘head’
Undefined global functions or variables:
  as.dist combn dist head integrate
Consider adding
  importFrom("stats", "as.dist", "dist", "integrate")
  importFrom("utils", "combn", "head")
to your NAMESPACE file.
'library' or 'require' call to ‘ape’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘ape’ ‘hash’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'HAP.ROR-package.Rd':
  \examples lines wider than 100 characters:
     ODS.ror(case.sub=case.sub, ctl.sub=ctl.sub, lib.sub=lib.sub, lib.sub.names=lib.sub.names, records=ror.res$records, dev.list=ror.res$dev ... [TRUNCATED]

Rd file 'HAP.ror.Rd':
  \usage lines wider than 90 characters:
     HAP.ror(case.sub, ctl.sub, lib.sub, lib.sub.names, alpha = 0.01, ref.level = NA, display.proc = TRUE)

Rd file 'ODS.ror.Rd':
  \usage lines wider than 90 characters:
     ODS.ror(case.sub, ctl.sub, lib.sub, lib.sub.names, records, dev.list, AIC.list, deleted.snps.ls, proteinf, locus = "DRB1*", ref.level = ... [TRUNCATED]
  \examples lines wider than 100 characters:
     ODS.ror(case.sub=case.sub, ctl.sub=ctl.sub, lib.sub=lib.sub, lib.sub.names=lib.sub.names, records=ror.res$records, dev.list=ror.res$dev ... [TRUNCATED]

Rd file 'cc.sim.Rd':
  \usage lines wider than 90 characters:
     cc.sim(n.ctrl, n.case, beta0, beta1, case.sub, ctl.sub, lib.sub, lib.sub.names, risk.type = "AA", risk.inx = 2, risk.names = c("301", " ... [TRUNCATED]

Rd file 'deletion.Rd':
  \usage lines wider than 90 characters:
     deletion(lib, lib.names, case.sub, ctl.sub, aic.now, dev.now, df.now, rank = FALSE, cut = -1, delete.snp = -1, ref = "NA", alpha = 0.05 ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Namespace with empty importFrom: ‘utils’
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  ‘dev’
Found the following apparent S3 methods exported but not registered:
  as.list.hash names.hash
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
hash: no visible global function definition for ‘new’
is.hash: no visible global function definition for ‘is’
Undefined global functions or variables:
  is new
Consider adding
  importFrom("methods", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
extract_hazus_functions: no visible global function definition for
  ‘data’
Undefined global functions or variables:
  data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
detect.movement: no visible global function definition for ‘t.test’
generate.random.conf: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm t.test
Consider adding
  importFrom("stats", "rnorm", "t.test")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'BiocInstaller' and 'biocLite()' are deprecated, use the 'BiocManager' CRAN
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/HBP.Rcheck/00install.out’ for details.
Rd file 'fSAE.Rd':
  \examples lines wider than 100 characters:
     est.global <- fSAE(y0 ~ x + area2, data=d$sam, area=NULL, popdata=colSums(d$Xpop), method="synthetic")

Rd file 'plot.sae.Rd':
  \usage lines wider than 90 characters:
         main = switch(type, coef = "coefficients", raneff = "random effects", "SAE estimates"),

Rd file 'uweights.Rd':
  \examples lines wider than 100 characters:
     sae <- fSAE(y0 ~ x + area2, data=d$sam, area="area", popdata=d$Xpop, method="hybrid", keep.data=TRUE)

These lines will be truncated in the PDF manual.
PoincarePlot: no visible global function definition for ‘plot’
PoincarePlot: no visible global function definition for ‘lines’
PoincarePlot: no visible global function definition for ‘lowess’
hctest: no visible global function definition for ‘cor.test’
rdplot: no visible global function definition for ‘plot’
rdplot: no visible global function definition for ‘lines’
rdplot: no visible global function definition for ‘lowess’
rdplot: no visible global function definition for ‘rgb’
simer: no visible global function definition for ‘runif’
simer: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  cor.test lines lowess plot rgb rnorm runif
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "cor.test", "lowess", "rnorm", "runif")
to your NAMESPACE file.
Promax.only: no visible global function definition for ‘lm.fit’
factor.pa.ginv: no visible binding for global variable ‘median’
factor.pa.ginv: no visible global function definition for ‘cor’
factor.pa.ginv: no visible global function definition for ‘varimax’
factor.pa.ginv: no visible global function definition for ‘pchisq’
pairwise.mahalanobis: no visible global function definition for ‘cor’
pairwise.mahalanobis: no visible global function definition for
  ‘mahalanobis’
Undefined global functions or variables:
  cor lm.fit mahalanobis median pchisq varimax
Consider adding
  importFrom("stats", "cor", "lm.fit", "mahalanobis", "median", "pchisq",
             "varimax")
to your NAMESPACE file.
Rd file 'AminoAcids.Rd':
  \examples lines wider than 100 characters:
     Factor54 = factor.pa.ginv(AA54, nfactors = 5, m=3, prerotate=TRUE, rotate="Promax", scores="regression")
       Factor3d =scatterplot3d(Factor54$scores[,1:3], pch = AminoAcids, main="Factor Scores", box = FALSE, grid=FALSE, xlab="pah", ylab="pss ... [TRUNCATED]
       legend(x=5, y=4.5, legend=c("hydrophobic", "polar", "small"), col=c("blue", "green", "orange"), pch=21, box.lty =0)

Rd file 'FactorTransform.Rd':
  \usage lines wider than 90 characters:
     FactorTransform(Source, Search = AminoAcids, Replace = AAMetric.Atchley, Factor = 1, bycol = TRUE, SeqName = NULL,  alignment=FALSE, fi ... [TRUNCATED]

Rd file 'HDMD-package.Rd':
  \examples lines wider than 100 characters:
     Factor54 = factor.pa.ginv(AA54, nfactors = 5, m=3, prerotate=TRUE, rotate="Promax", scores="regression")
     plot(-1*AA54_lda_RawMetric1Centered[,1], -1*AA54_lda_RawMetric1Centered[,2], pch = grouping, xlab="Canonical Variate 1", ylab="Canonica ... [TRUNCATED]

Rd file 'NMI.Rd':
  \usage lines wider than 90 characters:
     NMI(Hx, Hy, Hxy, type = c("NULL", "marginal", "joint", "min.marginal", "max.marginal", "min.conditional", "max.conditional"))

Rd file 'factor.pa.ginv.Rd':
  \usage lines wider than 90 characters:
     factor.pa.ginv(r, nfactors = 1, residuals = FALSE, prerotate = FALSE, rotate = "varimax", m = 4, n.obs = NA, scores = c("none", "regres ... [TRUNCATED]
  \examples lines wider than 100 characters:
     Factor54 = factor.pa.ginv(AA54, nfactors = 5, m=3, prerotate=TRUE, rotate="Promax", scores="regression")
       Factor3d =scatterplot3d(Factor54$scores[,1:3], pch = AminoAcids, main="Factor Scores", box = FALSE, grid=FALSE, xlab="pah", ylab="pss ... [TRUNCATED]
       legend(x=5, y=4.5, legend=c("hydrophobic", "polar", "small"), col=c("blue", "green", "orange"), pch=21, box.lty =0)

These lines will be truncated in the PDF manual.
coef.HDtweedie: no visible global function definition for ‘rbind2’
coef.cv.HDtweedie: no visible global function definition for ‘coef’
cv.tweediegrppath: no visible global function definition for ‘predict’
cv.tweediegrppath: no visible binding for global variable
  ‘weighted.mean’
cvcompute: no visible binding for global variable ‘weighted.mean’
error.bars: no visible global function definition for ‘segments’
lambda.interp: no visible global function definition for ‘approx’
plot.HDtweedie: no visible global function definition for ‘par’
plot.HDtweedie: no visible binding for global variable ‘plot.default’
plot.HDtweedie: no visible global function definition for ‘gray.colors’
plot.HDtweedie: no visible global function definition for ‘abline’
plot.cv.HDtweedie: no visible global function definition for ‘points’
plot.cv.HDtweedie: no visible global function definition for ‘axis’
plot.cv.HDtweedie: no visible global function definition for ‘abline’
predict.HDtweedie: no visible global function definition for ‘rbind2’
predict.HDtweedie: no visible global function definition for ‘cbind2’
predict.cv.HDtweedie: no visible global function definition for
  ‘predict’
Undefined global functions or variables:
  abline approx axis cbind2 coef gray.colors par plot.default points
  predict rbind2 segments weighted.mean
Consider adding
  importFrom("grDevices", "gray.colors")
  importFrom("graphics", "abline", "axis", "par", "plot.default",
             "points", "segments")
  importFrom("methods", "cbind2", "rbind2")
  importFrom("stats", "approx", "coef", "predict", "weighted.mean")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
heatmap.plus: no visible binding for global variable ‘dist’
heatmap.plus: no visible binding for global variable ‘hclust’
heatmap.plus : <anonymous>: no visible global function definition for
  ‘reorder’
heatmap.plus: no visible global function definition for ‘as.dendrogram’
heatmap.plus: no visible global function definition for
  ‘order.dendrogram’
heatmap.plus: no visible binding for global variable ‘sd’
heatmap.plus: no visible global function definition for ‘par’
heatmap.plus: no visible global function definition for ‘layout’
heatmap.plus: no visible global function definition for ‘image’
heatmap.plus: no visible global function definition for ‘axis’
heatmap.plus: no visible global function definition for ‘mtext’
heatmap.plus: no visible global function definition for ‘plot’
heatmap.plus: no visible global function definition for ‘frame’
heatmap.plus: no visible global function definition for ‘title’
Undefined global functions or variables:
  as.dendrogram axis dist frame hclust image layout mtext
  order.dendrogram par plot reorder sd title
Consider adding
  importFrom("graphics", "axis", "frame", "image", "layout", "mtext",
             "par", "plot", "title")
  importFrom("stats", "as.dendrogram", "dist", "hclust",
             "order.dendrogram", "reorder", "sd")
to your NAMESPACE file.
prepare_Rd: heatmap.plus.package.Rd:69: Dropping empty section \details
prepare_Rd: heatmap.plus.package.Rd:70: Dropping empty section \value
prepare_Rd: heatmap.plus.package.Rd:73: Dropping empty section \note
prepare_Rd: heatmap.plus.package.Rd:71: Dropping empty section \references
Rd file 'heatmap.plus.package.Rd':
  \usage lines wider than 90 characters:
     heatmap.plus(x, Rowv = NULL, Colv = if (symm) "Rowv" else NULL, distfun = dist, hclustfun = hclust, reorderfun = function(d, w) reorder ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/Analysis.Rmd’
(Is a VignetteBuilder field missing?)
Package suggested but not available for checking: ‘FRB’
Running examples in ‘hetGP-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: LOO_preds
> ### Title: Leave one out predictions
> ### Aliases: LOO_preds
> 
> ### ** Examples
> 
> set.seed(32)
> ## motorcycle data
> library(MASS)
> X <- matrix(mcycle$times, ncol = 1)
> Z <- mcycle$accel
> nvar <- 1
> plot(X, Z, ylim = c(-160, 90), ylab = 'acceleration', xlab = "time")
> 
> ## Model fitting
> model <- mleHomGP(X = X, Z = Z, lower = rep(0.1, nvar), upper = rep(50, nvar),
+                   covtype = "Matern5_2", known = list(beta0 = 0))
Error in chol.default(C + diag(eps + g/mult)) : 
  the leading minor of order 26 is not positive definite
Calls: mleHomGP ... <Anonymous> -> fn -> logLikHom -> chol -> chol.default
Execution halted
Warning: no function found corresponding to methods exports from ‘het.test’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
Packages in Depends field not imported from:
  ‘methods’ ‘vars’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
whites.htest: no visible global function definition for ‘residuals’
whites.htest: no visible global function definition for ‘lm’
whites.htest: no visible global function definition for ‘pchisq’
whites.htest: no visible global function definition for ‘new’
Undefined global functions or variables:
  lm new pchisq residuals
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "lm", "pchisq", "residuals")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages in Depends field not imported from:
  ‘grplasso’ ‘lattice’ ‘rgl’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HubNetwork: no visible global function definition for ‘rbinom’
HubNetwork: no visible global function definition for ‘runif’
HubNetwork: no visible global function definition for ‘cov2cor’
binaryMCMC: no visible global function definition for ‘rbinom’
image.hbn: no visible global function definition for ‘col2rgb’
image.hbn: no visible global function definition for ‘rgb’
image.hbn: no visible global function definition for ‘dev.new’
image.hbn: no visible global function definition for ‘par’
image.hbn: no visible global function definition for ‘image’
image.hcov: no visible global function definition for ‘col2rgb’
image.hcov: no visible global function definition for ‘rgb’
image.hcov: no visible global function definition for ‘dev.new’
image.hcov: no visible global function definition for ‘par’
image.hcov: no visible global function definition for ‘image’
image.hglasso: no visible global function definition for ‘col2rgb’
image.hglasso: no visible global function definition for ‘rgb’
image.hglasso: no visible global function definition for ‘dev.new’
image.hglasso: no visible global function definition for ‘par’
image.hglasso: no visible global function definition for ‘image’
plot.hbn: no visible global function definition for ‘rgb’
plot.hbn: no visible global function definition for ‘plot’
plot.hcov: no visible global function definition for ‘rgb’
plot.hcov: no visible global function definition for ‘plot’
plot.hglasso: no visible global function definition for ‘rgb’
plot.hglasso: no visible global function definition for ‘plot’
Undefined global functions or variables:
  col2rgb cov2cor dev.new image par plot rbinom rgb runif
Consider adding
  importFrom("grDevices", "col2rgb", "dev.new", "rgb")
  importFrom("graphics", "image", "par", "plot")
  importFrom("stats", "cov2cor", "rbinom", "runif")
to your NAMESPACE file.
Unexported objects imported by ':::' calls:
  ‘ggplot2:::build_guides’ ‘ggplot2:::guide_axis’
  ‘ggplot2:::scales_list’
  See the note in ?`:::` about the use of this operator.
banded: no visible global function definition for ‘toeplitz’
gpband: no visible global function definition for ‘toeplitz’
hierband.cv: no visible global function definition for ‘cov’
hierband.cv: no visible binding for global variable ‘sd’
subdiag.thresh: no visible global function definition for ‘uniroot’
subdiag.thresh: no visible global function definition for ‘toeplitz’
Undefined global functions or variables:
  cov sd toeplitz uniroot
Consider adding
  importFrom("stats", "cov", "sd", "toeplitz", "uniroot")
to your NAMESPACE file.
booties: no visible binding for global variable ‘sd’
booties: no visible binding for global variable ‘quantile’
hierDiversity: no visible global function definition for
  ‘txtProgressBar’
hierDiversity: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  quantile sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "quantile", "sd")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
calcPower: no visible global function definition for ‘pchisq’
calcPower: no visible global function definition for ‘qchisq’
delta2 : K1: no visible global function definition for ‘qnorm’
delta2: no visible global function definition for ‘qnorm’
delta2: no visible global function definition for ‘pnorm’
delta2: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm pchisq pnorm qchisq qnorm
Consider adding
  importFrom("stats", "dnorm", "pchisq", "pnorm", "qchisq", "qnorm")
to your NAMESPACE file.
'library' or 'require' call to ‘gtools’ which was already attached by Depends.
  Please remove these calls from your code.
all.regs: no visible global function definition for ‘glm’
all.regs: no visible global function definition for ‘logLik’
combos: no visible global function definition for ‘menu’
current.model: no visible global function definition for ‘formula’
current.model: no visible global function definition for ‘glm’
current.model: no visible global function definition for ‘logLik’
current.model: no visible global function definition for ‘lm’
rand.hp: no visible global function definition for ‘runif’
rand.hp: no visible global function definition for ‘sd’
Undefined global functions or variables:
  formula glm lm logLik menu runif sd
Consider adding
  importFrom("stats", "formula", "glm", "lm", "logLik", "runif", "sd")
  importFrom("utils", "menu")
to your NAMESPACE file.
compute.contrasts: no visible binding for global variable ‘sd’
compute.contrasts: no visible global function definition for ‘cor’
compute.contrasts: no visible global function definition for ‘sd’
plot.estfdr: no visible global function definition for ‘plot’
plot.hiertest: no visible global function definition for ‘plot’
plot.hiertest: no visible global function definition for ‘legend’
Undefined global functions or variables:
  cor legend plot sd
Consider adding
  importFrom("graphics", "legend", "plot")
  importFrom("stats", "cor", "sd")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘nnet’ ‘stats’
  Please remove these calls from your code.
Package in Depends field not imported from: ‘nnet’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'HItest3.Rd':
  \examples lines wider than 100 characters:
                                                     # individuals will have nonzero contributions from each of the

Rd file 'spatial.AD.Rd':
  \examples lines wider than 100 characters:
     # simulate secondary contact by sorting aling the x dimension and assigning parental genotypes on each side of the centerline:
     # selection, inlcuding heterozygote disadvantage at locus 2 and a DM incompatibility between 3 and 4:
     G10 <- spatial.AD(minX,minY,maxX,maxY,XY,Genotypes,beta,sel,mid,h,DM,sigmac,R,M,gens=10,immigrants=TRUE)

Rd file 'spatial.HZ.Rd':
  \examples lines wider than 100 characters:
     # simulate secondary contact by sorting aling the x dimension and assigning parental genotypes on each side of the centerline:
     # selection, inlcuding heterozygote disadvantage at locus 2 and a DM incompatibility between 3 and 4:
     G10 <- spatial.HZ(minX,minY,maxX,maxY,XY,Genotypes,beta,sel,mid,h,DM,sigmad,sigmac,sigmam,R,M,gens=10,immigrants=TRUE)

Rd file 'thirdclass.Rd':
  \examples lines wider than 100 characters:
                                                     # individuals will have nonzero contributions from each of the 

These lines will be truncated in the PDF manual.
CLX.sim.Covtest: no visible global function definition for ‘cov’
CLX.sim.equalcov: no visible global function definition for ‘cov’
CLX.sim.unequalcov: no visible global function definition for ‘cov’
CLX.test.equalcov: no visible global function definition for ‘cov’
CLX.test.unequalcov: no visible global function definition for ‘cov’
ChenQin.sim: no visible global function definition for ‘pnorm’
ChenQin.test: no visible global function definition for ‘pnorm’
GCT.sim: no visible binding for global variable ‘var’
GCT.sim: no visible global function definition for ‘acf’
GCT.sim: no visible global function definition for ‘pnorm’
GCT.test: no visible binding for global variable ‘var’
GCT.test: no visible global function definition for ‘acf’
GCT.test: no visible global function definition for ‘pnorm’
GCT.test.missing: no visible binding for global variable ‘var’
GCT.test.missing: no visible global function definition for ‘acf’
GCT.test.missing: no visible global function definition for ‘pnorm’
SK.sim: no visible global function definition for ‘cov’
SK.sim: no visible global function definition for ‘pnorm’
SK.test: no visible global function definition for ‘cov’
SK.test: no visible global function definition for ‘pnorm’
build2popData : <anonymous>: no visible global function definition for
  ‘rnorm’
build2popData: no visible global function definition for ‘arima.sim’
build2popData_muYafunction : <anonymous>: no visible global function
  definition for ‘rnorm’
build2popData_muYafunction: no visible global function definition for
  ‘arima.sim’
innovate: no visible binding for global variable ‘rnorm’
rdblepareto: no visible global function definition for ‘runif’
rgammashift: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  acf arima.sim cov pnorm rgamma rnorm runif var
Consider adding
  importFrom("stats", "acf", "arima.sim", "cov", "pnorm", "rgamma",
             "rnorm", "runif", "var")
to your NAMESPACE file.
Func.ABOD: no visible global function definition for ‘combn’
Func.ABOD: no visible global function definition for ‘var’
Func.SOD: no visible global function definition for ‘var’
Func.trans : erf: no visible global function definition for ‘pnorm’
Func.trans: no visible global function definition for ‘sd’
Undefined global functions or variables:
  combn pnorm sd var
Consider adding
  importFrom("stats", "pnorm", "sd", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
BenjaminiHochberg: no visible global function definition for ‘p.adjust’
CaoKosorok : CKfunc: no visible global function definition for ‘pnorm’
CaoKosorok : <anonymous>: no visible global function definition for
  ‘pnorm’
StoreyTibshirani: no visible global function definition for
  ‘smooth.spline’
plotI_Lines: no visible global function definition for ‘par’
plotI_Lines: no visible global function definition for ‘lines’
plotI_Lines: no visible global function definition for ‘legend’
plotI_Points: no visible global function definition for ‘points’
plotI_Points: no visible global function definition for ‘legend’
tStatistic : <anonymous>: no visible global function definition for
  ‘t.test’
venn2: no visible global function definition for ‘plot.new’
venn3: no visible global function definition for ‘plot.new’
Undefined global functions or variables:
  legend lines p.adjust par plot.new pnorm points smooth.spline t.test
Consider adding
  importFrom("graphics", "legend", "lines", "par", "plot.new", "points")
  importFrom("stats", "p.adjust", "pnorm", "smooth.spline", "t.test")
to your NAMESPACE file.
occupancy: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
data_simu: no visible global function definition for ‘runif’
data_simu: no visible global function definition for ‘rbinom’
data_simu: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rbinom rnorm runif
Consider adding
  importFrom("stats", "rbinom", "rnorm", "runif")
to your NAMESPACE file.
overlay.sim: no visible global function definition for ‘points’
plotDistr: no visible global function definition for ‘dev.hold’
plotDistr: no visible global function definition for ‘dev.flush’
plotDistr: no visible global function definition for ‘plot’
plotDistr: no visible global function definition for ‘segments’
Undefined global functions or variables:
  dev.flush dev.hold plot points segments
Consider adding
  importFrom("grDevices", "dev.flush", "dev.hold")
  importFrom("graphics", "plot", "points", "segments")
to your NAMESPACE file.
PlotOptPower: no visible global function definition for ‘bmp’
PlotOptPower: no visible global function definition for
  ‘filled.contour’
PlotOptPower: no visible global function definition for ‘title’
PlotOptPower: no visible global function definition for ‘grey.colors’
PlotOptPower: no visible global function definition for ‘axis’
PlotOptPower: no visible global function definition for ‘polygon’
PlotOptPower: no visible global function definition for ‘legend’
PlotOptPower: no visible global function definition for ‘mtext’
PlotOptPower: no visible global function definition for ‘dev.off’
PlotOptPower: no visible global function definition for
  ‘terrain.colors’
ShowOptDesign: no visible global function definition for ‘head’
diffVariantError: no visible global function definition for ‘pbinom’
predictPoolNCP: no visible global function definition for ‘data’
probDetEqual3: no visible global function definition for ‘dbinom’
probDetEqual3: no visible global function definition for ‘pbinom’
Undefined global functions or variables:
  axis bmp data dbinom dev.off filled.contour grey.colors head legend
  mtext pbinom polygon terrain.colors title
Consider adding
  importFrom("grDevices", "bmp", "dev.off", "grey.colors",
             "terrain.colors")
  importFrom("graphics", "axis", "filled.contour", "legend", "mtext",
             "polygon", "title")
  importFrom("stats", "dbinom", "pbinom")
  importFrom("utils", "data", "head")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘hiPOD/R/predictPoolNCP.R’:
  data(ncp.pool.pred)
See section ‘Good practice’ in ‘?data’.
arms: no visible global function definition for ‘rnorm’
rballunif: no visible global function definition for ‘rnorm’
rballunif: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: ‘FGN’
Found the following apparent S3 methods exported but not registered:
  summary.hmeasure
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
HMeasure: no visible global function definition for ‘complete.cases’
HMeasure : HMeasure.single: no visible global function definition for
  ‘chull’
HMeasure : HMeasure.single: no visible global function definition for
  ‘pbeta’
plotROC: no visible global function definition for ‘plot’
plotROC: no visible global function definition for ‘lines’
plotROC: no visible global function definition for ‘legend’
plotROC: no visible global function definition for ‘dbeta’
plotROC: no visible global function definition for ‘density’
Undefined global functions or variables:
  chull complete.cases dbeta density legend lines pbeta plot
Consider adding
  importFrom("grDevices", "chull")
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "complete.cases", "dbeta", "density", "pbeta")
to your NAMESPACE file.
The following files look like leftovers/mistakes:
  ‘hmeasure.dvi’
Please remove them from your package.
baumwelchcont: no visible global function definition for ‘dnorm’
hmmcontSimul: no visible global function definition for ‘rnorm’
hmmcontSimul: no visible global function definition for ‘rbinom’
plot.ContObservHMM: no visible global function definition for ‘plot’
plot.ContObservHMM: no visible global function definition for ‘lines’
statesDistributionsPlot: no visible global function definition for
  ‘dnorm’
statesDistributionsPlot: no visible global function definition for ‘sd’
statesDistributionsPlot: no visible global function definition for
  ‘plot’
statesDistributionsPlot: no visible global function definition for
  ‘lines’
statesDistributionsPlot: no visible global function definition for
  ‘legend’
summary.ContObservHMM: no visible global function definition for ‘sd’
Undefined global functions or variables:
  dnorm legend lines plot rbinom rnorm sd
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "dnorm", "rbinom", "rnorm", "sd")
to your NAMESPACE file.
dishonestCasino: no visible global function definition for ‘plot’
dishonestCasino: no visible global function definition for ‘axis’
dishonestCasino: no visible global function definition for ‘text’
dishonestCasino: no visible global function definition for ‘rect’
dishonestCasino: no visible global function definition for ‘rgb’
dishonestCasino: no visible global function definition for ‘points’
Undefined global functions or variables:
  axis plot points rect rgb text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "plot", "points", "rect", "text")
to your NAMESPACE file.
PlotBasic: no visible global function definition for ‘dev.new’
PlotBasic: no visible global function definition for ‘par’
PlotBasic: no visible global function definition for ‘plot’
PlotBasic: no visible global function definition for ‘grid’
PlotBasic: no visible global function definition for ‘lines’
PlotChoice : plotgraph: no visible global function definition for ‘par’
PlotChoice : plotgraph: no visible global function definition for
  ‘plot’
PlotChoice : plotgraph: no visible global function definition for
  ‘grid’
PlotChoice : plotgraph: no visible global function definition for
  ‘points’
PlotChoice : plotgraph: no visible global function definition for
  ‘lines’
PlotChoice : plotgraph: no visible global function definition for
  ‘axis’
PlotChoice : plotgraph: no visible global function definition for
  ‘mtext’
Undefined global functions or variables:
  axis dev.new grid lines mtext par plot points
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "axis", "grid", "lines", "mtext", "par", "plot",
             "points")
to your NAMESPACE file.
hornpa: no visible global function definition for ‘rnorm’
hornpa: no visible global function definition for ‘cor’
hornpa: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  cor quantile rnorm
Consider adding
  importFrom("stats", "cor", "quantile", "rnorm")
to your NAMESPACE file.
hpbayes.plot: no visible global function definition for ‘par’
hpbayes.plot: no visible global function definition for ‘plot’
hpbayes.plot: no visible global function definition for ‘points’
postpri.plot: no visible global function definition for ‘par’
postpri.plot: no visible global function definition for ‘plot’
postpri.plot: no visible global function definition for ‘points’
postpri.plot: no visible global function definition for ‘segments’
postpri.plot: no visible global function definition for ‘boxplot’
Undefined global functions or variables:
  boxplot par plot points segments
Consider adding
  importFrom("graphics", "boxplot", "par", "plot", "points", "segments")
to your NAMESPACE file.
ApproxC: no visible global function definition for ‘convolve’
DMC: no visible global function definition for ‘median’
DMC: no visible global function definition for ‘ecdf’
ToSWF: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  convolve ecdf median write.table
Consider adding
  importFrom("stats", "convolve", "ecdf", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
bracket: no visible global function definition for ‘segments’
Undefined global functions or variables:
  segments
Consider adding
  importFrom("graphics", "segments")
to your NAMESPACE file.
Found the following significant warnings:
  sar.cpp:210:32: warning: explicitly assigning value of variable of type 'arma::sp_mat' (aka 'SpMat<double>') to itself [-Wself-assign-overloaded]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/HSAR.Rcheck/00install.out’ for details.
File ‘hSDM/libs/hSDM.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘useful.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Objects: ‘hSDM.Nmixture.o’, ‘hSDM.Nmixture.iCAR.o’, ‘hSDM.ZIB.o’,
      ‘hSDM.ZIB.iCAR.alteration.o’, ‘hSDM.ZIB.iCAR.o’, ‘hSDM.ZIP.o’,
      ‘hSDM.ZIP.iCAR.alteration.o’, ‘hSDM.ZIP.iCAR.o’,
      ‘hSDM.binomial.o’, ‘hSDM.binomial.iCAR.o’, ‘hSDM.poisson.o’,
      ‘hSDM.poisson.iCAR.o’, ‘hSDM.siteocc.o’, ‘hSDM.siteocc.iCAR.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
hsicCCA: no visible global function definition for ‘median’
hsicCCA: no visible global function definition for ‘dist’
hsicCCAfunc: no visible global function definition for ‘rnorm’
hsicCCAfunc: no visible global function definition for ‘runif’
hsicCCAfunc: no visible global function definition for ‘optim’
ktaCCA: no visible global function definition for ‘median’
ktaCCA: no visible global function definition for ‘dist’
ktaCCAfunc: no visible global function definition for ‘rnorm’
ktaCCAfunc: no visible global function definition for ‘runif’
ktaCCAfunc: no visible global function definition for ‘optim’
Undefined global functions or variables:
  dist median optim rnorm runif
Consider adding
  importFrom("stats", "dist", "median", "optim", "rnorm", "runif")
to your NAMESPACE file.
Rd file 'hsicCCA.Rd':
  \usage lines wider than 90 characters:
     hsicCCA(x, y, M, sigmax = NULL, sigmay = NULL, numrepeat = 5, numiter = 100, reltolstop = 1e-04)

Rd file 'ktaCCA.Rd':
  \usage lines wider than 90 characters:
     ktaCCA(x, y, M, sigmax = NULL, sigmay = NULL, numrepeat = 5, numiter = 100, reltolstop = 1e-04)

These lines will be truncated in the PDF manual.
get.d: no visible global function definition for ‘dgeom’
get.d: no visible global function definition for ‘dnbinom’
get.d: no visible global function definition for ‘dpois’
get.pdf: no visible global function definition for ‘dnorm’
get.pdf: no visible global function definition for ‘dpois’
get.pdf: no visible global function definition for ‘dmvnorm’
hsmm: no visible global function definition for ‘uniroot’
hsmm.sim: no visible global function definition for ‘rbinom’
hsmm.sim: no visible global function definition for ‘rnorm’
hsmm.sim: no visible global function definition for ‘rpois’
hsmm.sim: no visible global function definition for ‘rmvnorm’
loggeom.update: no visible global function definition for ‘plogis’
rmt: no visible global function definition for ‘rt’
rmt: no visible global function definition for ‘rnorm’
rmt: no visible global function definition for ‘rchisq’
rvm: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dgeom dmvnorm dnbinom dnorm dpois plogis rbinom rchisq rmvnorm rnorm
  rpois rt runif uniroot
Consider adding
  importFrom("stats", "dgeom", "dnbinom", "dnorm", "dpois", "plogis",
             "rbinom", "rchisq", "rnorm", "rpois", "rt", "runif",
             "uniroot")
to your NAMESPACE file.
Huber: no visible global function definition for ‘quantile’
SSVD.iter.thresh: no visible global function definition for ‘mad’
error.est.full: no visible global function definition for ‘mad’
error.est.full : <anonymous>: no visible global function definition for
  ‘median’
low_rank: no visible global function definition for ‘median’
low_rank: no visible global function definition for ‘mad’
low_rank: no visible global function definition for ‘sd’
select.indices: no visible global function definition for ‘mad’
select.indices: no visible global function definition for ‘median’
select.indices: no visible global function definition for ‘pnorm’
select.indices: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  mad median p.adjust pnorm quantile sd
Consider adding
  importFrom("stats", "mad", "median", "p.adjust", "pnorm", "quantile",
             "sd")
to your NAMESPACE file.
Found the following significant warnings:
  language.c:41:5: warning: flexible array initialization is a GNU extension [-Wgnu-flexible-array-initializer]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/htmltidy.Rcheck/00install.out’ for details.
BasicHTML: no visible global function definition for ‘png’
BasicHTML: no visible global function definition for ‘dev.list’
BasicHTML: no visible global function definition for ‘dev.off’
FramedHTML: no visible global function definition for ‘graphics.off’
Undefined global functions or variables:
  dev.list dev.off graphics.off png
Consider adding
  importFrom("grDevices", "dev.list", "dev.off", "graphics.off", "png")
to your NAMESPACE file.
getToHost: no visible global function definition for ‘make.socket’
getToHost: no visible global function definition for ‘write.socket’
getToHost: no visible global function definition for ‘read.socket’
getToHost: no visible global function definition for ‘close.socket’
postToHost: no visible global function definition for ‘runif’
simplePostToHost: no visible global function definition for
  ‘make.socket’
simplePostToHost: no visible global function definition for
  ‘write.socket’
simplePostToHost: no visible global function definition for
  ‘read.socket’
simplePostToHost: no visible global function definition for
  ‘close.socket’
Undefined global functions or variables:
  close.socket make.socket read.socket runif write.socket
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "close.socket", "make.socket", "read.socket",
             "write.socket")
to your NAMESPACE file.
Package in Depends field not imported from: ‘testthat’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Calculate3D: no visible global function definition for ‘persp’
CalculateHUM_Ex: no visible global function definition for ‘combn’
CalculateHUM_Plot: no visible global function definition for ‘plot’
CalculateHUM_Plot: no visible global function definition for ‘polygon’
CalculateHUM_Plot: no visible global function definition for ‘text’
CalculateHUM_Plot: no visible global function definition for ‘points’
CalculateHUM_Plot: no visible global function definition for ‘lines’
Undefined global functions or variables:
  combn lines persp plot points polygon text
Consider adding
  importFrom("graphics", "lines", "persp", "plot", "points", "polygon",
             "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
Package suggested but not available for checking: ‘hurricaneexposuredata’
HWEImportSamp: no visible global function definition for ‘dnorm’
HWEImportSamp: no visible global function definition for ‘rnorm’
HWEmodelsMLE: no visible global function definition for ‘optim’
HWEsimdat: no visible global function definition for ‘rmultinom’
LambdaOptim: no visible global function definition for ‘rnorm’
LambdaOptim : LambdaPriorChoice: no visible global function definition
  for ‘quantile’
LambdaOptim: no visible global function definition for ‘optim’
SinglefPrior: no visible global function definition for ‘rnorm’
SinglefReject: no visible global function definition for ‘runif’
TriangNormHWE: no visible global function definition for ‘pbeta’
Undefined global functions or variables:
  dnorm optim pbeta quantile rmultinom rnorm runif
Consider adding
  importFrom("stats", "dnorm", "optim", "pbeta", "quantile", "rmultinom",
             "rnorm", "runif")
to your NAMESPACE file.
HW.plain: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
getHwriterVersion: no visible global function definition for
  ‘sessionInfo’
hmapRowCol: no visible global function definition for ‘na.omit’
hwriteImage: no visible global function definition for ‘dev.print’
hwriteImage: no visible binding for global variable ‘png’
showExample: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL dev.print na.omit png sessionInfo
Consider adding
  importFrom("grDevices", "dev.print", "png")
  importFrom("stats", "na.omit")
  importFrom("utils", "browseURL", "sessionInfo")
to your NAMESPACE file.
hybridMC: no visible global function definition for ‘txtProgressBar’
hybridMC : pbFun: no visible global function definition for
  ‘setTxtProgressBar’
hybridMC: no visible global function definition for ‘mcmc’
Undefined global functions or variables:
  mcmc setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Rd file 'hybridMC.Rd':
  \usage lines wider than 90 characters:
     hybridMC(y.start, n.samp=1, logDens, dLogDens, epsilon, LFsteps, compWeights=NULL, MPwidth=1, MPweights=NULL, progress=0 ,...)

These lines will be truncated in the PDF manual.
ARPIEM2012.Lmom.sample: no visible global function definition for ‘var’
ARPIEM2012.freq: no visible binding for global variable ‘quantile’
ARPIEM2012.sim.Lmoments : ARPIEM2012.sim.Qind_camp: no visible global
  function definition for ‘rnorm’
ARPIEM2012.sim.Lmoments : ARPIEM2012.sim.Qind_reg_moltiplicativo: no
  visible global function definition for ‘rnorm’
ARPIEM2012.sim.Lmoments : ARPIEM2012.sim.LCV_camp.LCA_camp: no visible
  global function definition for ‘rnorm’
ARPIEM2012.sim.Lmoments : ARPIEM2012.sim.LCV_camp.LCA_reg_additivo: no
  visible global function definition for ‘rnorm’
ARPIEM2012.sim.Lmoments :
  ARPIEM2012.sim.LCV_reg_moltiplicativo.LCA_reg_additivo: no visible
  global function definition for ‘rnorm’
Undefined global functions or variables:
  quantile rnorm var
Consider adding
  importFrom("stats", "quantile", "rnorm", "var")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘minpack.lm’ ‘nlme’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Dstart: no visible global function definition for ‘coef’
Dstart: no visible global function definition for ‘lm’
SSkosugi: no visible global function definition for ‘pnorm’
SSkosugi: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  coef dnorm lm pnorm
Consider adding
  importFrom("stats", "coef", "dnorm", "lm", "pnorm")
to your NAMESPACE file.
Rd file 'Brook.Rd':
  \examples lines wider than 100 characters:
     brook.ns=nlsLM(y~Brook(x,thr,ths,alp,nscal),data=pf, control=nls.lm.control(maxiter=200),start=c(thr=Dstart(pf)[1],ths=Dstart(pf)[2], a ... [TRUNCATED]

Rd file 'Expo.Rd':
  \examples lines wider than 100 characters:
     expo.ns=nlsLM(y~Expo(x,thr,ths,alp),data=pf, control=nls.lm.control(maxiter=200),start=c(thr=Dstart(pf)[1],ths=Dstart(pf)[2], alp=Dstar ... [TRUNCATED]

Rd file 'Ruso.Rd':
  \examples lines wider than 100 characters:
     ruso.ns=nlsLM(y~Ruso(x,thr,ths,alp,nscal),data=pf, control=nls.lm.control(maxiter=200),start=c(thr=Dstart(pf)[1],ths=Dstart(pf)[2], alp ... [TRUNCATED]

Rd file 'SSfredlund.Rd':
  \examples lines wider than 100 characters:
     fredlund.ns=nlsLM(y~SSfredlund(x,thr,ths,alp,nscal,mscal),data=pf,control=nls.lm.control(maxiter=200,options(warn=-1)))

Rd file 'SSkosugi.Rd':
  \examples lines wider than 100 characters:
     kosugi.ns=nlsLM(y~SSkosugi(x,thr,ths,alp,nscal),data=subset(isric, Sample=="Benin2"),control=nls.lm.control(maxiter=200,options(warn=-1 ... [TRUNCATED]

Rd file 'SSvgm.Rd':
  \examples lines wider than 100 characters:
     vn.ns=nlsLM(y~SSvgm(x,thr,ths,alp,nscal,mscal),data=subset(isric, Sample=="Benin2"),control=nls.lm.control(maxiter=200,options(warn=-1) ... [TRUNCATED]

Rd file 'Tani.Rd':
  \examples lines wider than 100 characters:
     tani.ns=nlsLM(y~Tani(x,thr,ths,alp),data=pf, control=nls.lm.control(maxiter=200),start=c(thr=Dstart(pf)[1],ths=Dstart(pf)[2], alp=Dstar ... [TRUNCATED]

These lines will be truncated in the PDF manual.
hyper.plot2d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  ‘lo’ to ‘locut’
hyper.plot2d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  ‘hi’ to ‘hicut’
hyper.plot2d: warning in magmap(seq(sigscale[1], sigscale[2], len =
  100), lo = sigscale[1], hi = sigscale[2], flip = TRUE, type = "num"):
  partial argument match of ‘lo’ to ‘locut’
hyper.plot2d: warning in magmap(seq(sigscale[1], sigscale[2], len =
  100), lo = sigscale[1], hi = sigscale[2], flip = TRUE, type = "num"):
  partial argument match of ‘hi’ to ‘hicut’
hyper.plot3d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  ‘lo’ to ‘locut’
hyper.plot3d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  ‘hi’ to ‘hicut’
src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_CFLAGS but not in PKG_LIBS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
Packages in Depends field not imported from:
  ‘R.utils’ ‘ape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
requiprobable: no visible global function definition for ‘extract’
requiprobable : make.tree: no visible global function definition for
  ‘extract’
requiprobable : make.tree: no visible global function definition for
  ‘runif’
rgenetree: no visible global function definition for ‘dbinom’
rgenetree: no visible global function definition for ‘dnbinom’
rgenetree: no visible global function definition for ‘runif’
rgenetree: no visible global function definition for ‘rbinom’
rgenetree: no visible global function definition for ‘rnbinom’
Undefined global functions or variables:
  dbinom dnbinom extract rbinom rnbinom runif
Consider adding
  importFrom("stats", "dbinom", "dnbinom", "rbinom", "rnbinom", "runif")
to your NAMESPACE file.
Rd file 'requiprobable.Rd':
  \examples lines wider than 100 characters:
     for (i in 1:10) unlabeled[[i]]$tip.label<-sample(c("A1","A2","B1","B2","B3","C1","C2","C3","C4","C5"))

Rd file 'rgenetree.Rd':
  \examples lines wider than 100 characters:
     ##Now lets start with 3 genes, set the number of genes at each tip of spec and vary mu between the branches of spec 

These lines will be truncated in the PDF manual.
conint: no visible global function definition for ‘sd’
findroot: no visible global function definition for ‘integrate’
hypothesis: no visible global function definition for ‘sd’
hypothesis: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate sd
Consider adding
  importFrom("stats", "integrate", "sd")
to your NAMESPACE file.
Rd file 'conint.Rd':
  \usage lines wider than 90 characters:
     conint(TrnX = NULL, TrnY = NULL, m, n1, n2, s1, s2, side = "both", alpha = 0.95, method = "n")

Rd file 'hypothesis-package.Rd':
  \examples lines wider than 100 characters:
     hypothesis(TrnX=c(3,4,5),TrnY=c(4,5,6),m,u0=4,3,3,s1=NULL,s2=NULL,sigma1=NULL,sigma2=NULL,alpha=0.05,method="n",H0="u=u0",p)

Rd file 'hypothesis.Rd':
  \usage lines wider than 90 characters:
     hypothesis(TrnX = NULL, TrnY = NULL, m, u0, n1, n2, s1 = NULL, s2 = NULL, sigma1 = NULL, sigma2 = NULL, alpha = 0.05, method = "n", H0  ... [TRUNCATED]
  \examples lines wider than 100 characters:
      hypothesis(TrnX=c(3,4,5),TrnY=c(4,5,6),m,u0=4,3,3,s1=NULL,s2=NULL,sigma1=NULL,sigma2=NULL,alpha=0.05,method="n",H0="u=u0",p)

These lines will be truncated in the PDF manual.
Packages in Depends field not imported from:
  ‘MCMCpack’ ‘coda’ ‘foreach’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ibdhap.barplot: no visible global function definition for ‘plot’
ibdhap.barplot: no visible global function definition for ‘rect’
ibdhap.compare.loci: no visible global function definition for ‘hist’
ibdhap.compare.segs: no visible global function definition for ‘tail’
ibdhap.make.calls: no visible global function definition for
  ‘count.fields’
ibdhap.make.calls: no visible global function definition for
  ‘read.table’
ibdhap.make.true: no visible global function definition for
  ‘read.table’
ibdhap.names: no visible global function definition for ‘count.fields’
ibdhap.names: no visible global function definition for ‘read.table’
ibdhap.reduce.states: no visible global function definition for
  ‘read.table’
ibdhap.reduce.states: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  count.fields hist plot read.table rect tail write.table
Consider adding
  importFrom("graphics", "hist", "plot", "rect")
  importFrom("utils", "count.fields", "read.table", "tail",
             "write.table")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘perl’
create.ibd.dat: no visible global function definition for ‘read.table’
create.pairs.frame: no visible global function definition for ‘terms’
ibd.moments: no visible global function definition for ‘var’
ibdreg: no visible global function definition for ‘terms’
ibdreg: no visible global function definition for ‘as.formula’
linkage.tests: no visible global function definition for ‘pchisq’
pchibar: no visible global function definition for ‘pchisq’
plot.linkage.all: no visible global function definition for ‘plot’
plot.linkage.all: no visible global function definition for ‘title’
plotpval: no visible global function definition for ‘plot’
plotpval: no visible global function definition for ‘lines’
sim.ibd.var: no visible global function definition for ‘read.table’
sim.mark.prop: no visible global function definition for ‘runif’
Undefined global functions or variables:
  as.formula lines pchisq plot read.table runif terms title var
Consider adding
  importFrom("graphics", "lines", "plot", "title")
  importFrom("stats", "as.formula", "pchisq", "runif", "terms", "var")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following significant warnings:
  IBDsim.c:27:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:39:20: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:54:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:61:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/IBDsim.Rcheck/00install.out’ for details.
CreateVoronoi: no visible global function definition for ‘slot’
CreateVoronoi : <anonymous>: no visible global function definition for
  ‘slot’
CreateVoronoi: no visible global function definition for ‘chull’
ExtractIMFi2D: no visible global function definition for ‘par’
LocatedAtBoundary: no visible global function definition for
  ‘txtProgressBar’
LocatedAtBoundary: no visible global function definition for
  ‘setTxtProgressBar’
PlotFit: no visible global function definition for ‘par’
iBEEMD: no visible global function definition for ‘is’
iBEEMD: no visible global function definition for ‘sd’
iBEEMD: no visible global function definition for ‘txtProgressBar’
iBEEMD: no visible global function definition for ‘rnorm’
iBEEMD: no visible global function definition for ‘setTxtProgressBar’
iBEEMD: no visible global function definition for ‘terrain.colors’
rbfcreate: no visible global function definition for ‘is’
rbfcreate : rbfAssemble: no visible global function definition for
  ‘dist’
rbfinterp: no visible global function definition for ‘is’
rbfinterp: no visible global function definition for ‘dist’
Undefined global functions or variables:
  chull dist is par rnorm sd setTxtProgressBar slot terrain.colors
  txtProgressBar
Consider adding
  importFrom("grDevices", "chull", "terrain.colors")
  importFrom("graphics", "par")
  importFrom("methods", "is", "slot")
  importFrom("stats", "dist", "rnorm", "sd")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package suggested but not available for checking: ‘SparkR’
Iboot: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
..placeOrder: no visible global function definition for ‘str’
.reqMktData.vignette: no visible global function definition for
  ‘flush.console’
e_portfolio_value: no visible global function definition for ‘str’
print.eventPortfolioValue: no visible global function definition for
  ‘str’
print.twsContract: no visible global function definition for ‘str’
print.twsContractDetails: no visible global function definition for
  ‘str’
print.twsOrder: no visible global function definition for ‘str’
print.twsOrderState: no visible global function definition for ‘str’
print.twsScannerSubscription: no visible global function definition for
  ‘str’
reqAccountUpdates: no visible binding for global variable ‘timestamp’
reqContractDetails: no visible binding for global variable ‘timestamp’
reqHistoricalData: no visible global function definition for
  ‘flush.console’
reqHistoricalData: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  flush.console str timestamp write.table
Consider adding
  importFrom("utils", "flush.console", "str", "timestamp", "write.table")
to your NAMESPACE file.
Registration problems:
  symbol ‘nom1’ in the local frame:
   .C(nom1, as.double(xord), as.integer(length(xord)), as.double(yord), 
       as.double(gridbw), as.integer(length(gridbw)), as.integer(effold), 
       as.integer(neffold), double(length(gridbw)), double(length(gridbw)))
  symbol ‘nom2’ in the local frame:
   .C(nom2, as.double(x), as.integer(n), as.double(y), as.double(bandwidth), 
       as.double(x), as.integer(n), double(n), double(1))
  symbol ‘nom2’ in the local frame:
   .C(nom2, as.double(x), as.integer(n), as.double(y), as.double(bandwidth), 
       as.double(x), as.integer(n), double(n), double(1), double(n))
  symbol ‘nom’ in the local frame:
   .C(nom, as.double(x), as.integer(length(x)), as.double(y), as.double(object$bandwidth), 
       as.double(newdata), as.integer(length(newdata)), double(length(newdata)), 
       double(1))
  symbol ‘nom’ in the local frame:
   .C(nom, as.double(x), as.integer(length(x)), as.double(y), as.double(object$bandwidth), 
       as.double(newdata), as.integer(length(newdata)), double(length(newdata)), 
       double(1), double(length(newdata)))
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Rd file 'curveConcent.Rd':
  \examples lines wider than 100 characters:
     curveConcent(x=hhbudgets[, "transporte"], y=hhbudgets[,"ingreso"], w=hhbudgets[,"factor"], col="red", xlab="Ranking by income")
     curveConcent(x=hhbudgets[, "mantenimiento"], y=hhbudgets[,"ingreso"], w=hhbudgets[,"factor"], col="blue", add=TRUE)
     curveConcent(x=hhbudgets[, "publico"], y=hhbudgets[,"ingreso"], w=hhbudgets[,"factor"], col="green", add=TRUE)
     legend("topleft", legend = c("All transport", "Private: Maintenance and repair", "Public transport"), col=c("red", "blue", "green"), lt ... [TRUNCATED]

Rd file 'decompAtkinson.Rd':
  \examples lines wider than 100 characters:
     summary(decompAtkinson(x=hhbudgets[,"transporte"], z=hhbudgets[,"tenencia"], w=hhbudgets[,"factor"], decomp="DP", ELMO=FALSE))
     summary(decompAtkinson(x=hhbudgets[,"transporte"], z=hhbudgets[,"tenencia"], w=hhbudgets[,"factor"], decomp="DP", epsilon=0.25))

Rd file 'decompGEI.Rd':
  \examples lines wider than 100 characters:
     summary(decompGEI(x=hhbudgets[,"transporte"], z=hhbudgets[,"tenencia"], w=hhbudgets[,"factor"], alpha=1.5))

Rd file 'decompSGini.Rd':
  \examples lines wider than 100 characters:
     decompSGini(x=hhbudgets[,"transporte"], z=hhbudgets[,"estructura"], w=hhbudgets[,"factor"], decomp="YL", ELMO=FALSE)
     summary(decompSGini(x=hhbudgets[,"transporte"], z=hhbudgets[,"tenencia"], w=hhbudgets[,"factor"], param=1.5))

These lines will be truncated in the PDF manual.
'library' or 'require' call to ‘tcltk’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'hts.Rd':
  \examples lines wider than 100 characters:
                   measure="mpi384_measure.txt",control="mpi384_control.txt",dilution="mpi384_dilution.txt",

Rd file 'ic50.Rd':
  \examples lines wider than 100 characters:
                    measure="mpi384_measure.txt",control="mpi384_control.txt",dilution="mpi384_dilution.txt",

These lines will be truncated in the PDF manual.
ICA: no visible global function definition for ‘runif’
plot.ICA: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
to your NAMESPACE file.
ICCbare: no visible global function definition for ‘na.omit’
ICCbare: no visible global function definition for ‘formula’
ICCbare: no visible global function definition for ‘replications’
ICCbare: no visible global function definition for ‘aggregate’
ICCbare: no visible global function definition for ‘anova’
ICCbare: no visible global function definition for ‘aov’
ICCbareF: no visible global function definition for ‘aggregate’
ICCest: no visible global function definition for ‘na.omit’
ICCest: no visible global function definition for ‘anova’
ICCest: no visible global function definition for ‘aov’
ICCest: no visible global function definition for ‘aggregate’
ICCest: no visible global function definition for ‘qf’
ICCest: no visible global function definition for ‘qnorm’
Nest: no visible global function definition for ‘qnorm’
effort : CIW: no visible global function definition for ‘qf’
effort: no visible global function definition for ‘plot’
effort: no visible global function definition for ‘axis’
effort: no visible global function definition for ‘lines’
effort: no visible global function definition for ‘legend’
Undefined global functions or variables:
  aggregate anova aov axis formula legend lines na.omit plot qf qnorm
  replications
Consider adding
  importFrom("graphics", "axis", "legend", "lines", "plot")
  importFrom("stats", "aggregate", "anova", "aov", "formula", "na.omit",
             "qf", "qnorm", "replications")
to your NAMESPACE file.
'library' or 'require' call to ‘KernSmooth’ which was already attached by Depends.
  Please remove these calls from your code.
bickde: no visible global function definition for ‘optimize’
iclocpoly: no visible global function definition for ‘approx’
iclocpoly: no visible global function definition for ‘sd’
iclocpoly: no visible global function definition for ‘dnorm’
iclocpoly: no visible global function definition for ‘pnorm’
iclocpoly: no visible global function definition for ‘var’
inmost: no visible global function definition for ‘stack’
Undefined global functions or variables:
  approx dnorm optimize pnorm sd stack var
Consider adding
  importFrom("stats", "approx", "dnorm", "optimize", "pnorm", "sd",
             "var")
  importFrom("utils", "stack")
to your NAMESPACE file.
Rd file 'ickde.Rd':
  \usage lines wider than 90 characters:
     ickde(I, h, f, m, n.iterations = 10, x1, xm, right.limit = 10000,kernel="gaussian", old=TRUE)

These lines will be truncated in the PDF manual.
INCAncinner : dian: no visible global function definition for ‘cutree’
INCAncinner : bestela: no visible global function definition for
  ‘cutree’
center: no visible global function definition for ‘var’
dbhatta: no visible global function definition for ‘as.dist’
dcor: no visible global function definition for ‘cor’
dcor: no visible global function definition for ‘as.dist’
dgower: no visible global function definition for ‘as.dist’
dmahal: no visible global function definition for ‘as.dist’
dproc2: no visible global function definition for ‘as.dist’
plot.incaix: no visible global function definition for ‘barplot’
plot.incanc: no visible global function definition for ‘plot’
plot.incanc: no visible global function definition for ‘lines’
plot.incanc: no visible global function definition for ‘legend’
selectioncluster : dian: no visible global function definition for
  ‘cutree’
selectioncluster : bestela: no visible global function definition for
  ‘cutree’
Undefined global functions or variables:
  as.dist barplot cor cutree legend lines plot var
Consider adding
  importFrom("graphics", "barplot", "legend", "lines", "plot")
  importFrom("stats", "as.dist", "cor", "cutree", "var")
to your NAMESPACE file.
Depends: includes the non-default packages:
  'lattice', 'caTools', 'gdata', 'gtools', 'gplots', 'parallel'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  ‘caTools’ ‘gdata’ ‘gplots’ ‘gtools’ ‘lattice’ ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  RccpSource_.cpp:978:54: warning: explicitly assigning value of variable of type 'Rcpp::NumericVector' (aka 'Vector<14>') to itself [-Wself-assign-overloaded]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/icosa.Rcheck/00install.out’ for details.
PH.ICsurv.EM: no visible global function definition for ‘quantile’
PH.ICsurv.EM: no visible global function definition for ‘optim’
fast.PH.ICsurv.EM: no visible global function definition for ‘quantile’
fast.PH.ICsurv.EM: no visible global function definition for ‘optim’
Undefined global functions or variables:
  optim quantile
Consider adding
  importFrom("stats", "optim", "quantile")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

idbg.interact: no visible global function definition for
  ‘capture.output’
idbg.interact: no visible global function definition for ‘timestamp’
idbg.print_breakpoints: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  capture.output timestamp
Consider adding
  importFrom("utils", "capture.output", "timestamp")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘README.Idcoefs2b1.txt’
comp.uri: no visible global function definition for ‘quantile’
est.IDR: no visible global function definition for ‘ecdf’
get.pseudo.mix: no visible global function definition for ‘pnorm’
get.uri.2d: no visible global function definition for ‘smooth.spline’
get.uri.2d: no visible global function definition for ‘predict’
Undefined global functions or variables:
  ecdf pnorm predict quantile smooth.spline
Consider adding
  importFrom("stats", "ecdf", "pnorm", "predict", "quantile",
             "smooth.spline")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘XML’ ‘vegan’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: ‘ie2miscdata’
Package suggested but not available for checking: ‘financial’
ROC_plot: no visible global function definition for ‘pdf’
ROC_plot: no visible global function definition for ‘par’
ROC_plot: no visible global function definition for ‘dev.off’
Ymean_compare: no visible binding for global variable ‘sd’
Ymean_compare: no visible global function definition for ‘pdf’
Ymean_compare: no visible global function definition for ‘par’
Ymean_compare: no visible global function definition for ‘dev.off’
data_simulation: no visible global function definition for ‘rnorm’
gibbs_sampling: no visible global function definition for ‘rnorm’
mcmc_trace_plot: no visible global function definition for ‘pdf’
mcmc_trace_plot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off par pdf rnorm sd
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par")
  importFrom("stats", "rnorm", "sd")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

ifa.em: no visible global function definition for ‘runif’
ifa.init.pca: no visible global function definition for ‘var’
ifa.init.pca: no visible global function definition for ‘cor’
ifa.init.pca: no visible global function definition for ‘runif’
ifa.init.random: no visible global function definition for ‘runif’
ifa.init.random: no visible global function definition for ‘var’
Undefined global functions or variables:
  cor runif var
Consider adding
  importFrom("stats", "cor", "runif", "var")
to your NAMESPACE file.
Found the following assignments to the global environment:
File ‘IgorR/R/ReadIgorBinary.R’:
  assign(WaveName, rval, envir = .GlobalEnv)
ihs.mle: no visible global function definition for ‘as.formula’
pihs: no visible global function definition for ‘pnorm’
qihs: no visible global function definition for ‘qnorm’
rihs: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  as.formula pnorm qnorm rnorm
Consider adding
  importFrom("stats", "as.formula", "pnorm", "qnorm", "rnorm")
to your NAMESPACE file.
src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but not in PKG_CFLAGS
  src/Makevars.win: it is not portable to include SHLIB_OPENMP_*' macros in PKG_CPPFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
PKG_CPPFLAGS is used for both C and C++ code so it is not portable to
use it for these macros.
IMIS: no visible global function definition for ‘sample.prior’
IMIS: no visible global function definition for ‘var’
IMIS: no visible global function definition for ‘cov’
IMIS: no visible global function definition for ‘prior’
IMIS: no visible global function definition for ‘likelihood’
IMIS : posterior: no visible global function definition for ‘prior’
IMIS : posterior: no visible global function definition for
  ‘likelihood’
IMIS: no visible global function definition for ‘optim’
IMIS: no visible global function definition for ‘rnorm’
IMIS: no visible global function definition for ‘mahalanobis’
IMIS: no visible global function definition for ‘cov.wt’
IMIS: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  cov cov.wt dnorm likelihood mahalanobis optim prior rnorm
  sample.prior var
Consider adding
  importFrom("stats", "cov", "cov.wt", "dnorm", "mahalanobis", "optim",
             "rnorm", "var")
to your NAMESPACE file.
prepare_Rd: IMIS.Rd:26: Dropping empty section \keyword
Found the following significant warnings:
  IM4ECpp.cpp:24:54: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:24:65: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:33:54: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:33:65: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:25:62: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:25:73: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:35:62: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:35:73: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:59: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:67: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:78: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:59: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:67: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:78: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Immigrate.Rcheck/00install.out’ for details.
heter_IV2: no visible global function definition for ‘poly’
heter_IV2: no visible global function definition for ‘lm’
heter_IV2: no visible global function definition for ‘step’
heter_IV2: no visible global function definition for ‘pnorm’
heter_IV2: no visible global function definition for ‘qnorm’
homo_IV1: no visible global function definition for ‘coef’
homo_IV1: no visible global function definition for ‘pnorm’
homo_IV1: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  coef lm pnorm poly qnorm step
Consider adding
  importFrom("stats", "coef", "lm", "pnorm", "poly", "qnorm", "step")
to your NAMESPACE file.
prepare_Rd: heter_IV2.Rd:82-84: Dropping empty section \note
prepare_Rd: heter_IV2.Rd:88-90: Dropping empty section \seealso
prepare_Rd: homo_IV1.Rd:65-67: Dropping empty section \note
prepare_Rd: homo_IV1.Rd:71-73: Dropping empty section \seealso
prepare_Rd: impact.Rd:31-33: Dropping empty section \source
'library' or 'require' calls to packages already attached by Depends:
  ‘inline’ ‘lpSolve’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘inline’ ‘lpSolve’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
FctReducedNodevalues: no visible global function definition for
  ‘signature’
FctReducedNodevalues: no visible global function definition for
  ‘cfunction’
TotalVar: no visible global function definition for ‘lp’
Undefined global functions or variables:
  cfunction lp signature
Consider adding
  importFrom("methods", "signature")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
generate.ExpressionData: no visible global function definition for
  ‘rnorm’
impute.MinDet: no visible binding for global variable ‘quantile’
impute.MinProb: no visible binding for global variable ‘quantile’
impute.MinProb: no visible binding for global variable ‘sd’
impute.MinProb: no visible global function definition for ‘median’
impute.MinProb: no visible global function definition for ‘rnorm’
impute.QRILC: no visible global function definition for ‘qnorm’
impute.QRILC: no visible global function definition for ‘quantile’
impute.QRILC: no visible global function definition for ‘lm’
insertMVs: no visible global function definition for ‘rnorm’
model.Selector: no visible global function definition for ‘qnorm’
model.Selector: no visible global function definition for ‘quantile’
model.Selector: no visible global function definition for ‘lm’
model.Selector: no visible global function definition for ‘ecdf’
model.Selector: no visible global function definition for ‘pnorm’
pep2prot: no visible binding for global variable ‘median’
Undefined global functions or variables:
  ecdf lm median pnorm qnorm quantile rnorm sd
Consider adding
  importFrom("stats", "ecdf", "lm", "median", "pnorm", "qnorm",
             "quantile", "rnorm", "sd")
to your NAMESPACE file.
impute.mdr: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Rd file 'impute.mdr.Rd':
  \usage lines wider than 90 characters:
     impute.mdr(dataset, colresp, cs, combi, cv.fold = 10, na.method = 0, max_iter = 30, randomize = FALSE)

These lines will be truncated in the PDF manual.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘count_compare’
heal_data: no visible global function definition for ‘optimum_k’
heal_data: no visible global function definition for ‘optimum_w’
heal_data: no visible global function definition for ‘pred_for_w’
Undefined global functions or variables:
  optimum_k optimum_w pred_for_w
Warning: no function found corresponding to methods exports from ‘IM’ for: ‘initialize’

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

Probably some imports need to be declared in the NAMESPACE file.
Packages in Depends field not imported from:
  ‘bmp’ ‘jpeg’ ‘methods’ ‘png’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'MultiIm-class.Rd':
  \examples lines wider than 100 characters:
     #create MultiIm object, calculate generalized Pseudo-Zernike moments, invariants, and reconstruction for all images
             #create MultiIm object, calculate discrete Chebyshev moments, invariants, and reconstruction for all images
             #create MultiIm object, calculate continuous Chebyshev - Legendre moments, invariants, and reconstruction for all images

Rd file 'demoPoly.Rd':
  \examples lines wider than 100 characters:
             #display generalized Pseudo-Zernike polynomials of order and repetition (3,2), (4,2), (5,3), (6,3) 

Rd file 'momentObj.Rd':
  \examples lines wider than 100 characters:
             #calculate bivariate Legendre/Gegenbauer moments up to orders 50 and 100 with parameter 1 for Gegenbauer moments.
             #compute Radial Harmonic-Fourier moment invariants of a list of images, using up to order 10 and repetition 10

These lines will be truncated in the PDF manual.
GenerateMixData: no visible global function definition for ‘rnbinom’
GenerateMixData: no visible global function definition for ‘rbeta’
GenerateMixData: no visible global function definition for ‘rbinom’
GenerateMixData: no visible global function definition for ‘rpois’
InitializePars: no visible global function definition for ‘aggregate’
InitializePars: no visible global function definition for ‘rnorm’
MultiStart: no visible global function definition for ‘rnorm’
MultiStart: no visible global function definition for ‘runif’
inarmix: no visible global function definition for ‘terms’
inarmix: no visible global function definition for ‘model.frame’
inarmix: no visible global function definition for ‘model.response’
inarmix: no visible global function definition for ‘model.matrix’
print.diagnose.inarmix: no visible global function definition for
  ‘plot’
print.diagnose.inarmix: no visible global function definition for
  ‘lines’
print.summary.inarmix: no visible global function definition for
  ‘printCoefmat’
summary.inarmix: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  aggregate lines model.frame model.matrix model.response plot pnorm
  printCoefmat rbeta rbinom rnbinom rnorm rpois runif terms
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "aggregate", "model.frame", "model.matrix",
             "model.response", "pnorm", "printCoefmat", "rbeta",
             "rbinom", "rnbinom", "rnorm", "rpois", "runif", "terms")
to your NAMESPACE file.
Package suggested but not available for checking: ‘rsprng’
'library' or 'require' call to ‘xtable’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘Rmpi’ ‘rsprng’ ‘snow’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
A.dep.tests: no visible global function definition for ‘combn’
A.dep.tests: no visible global function definition for ‘pchisq’
dependogram: no visible global function definition for ‘makeCluster’
dependogram: no visible global function definition for
  ‘clusterSetupSPRNG’
dependogram: no visible global function definition for ‘clusterCall’
dependogram: no visible global function definition for ‘stopCluster’
dependogram: no visible global function definition for ‘combn’
dependogram: no visible global function definition for ‘plot’
dependogram: no visible global function definition for ‘points’
dependogram: no visible global function definition for ‘segments’
Undefined global functions or variables:
  clusterCall clusterSetupSPRNG combn makeCluster pchisq plot points
  segments stopCluster
Consider adding
  importFrom("graphics", "plot", "points", "segments")
  importFrom("stats", "pchisq")
  importFrom("utils", "combn")
to your NAMESPACE file.
IDM.bootCI: no visible global function definition for ‘cov’
IDM.bootCI: no visible global function definition for ‘cor’
IDM.bootCI: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  cor cov quantile
Consider adding
  importFrom("stats", "cor", "cov", "quantile")
to your NAMESPACE file.
Rd file 'IDM.bootCI.Rd':
  \examples lines wider than 100 characters:
     #a built-in dataset fish is used. This data gives sizes of 53 female stickleback measured at the age of 17, 45, 80, and 115 days.
     #figure showing first two trajectories and percentages of variations accounted for by each trajectory.
     barplot(out$Percent.trajectory,ylim=c(0,105),las=1,names.arg=c("1","2","3","4"), ylab="Percentage of variation",cex.lab=1.35,cex.axis=1 ... [TRUNCATED]
     plot(age,out$Trajectories97.5CI[,1],type="l",lty=2,ylim=c(-1,1),las=1,ylab="Trajectory value",xlab="Age (days)",cex.lab=1.35,cex.axis=1 ... [TRUNCATED]
     plot(age,out$Trajectories97.5CI[,2],type="l",lty=2,ylim=c(-1,1),las=1,ylab="Trajectory value",xlab="Age (days)",cex.lab=1.35,cex.axis=1 ... [TRUNCATED]

Rd file 'p.function.Rd':
  \examples lines wider than 100 characters:
     temp2b=(-1)^i*factorial(j)/(factorial(i)*factorial(j-i))*factorial(2*j-2*i)/(factorial(j)*factorial(2*j-2*i-j))*x^(j-2*i)

These lines will be truncated in the PDF manual.
Package in Depends field not imported from: ‘sandwich’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
infer,coxph: no visible global function definition for ‘coef’
infer,coxph: no visible global function definition for ‘vcov’
infer,coxph: no visible global function definition for ‘sandwich’
infer,coxph: no visible global function definition for ‘pnorm’
infer,coxph: no visible global function definition for ‘qnorm’
infer,gee: no visible global function definition for ‘coef’
infer,gee: no visible global function definition for ‘pnorm’
infer,gee: no visible global function definition for ‘qnorm’
infer,glm: no visible global function definition for ‘coef’
infer,glm: no visible global function definition for ‘sandwich’
infer,glm: no visible global function definition for ‘vcov’
infer,glm: no visible global function definition for ‘pnorm’
infer,glm: no visible global function definition for ‘qnorm’
infer,lm: no visible global function definition for ‘coef’
infer,lm: no visible global function definition for ‘sandwich’
infer,lm: no visible global function definition for ‘vcov’
infer,lm: no visible global function definition for ‘pnorm’
infer,lm: no visible global function definition for ‘qnorm’
infer,lme: no visible global function definition for ‘coef’
infer,lme: no visible global function definition for ‘fixed.effects’
infer,lme: no visible global function definition for ‘vcov’
infer,lme: no visible global function definition for ‘pnorm’
infer,lme: no visible global function definition for ‘qnorm’
infer,mer: no visible global function definition for ‘coef’
infer,mer: no visible global function definition for ‘vcov’
infer,mer: no visible global function definition for ‘pnorm’
infer,mer: no visible global function definition for ‘qnorm’
infer,mer: no visible binding for global variable ‘fm1’
Undefined global functions or variables:
  coef fixed.effects fm1 pnorm qnorm sandwich vcov
Consider adding
  importFrom("stats", "coef", "pnorm", "qnorm", "vcov")
to your NAMESPACE file.
contrib: no visible global function definition for ‘aggregate’
est.expDeath : surv_p: no visible global function definition for
  ‘survfit’
est.expDeath : surv_p: no visible global function definition for
  ‘approx’
function1: no visible global function definition for ‘coxph.detail’
inference.SMR: no visible global function definition for ‘qnorm’
var.expDeath : surv_p: no visible global function definition for
  ‘survfit’
var.expDeath : surv_p: no visible global function definition for
  ‘approx’
Undefined global functions or variables:
  aggregate approx coxph.detail qnorm survfit
Consider adding
  importFrom("stats", "aggregate", "approx", "qnorm")
to your NAMESPACE file.
Package unavailable to check Rd xrefs: ‘minfi’
BugReports field should be the URL of a single webpage
gen.intercepts: no visible global function definition for ‘contr.SAS’
Undefined global functions or variables:
  contr.SAS
Consider adding
  importFrom("stats", "contr.SAS")
to your NAMESPACE file.
entropy: no visible global function definition for ‘na.omit’
interinformation: no visible global function definition for ‘na.omit’
multiinformation: no visible global function definition for ‘na.omit’
mutinformation: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
getInfra: no visible global function definition for ‘txtProgressBar’
getInfra: no visible global function definition for ‘download.file’
getInfra: no visible global function definition for ‘setTxtProgressBar’
getInfra : <anonymous>: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "download.file", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
Unexported object imported by a ':::' call: ‘ltm:::crf.GPCM’
  See the note in ?`:::` about the use of this operator.
Jeffreys: no visible global function definition for ‘integrate’
Jeffreys: no visible global function definition for ‘splinefun’
count.rows: no visible global function definition for ‘tail’
count.rows: no visible global function definition for ‘head’
cprobs : <anonymous>: no visible global function definition for
  ‘plogis’
inf.func.ltm : f: no visible global function definition for ‘plogis’
iota: no visible global function definition for ‘integrate’
iota: no visible global function definition for ‘optimize’
iota: no visible global function definition for ‘pchisq’
iota.c : rirm: no visible global function definition for ‘coef’
iota.c: no visible global function definition for ‘integrate’
iota.c: no visible global function definition for ‘sd’
iota.u: no visible global function definition for ‘integrate’
iprobs : <anonymous>: no visible global function definition for
  ‘plogis’
logL.ltm : logL: no visible global function definition for ‘dbinom’
logL.ltm : logL: no visible global function definition for ‘plogis’
logL.ltm : logL : <anonymous>: no visible global function definition
  for ‘plogis’
rJeffreys : Jpinv.min: no visible global function definition for
  ‘integrate’
rJeffreys : Jpinv: no visible global function definition for ‘nlminb’
rJeffreys : Jpinv: no visible global function definition for ‘qnorm’
rJeffreys: no visible global function definition for ‘runif’
Undefined global functions or variables:
  coef dbinom head integrate nlminb optimize pchisq plogis qnorm runif
  sd splinefun tail
Consider adding
  importFrom("stats", "coef", "dbinom", "integrate", "nlminb",
             "optimize", "pchisq", "plogis", "qnorm", "runif", "sd",
             "splinefun")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Rd file 'Jeffreys.Rd':
  \usage lines wider than 90 characters:
     Jeffreys(ltm.obj = NULL, inf.mat = NULL, inf.func = NULL, return = "prior", spl.method = "natural", range.int = c(-Inf, Inf))

Rd file 'iota.Rd':
  \usage lines wider than 90 characters:
     iota(ltm.obj, logL.fun, fscore.obj = NULL, data = NULL, prior = NULL, theta0 = NULL, range.int = c(-Inf, Inf), range.theta = c(-10, 10) ... [TRUNCATED]

Rd file 'iota.c.Rd':
  \usage lines wider than 90 characters:
     iota.c(ltm.obj, M = NULL, prior = NULL, logL.fun = NULL, rirm = NULL, range.int = c(-Inf, Inf))

These lines will be truncated in the PDF manual.
Package unavailable to check Rd xrefs: ‘INLA’
Found the following apparent S3 methods exported but not registered:
  combine.NULL print.allfun
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Packages in Depends field not imported from:
  ‘ExPosition’ ‘prettyGraphs’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  print.epCA.inference.battery print.epGPCA.inference.battery
  print.epMCA.inference.battery print.epPCA.inference.battery
  print.inpoBoot print.inpoBootTests print.inpoComponents
  print.inpoOmni print.inpoOutput
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘compiler’ ‘deSolve’ ‘lattice’ ‘nlme’
  Please remove these calls from your code.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘insideRODE/R/zzz.r’:
  .First.lib calls:
    require(nlme)
    require(lattice)
    require(deSolve)
    require(compiler)

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

cfLSODE: no visible global function definition for ‘deriv’
cfODE: no visible global function definition for ‘deriv’
cfVODE: no visible global function definition for ‘deriv’
cpLSODE: no visible global function definition for ‘deriv’
cpODE: no visible global function definition for ‘deriv’
cpVODE: no visible global function definition for ‘deriv’
nlmLSODE: no visible global function definition for ‘deriv’
nlmLSODEcp: no visible global function definition for ‘deriv’
nlmODE: no visible global function definition for ‘deriv’
nlmODEcp: no visible global function definition for ‘deriv’
nlmVODE: no visible global function definition for ‘deriv’
nlmVODEcp: no visible global function definition for ‘deriv’
Undefined global functions or variables:
  deriv
Consider adding
  importFrom("stats", "deriv")
to your NAMESPACE file.
cgrad: no visible global function definition for ‘res’
doshade: no visible global function definition for ‘projection’
doshade: no visible global function definition for ‘extent’
doshade: no visible global function definition for ‘res’
doshade: no visible global function definition for ‘raster’
doshade: no visible global function definition for ‘extent<-’
Undefined global functions or variables:
  extent extent<- projection raster res
ClearBottomMenuPlot: no visible global function definition for ‘rect’
InteractiveIGraph : mousedown: no visible global function definition
  for ‘grconvertX’
InteractiveIGraph : mousedown: no visible global function definition
  for ‘grconvertY’
InteractiveIGraph : dragmousemove: no visible global function
  definition for ‘grconvertX’
InteractiveIGraph : dragmousemove: no visible global function
  definition for ‘grconvertY’
InteractiveIGraph : dragmousemove: no visible global function
  definition for ‘polygon’
InteractiveIGraph : mouseup: no visible global function definition for
  ‘grconvertX’
InteractiveIGraph : mouseup: no visible global function definition for
  ‘grconvertY’
InteractiveIGraph : keybd: no visible global function definition for
  ‘par’
PlotRegionGeneral: no visible global function definition for ‘polygon’
plot.InteractiveIGraph: no visible global function definition for
  ‘plot’
plot.InteractiveIGraph: no visible global function definition for ‘par’
plot.Menu: no visible global function definition for ‘par’
plot.Menu: no visible binding for global variable ‘rect’
plot.MenuItem: no visible binding for global variable ‘strwidth’
plot.MenuItem: no visible binding for global variable ‘strheight’
plot.MenuItem: no visible binding for global variable ‘rect’
plot.MenuItem: no visible binding for global variable ‘text’
plot.MenuLine: no visible binding for global variable ‘rect’
Undefined global functions or variables:
  grconvertX grconvertY par plot polygon rect strheight strwidth text
Consider adding
  importFrom("graphics", "grconvertX", "grconvertY", "par", "plot",
             "polygon", "rect", "strheight", "strwidth", "text")
to your NAMESPACE file.
Rd file 'InteractiveIGraph.Rd':
  \examples lines wider than 100 characters:
     # this is an 'InteractiveIGraph' object, up till now there is not much difference. Just some extra attributes.

Rd file 'MenuAddItems.Rd':
  \examples lines wider than 100 characters:
       Item = list(list(label=msg, RegionParams=list(XBufCof = 0, YBufCof=0.2), RecParams=list(lwd = NA, border=NA), TextParams=list(cex=0.8 ... [TRUNCATED]

These lines will be truncated in the PDF manual.
interact: no visible global function definition for ‘cor’
plot.interact: no visible global function definition for ‘plot’
standardize.matrix: no visible binding for global variable ‘var’
standardize.matrix: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  cor plot sd var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "cor", "sd", "var")
to your NAMESPACE file.
HH: no visible global function definition for ‘var’
HH: no visible global function definition for ‘qnorm’
exactCI: no visible global function definition for ‘quantile’
sample.n: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  qnorm quantile rbinom var
Consider adding
  importFrom("stats", "qnorm", "quantile", "rbinom", "var")
to your NAMESPACE file.
Interpol: no visible global function definition for ‘splinefun’
Undefined global functions or variables:
  splinefun
Consider adding
  importFrom("stats", "splinefun")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘Interpol/R/AAdescriptor.R’:
  data(AAindex)
See section ‘Good practice’ in ‘?data’.
prepare_Rd: AAdescriptor.Rd:25-27: Dropping empty section \details
prepare_Rd: AAdescriptor.Rd:39-41: Dropping empty section \note
prepare_Rd: AAdescriptor.Rd:45-47: Dropping empty section \seealso
prepare_Rd: AAindex.Rd:11-12: Dropping empty section \format
prepare_Rd: AAindex.Rd:1080-1081: Dropping empty section \source
prepare_Rd: AAindex.Rd:1085-1086: Dropping empty section \examples
prepare_Rd: Interpol.Rd:35-37: Dropping empty section \details
prepare_Rd: Interpol.Rd:47-49: Dropping empty section \note
prepare_Rd: Interpol.Rd:53-55: Dropping empty section \seealso
prepare_Rd: V3.Rd:11-12: Dropping empty section \format
prepare_Rd: V3.Rd:13-14: Dropping empty section \details
prepare_Rd: V3.Rd:15-16: Dropping empty section \source
prepare_Rd: V3.Rd:20-21: Dropping empty section \examples
Rd file 'Interpol.Rd':
  \examples lines wider than 100 characters:
             plot(unlist(b), type="l", col="darkgreen", ylim=c(-3,3), ylab="descriptor value", xlab="sequence position", lwd=2)
             lines(seq(1,length(unlist(b)),(length(unlist(b))/length(as.vector(c)))),as.vector(c), col="red", lwd=2)

These lines will be truncated in the PDF manual.
Packages in Depends field not imported from:
  ‘chron’ ‘date’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Mo.Th.Ra.: no visible global function definition for ‘aggregate’
daily_mean: no visible global function definition for ‘aggregate’
date.time: no visible global function definition for ‘chron’
date.time: no visible global function definition for ‘years’
date.time: no visible global function definition for ‘days’
date.time: no visible global function definition for ‘hours’
par_calibration: no visible global function definition for ‘date.mdy’
par_calibration: no visible global function definition for ‘as.date’
par_calibration: no visible global function definition for ‘aggregate’
plot_meas_sim: no visible global function definition for ‘as.date’
plot_meas_sim: no visible global function definition for ‘date.mdy’
plot_meas_sim: no visible global function definition for ‘plot’
plot_meas_sim: no visible global function definition for ‘par’
plot_meas_sim: no visible global function definition for ‘legend’
shape_calibration: no visible global function definition for ‘date.mdy’
shape_calibration: no visible global function definition for ‘as.date’
shape_calibration: no visible global function definition for
  ‘aggregate’
Undefined global functions or variables:
  aggregate as.date chron date.mdy days hours legend par plot years
Consider adding
  importFrom("graphics", "legend", "par", "plot")
  importFrom("stats", "aggregate")
to your NAMESPACE file.
icScoreTest: no visible global function definition for ‘pnorm’
icScoreTest: no visible global function definition for ‘pchisq’
icfit.formula: no visible global function definition for ‘terms’
icfit.formula: no visible global function definition for
  ‘model.extract’
icfitBootCI: no visible global function definition for ‘binom.test’
ictest.formula: no visible global function definition for
  ‘model.extract’
plot.icfit: no visible global function definition for ‘gray’
plot.icfit: no visible global function definition for ‘plot’
plot.icfit: no visible global function definition for ‘axis’
plot.icfit : polygon.icfit: no visible global function definition for
  ‘polygon’
scoresFromFit: no visible global function definition for ‘dnorm’
scoresFromFit: no visible global function definition for ‘qnorm’
wsrHLYpclt: no visible global function definition for ‘model.matrix’
wsrHLYpclt: no visible global function definition for ‘pchisq’
wsrHLYpclt: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  axis binom.test dnorm gray model.extract model.matrix pchisq plot
  pnorm polygon qnorm terms
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "axis", "plot", "polygon")
  importFrom("stats", "binom.test", "dnorm", "model.extract",
             "model.matrix", "pchisq", "pnorm", "qnorm", "terms")
to your NAMESPACE file.
interventionEffects: no visible binding for global variable ‘sd’
interventionEffects: no visible global function definition for ‘pt’
interventionEffects: no visible global function definition for ‘sd’
interventionalInference: no visible global function definition for ‘sd’
interventionalInferenceAdvanced: no visible global function definition
  for ‘sd’
linesROC: no visible global function definition for ‘segments’
plotMaxML: no visible global function definition for ‘plot’
plotMaxML: no visible global function definition for ‘segments’
Undefined global functions or variables:
  plot pt sd segments
Consider adding
  importFrom("graphics", "plot", "segments")
  importFrom("stats", "pt", "sd")
to your NAMESPACE file.
'library' or 'require' call to ‘maxLik’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘maxLik’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ILik : rbern: no visible global function definition for ‘runif’
ILik : q: no visible global function definition for ‘dnorm’
ILik : SlambdaG: no visible global function definition for ‘rnorm’
ILik : Pi_hat: no visible global function definition for ‘rnorm’
ILik : q: no visible global function definition for ‘dgamma’
ILik : SlambdaG: no visible global function definition for ‘rgamma’
ILik : Pi_hat: no visible global function definition for ‘rgamma’
ILik: no visible global function definition for ‘maxLik’
ILik: no visible global function definition for ‘coef’
ILik: no visible global function definition for ‘hessian’
ILik: no visible global function definition for ‘plot’
Undefined global functions or variables:
  coef dgamma dnorm hessian maxLik plot rgamma rnorm runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "dgamma", "dnorm", "rgamma", "rnorm",
             "runif")
to your NAMESPACE file.
intReg: no visible binding for global variable ‘plogis’
intReg: no visible binding for global variable ‘pnorm’
intReg: no visible binding for global variable ‘pcauchy’
intReg: no visible binding for global variable ‘dlogis’
intReg: no visible binding for global variable ‘dnorm’
intReg: no visible binding for global variable ‘dcauchy’
intReg: no visible global function definition for ‘model.matrix’
intReg: no visible global function definition for ‘model.weights’
intReg: no visible global function definition for ‘model.offset’
intReg: no visible global function definition for ‘model.response’
intReg: no visible global function definition for ‘glm.fit’
intReg: no visible global function definition for ‘binomial’
intReg: no visible binding for global variable ‘coef’
intReg: no visible global function definition for ‘lm’
intReg: no visible global function definition for ‘coef’
intReg: no visible global function definition for ‘var’
model.matrix.intReg: no visible global function definition for
  ‘model.frame’
print.intReg: no visible global function definition for ‘coef’
print.summary.intReg: no visible global function definition for
  ‘logLik’
print.summary.intReg: no visible global function definition for
  ‘printCoefmat’
summary.intReg: no visible global function definition for ‘coef’
Undefined global functions or variables:
  binomial coef dcauchy dlogis dnorm glm.fit lm logLik model.frame
  model.matrix model.offset model.response model.weights pcauchy plogis
  pnorm printCoefmat var
Consider adding
  importFrom("stats", "binomial", "coef", "dcauchy", "dlogis", "dnorm",
             "glm.fit", "lm", "logLik", "model.frame", "model.matrix",
             "model.offset", "model.response", "model.weights",
             "pcauchy", "plogis", "pnorm", "printCoefmat", "var")
to your NAMESPACE file.
f.B: no visible global function definition for ‘pnorm’
f.B.neglog.deriv: no visible global function definition for ‘pnorm’
f.B.neglog.deriv: no visible global function definition for ‘dnorm’
f.grovest3 : f.est: no visible global function definition for ‘survfit’
f.grovest3 : f.est: no visible global function definition for ‘plot’
f.grovest3 : f.est: no visible global function definition for ‘lines’
f.grovest3: no visible global function definition for ‘model.frame’
f.grovest3: no visible global function definition for ‘model.extract’
invGauss: no visible global function definition for ‘model.frame’
invGauss: no visible global function definition for ‘model.extract’
invGauss: no visible global function definition for ‘model.matrix’
predict.invGauss: no visible global function definition for
  ‘model.frame’
predict.invGauss: no visible global function definition for
  ‘model.extract’
predict.invGauss: no visible global function definition for
  ‘model.matrix’
predict.invGauss: no visible binding for global variable ‘formula’
predict.invGauss: no visible binding for global variable ‘data’
summary.invGauss: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  data dnorm formula lines model.extract model.frame model.matrix plot
  pnorm survfit
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "dnorm", "formula", "model.extract", "model.frame",
             "model.matrix", "pnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
flowsRandom: no visible global function definition for ‘dmultinom’
readBed: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  dmultinom read.table
Consider adding
  importFrom("stats", "dmultinom")
  importFrom("utils", "read.table")
to your NAMESPACE file.
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard file/directory found at top level:
  ‘beta’
Warning: no function found corresponding to methods exports from ‘ipdmeta’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
ipd.meta.power.base.function : power: no visible global function
  definition for ‘qnorm’
ipd.meta.power.base.function : power: no visible global function
  definition for ‘pnorm’
ipd.meta.power.base.function: no visible global function definition for
  ‘qnorm’
ipdlme.hetero: no visible global function definition for ‘new’
ipdlme.homo: no visible global function definition for ‘new’
plot_ipdlme: no visible global function definition for ‘par’
plot_ipdlme: no visible global function definition for ‘abline’
plot_ipdlme: no visible global function definition for ‘axis’
plot_ipdlme: no visible global function definition for ‘segments’
confint,ipdlme: no visible global function definition for ‘qt’
plot,ipdlme: no visible global function definition for ‘par’
plot,ipdlme: no visible global function definition for ‘abline’
plot,ipdlme: no visible global function definition for ‘axis’
plot,ipdlme: no visible global function definition for ‘segments’
summary,ipdlme: no visible global function definition for ‘pt’
Undefined global functions or variables:
  abline axis new par pnorm pt qnorm qt segments
Consider adding
  importFrom("graphics", "abline", "axis", "par", "segments")
  importFrom("methods", "new")
  importFrom("stats", "pnorm", "pt", "qnorm", "qt")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running ‘testthat.R’ [0m/17m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ipeaData)
  > 
  > test_check("ipeaData")
  [1] "NA. 05/1999 a 03/2009. Acesso em: 26/10/2018"
  ── 1. Error: ipeaData (@test_functions_ipea_data.R#19)  ────────────────────────
  Recv failure: Connection timed out
  1: suppressWarnings(result <- ipeadata("SERIE SEM RETORNO")) at testthat/test_functions_ipea_data.R:19
  2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  3: ipeadata("SERIE SEM RETORNO")
  4: get_metadata(serie)
  5: basic_call(api_call, type)
  6: GET(api)
  7: request_perform(req, hu$handle$handle)
  8: request_fetch(req$output, req$url, handle)
  9: request_fetch.write_memory(req$output, req$url, handle)
  10: curl::curl_fetch_memory(url, handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 6 SKIPPED: 0 FAILED: 1
  1. Error: ipeaData (@test_functions_ipea_data.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
Non-standard file/directory found at top level:
  ‘version’
'library' or 'require' calls in package code:
  ‘MCMCpack’ ‘mvtnorm’ ‘truncnorm’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
code.simple.gaps: no visible global function definition for ‘tail’
multistateMCMC: no visible global function definition for ‘write.table’
multistateMCMC: no visible global function definition for ‘read.table’
multistateMCMC: no visible global function definition for ‘tail’
multistateML: no visible global function definition for ‘tail’
multistateML: no visible global function definition for ‘write.table’
multistateML: no visible global function definition for ‘read.table’
phylo2mafft: no visible global function definition for ‘write.table’
read.beast : foo: no visible global function definition for ‘head’
read.beast: no visible global function definition for ‘tail’
read.starbeast: no visible global function definition for ‘head’
trimEnds : replaceWithN : getIndex: no visible global function
  definition for ‘head’
unresolve.clade: no visible global function definition for ‘tail’
unresolve.clade: no visible global function definition for ‘head’
write.fas: no visible global function definition for ‘tail’
Undefined global functions or variables:
  head read.table tail write.table
Consider adding
  importFrom("utils", "head", "read.table", "tail", "write.table")
to your NAMESPACE file.
gimli.7374hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Packages in Depends field not imported from:
  ‘RBGL’ ‘graph’ ‘igraph’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
convert_MITAB_to_edgeList: no visible global function definition for
  ‘combn’
convert_edgeList_to_graph: no visible global function definition for
  ‘ftM2graphNEL’
convert_edgeList_to_graph: no visible global function definition for
  ‘graph.data.frame’
convert_graph_to_edgeList: no visible global function definition for
  ‘edgeWeights’
convert_graph_to_edgeList: no visible global function definition for
  ‘get.edgelist’
convert_graph_to_edgeList: no visible global function definition for
  ‘E’
create_id_conversion_table: no visible global function definition for
  ‘write.table’
get_irefindex: no visible global function definition for ‘read.table’
get_irefindex: no visible global function definition for
  ‘download.file’
get_irefindex: no visible global function definition for ‘unzip’
summary_graph: no visible global function definition for
  ‘connectedComp’
summary_graph: no visible global function definition for ‘subGraph’
summary_graph: no visible global function definition for ‘clusters’
summary_graph: no visible global function definition for ‘subgraph’
summary_graph: no visible global function definition for ‘plot’
summary_graph: no visible binding for global variable
  ‘layout.fruchterman.reingold’
Undefined global functions or variables:
  E clusters combn connectedComp download.file edgeWeights ftM2graphNEL
  get.edgelist graph.data.frame layout.fruchterman.reingold plot
  read.table subGraph subgraph unzip write.table
Consider adding
  importFrom("graphics", "plot")
  importFrom("utils", "combn", "download.file", "read.table", "unzip",
             "write.table")
to your NAMESPACE file.
'library' or 'require' call to ‘lpSolve’ which was already attached by Depends.
  Please remove these calls from your code.
Found the following apparent S3 methods exported but not registered:
  print.icclist print.irrlist
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'N2.cohen.kappa.Rd':
  \examples lines wider than 100 characters:
       N2.cohen.kappa(c(0.2, 0.25, 0.55), k1=0.6, k0=0.4)                                                            

These lines will be truncated in the PDF manual.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  inst/irtppcpp/include/SPGO/makefile
  inst/irtppcpp/makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
dendrify: no visible binding for global variable ‘item’
dendrify: no visible binding for global variable ‘node’
dendrify: no visible binding for global variable ‘value’
exogenize: no visible binding for global variable ‘item’
Undefined global functions or variables:
  item node value
isbf: no visible global function definition for ‘var’
isbf: no visible global function definition for ‘qnorm’
isbfReg: no visible global function definition for ‘var’
isbfReg: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm var
Consider adding
  importFrom("stats", "qnorm", "var")
to your NAMESPACE file.
residualplot: no visible global function definition for ‘predict’
residualplot: no visible global function definition for ‘rstandard’
residualplot: no visible global function definition for
  ‘complete.cases’
residualplot: no visible global function definition for ‘plot’
residualplot: no visible global function definition for ‘points’
residualplot: no visible global function definition for ‘lines’
residualplot: no visible global function definition for ‘smooth.spline’
residualplot: no visible global function definition for ‘sd’
residualplot: no visible global function definition for ‘rgb’
residualplot: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  complete.cases lines plot points polygon predict rgb rstandard sd
  smooth.spline
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "plot", "points", "polygon")
  importFrom("stats", "complete.cases", "predict", "rstandard", "sd",
             "smooth.spline")
to your NAMESPACE file.
'library' or 'require' call to ‘scatterplot3d’ which was already attached by Depends.
  Please remove these calls from your code.
Found the following apparent S3 methods exported but not registered:
  summary.interval
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
histInterval : buildHist: no visible global function definition for
  ‘hist’
intervalGraph3D: no visible global function definition for ‘par’
regInterval: no visible global function definition for ‘lm’
Undefined global functions or variables:
  hist lm par
Consider adding
  importFrom("graphics", "hist", "par")
  importFrom("stats", "lm")
to your NAMESPACE file.
EstimateIsingLL: no visible global function definition for ‘combn’
EstimateIsingLL: no visible global function definition for ‘loglin’
EstimateIsingPL: no visible global function definition for ‘nlm’
EstimateIsingUni : <anonymous>: no visible global function definition
  for ‘glm’
EstimateIsingUni : <anonymous>: no visible binding for global variable
  ‘binomial’
EstimateIsingUni: no visible binding for global variable ‘coef’
Undefined global functions or variables:
  binomial coef combn glm loglin nlm
Consider adding
  importFrom("stats", "binomial", "coef", "glm", "loglin", "nlm")
  importFrom("utils", "combn")
to your NAMESPACE file.
C.cal: no visible global function definition for ‘as.stepfun’
bandwidth.choose.cv: no visible global function definition for ‘isoreg’
g.density: no visible global function definition for ‘as.stepfun’
g.density: no visible global function definition for ‘dnorm’
h.density: no visible global function definition for ‘dnorm’
iso.bt.unit: no visible global function definition for ‘quantile’
iso.bt.unit.sub: no visible global function definition for ‘isoreg’
iso.bt.unit.sub: no visible global function definition for ‘as.stepfun’
iso.bt.wald.unit: no visible global function definition for ‘var’
iso.ci: no visible global function definition for ‘isoreg’
iso.ci.transform.unit: no visible global function definition for
  ‘as.stepfun’
Undefined global functions or variables:
  as.stepfun dnorm isoreg quantile var
Consider adding
  importFrom("stats", "as.stepfun", "dnorm", "isoreg", "quantile", "var")
to your NAMESPACE file.
ACO : bordacircular: no visible global function definition for
  ‘medianCircular’
Undefined global functions or variables:
  medianCircular
'library' or 'require' call to ‘proxy’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
isopam : core: no visible global function definition for ‘dist’
isopam : core: no visible global function definition for ‘write.table’
isopam : core: no visible global function definition for ‘as.dist’
isopam : core: no visible global function definition for
  ‘txtProgressBar’
isopam : core: no visible global function definition for
  ‘setTxtProgressBar’
isopam : core: no visible global function definition for ‘aggregate’
isopam: no visible binding for global variable ‘var’
isopam: no visible global function definition for ‘na.omit’
isopam: no visible global function definition for ‘write.table’
isopam: no visible global function definition for ‘bmp’
isopam: no visible global function definition for ‘dev.off’
isotab: no visible global function definition for ‘aggregate’
isotab : fshtest: no visible global function definition for ‘dhyper’
isotab : fshtest : pnhyper: no visible global function definition for
  ‘phyper’
Undefined global functions or variables:
  aggregate as.dist bmp dev.off dhyper dist na.omit phyper
  setTxtProgressBar txtProgressBar var write.table
Consider adding
  importFrom("grDevices", "bmp", "dev.off")
  importFrom("stats", "aggregate", "as.dist", "dhyper", "dist",
             "na.omit", "phyper", "var")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar",
             "write.table")
to your NAMESPACE file.
ufit: no visible global function definition for ‘stepfun’
Undefined global functions or variables:
  stepfun
Consider adding
  importFrom("stats", "stepfun")
to your NAMESPACE file.
Depends: includes the non-default packages:
  'partitions', 'VGAM', 'MASS', 'ape', 'apTreeshape', 'geiger',
  'gtools'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  ‘MASS’ ‘VGAM’ ‘apTreeshape’ ‘ape’ ‘geiger’ ‘gtools’ ‘partitions’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Non-standard file/directory found at top level:
  ‘Readme’
Packages in Depends field not imported from:
  ‘Matching’ ‘R2jags’ ‘boot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bpsm: no visible global function definition for ‘glm’
bpsm: no visible global function definition for ‘binomial’
bpsm: no visible global function definition for ‘Match’
bpsm: no visible global function definition for ‘cov’
bpsm: no visible global function definition for ‘vcov’
bpsm : inits: no visible global function definition for ‘runif’
bpsm: no visible global function definition for ‘jags’
bpsr: no visible global function definition for ‘glm’
bpsr: no visible global function definition for ‘binomial’
bpsr: no visible global function definition for ‘lm’
bpsr : inits: no visible global function definition for ‘runif’
bpsr: no visible global function definition for ‘jags’
modelpsm: no visible binding for global variable ‘D’
modelpsr: no visible binding for global variable ‘D’
Undefined global functions or variables:
  D Match binomial cov glm jags lm runif vcov
Consider adding
  importFrom("stats", "D", "binomial", "cov", "glm", "lm", "runif",
             "vcov")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  summary.ivbma
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
ivbma.cv.study: no visible global function definition for ‘predict’
ivbma.diagnostics: no visible global function definition for ‘pchisq’
ivbma.init: no visible global function definition for ‘rbinom’
ivbma.init: no visible global function definition for ‘cov’
ivbma.score: no visible global function definition for ‘median’
ivbma.score: no visible global function definition for ‘var’
predict.ivbma: no visible global function definition for ‘rnorm’
rinvwish: no visible global function definition for ‘rchisq’
rinvwish: no visible global function definition for ‘rnorm’
rinvwish.old: no visible global function definition for ‘rchisq’
rinvwish.old: no visible global function definition for ‘rnorm’
rmvnorm: no visible global function definition for ‘rnorm’
rmvnorm.precision: no visible global function definition for ‘rnorm’
summary.ivbma: no visible global function definition for ‘quantile’
update.L: no visible global function definition for ‘runif’
update.M: no visible global function definition for ‘runif’
update.M.SUR: no visible global function definition for ‘runif’
Undefined global functions or variables:
  cov median pchisq predict quantile rbinom rchisq rnorm runif var
Consider adding
  importFrom("stats", "cov", "median", "pchisq", "predict", "quantile",
             "rbinom", "rchisq", "rnorm", "runif", "var")
to your NAMESPACE file.
ivFixed.formula: no visible global function definition for
  ‘model.matrix’
ivFixed.formula: no visible global function definition for
  ‘model.response’
summary.ivFixed: no visible global function definition for ‘coef’
summary.ivFixed: no visible global function definition for ‘pt’
Undefined global functions or variables:
  coef model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.matrix", "model.response", "pt")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  print.lewbel.model
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
clusterVCV: no visible global function definition for ‘estfun’
covc: no visible global function definition for ‘sandwich’
ftest: no visible global function definition for ‘vcovHC’
Undefined global functions or variables:
  estfun sandwich vcovHC
ARsensitivity.ci: no visible global function definition for ‘residuals’
ARsensitivity.ci: no visible global function definition for ‘lm’
ARsensitivity.ci: no visible global function definition for ‘qf’
ARsensitivity.ci: no visible global function definition for ‘fitted’
ARsensitivity.power: no visible global function definition for ‘qf’
ARsensitivity.power: no visible global function definition for ‘pf’
ARsensitivity.size: no visible global function definition for ‘qf’
ARsensitivity.size: no visible global function definition for ‘pf’
anderson.rubin.ci: no visible global function definition for ‘qf’
anderson.rubin.ci: no visible global function definition for ‘fitted’
anderson.rubin.ci: no visible global function definition for ‘lm’
power.iv: no visible global function definition for ‘qf’
power.iv: no visible global function definition for ‘pf’
Undefined global functions or variables:
  fitted lm pf qf residuals
Consider adding
  importFrom("stats", "fitted", "lm", "pf", "qf", "residuals")
to your NAMESPACE file.
hausman: no visible global function definition for ‘pchisq’
ivbe: no visible global function definition for ‘cor’
ivbe: no visible global function definition for ‘pt’
ivfixed: no visible global function definition for ‘cor’
ivfixed: no visible global function definition for ‘pt’
ivpan.formula: no visible global function definition for ‘model.matrix’
ivpan.formula: no visible global function definition for
  ‘model.response’
ivrandom: no visible global function definition for ‘cor’
ivrandom: no visible global function definition for ‘pt’
summary.ivpan: no visible global function definition for ‘printCoefmat’
Undefined global functions or variables:
  cor model.matrix model.response pchisq printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.matrix", "model.response", "pchisq",
             "printCoefmat", "pt")
to your NAMESPACE file.
histw: no visible global function definition for ‘plot.new’
histw: no visible global function definition for ‘plot.window’
histw: no visible global function definition for ‘axis’
histw: no visible global function definition for ‘rect’
histw: no visible global function definition for ‘lines’
Undefined global functions or variables:
  axis lines plot.new plot.window rect
Consider adding
  importFrom("graphics", "axis", "lines", "plot.new", "plot.window",
             "rect")
to your NAMESPACE file.
boxplot.james: no visible global function definition for ‘mtext’
getBestSolutionValues.james : <anonymous>: no visible global function
  definition for ‘tail’
isMinimizing: no visible global function definition for ‘head’
isMinimizing: no visible global function definition for ‘tail’
mergeJAMES.james: no visible global function definition for ‘glob2rx’
plotConvergence.james : <anonymous> : <anonymous>: no visible global
  function definition for ‘tail’
plotConvergence.james: no visible global function definition for ‘tail’
plotConvergence.james: no visible global function definition for ‘head’
plotConvergence.james : <anonymous>: no visible global function
  definition for ‘tail’
plotConvergence.james: no visible global function definition for
  ‘matplot’
plotConvergence.james: no visible global function definition for
  ‘mtext’
summary.james: no visible global function definition for ‘sd’
summary.james: no visible global function definition for ‘median’
summary.james: no visible global function definition for ‘IQR’
Undefined global functions or variables:
  IQR glob2rx head matplot median mtext sd tail
Consider adding
  importFrom("graphics", "matplot", "mtext")
  importFrom("stats", "IQR", "median", "sd")
  importFrom("utils", "glob2rx", "head", "tail")
to your NAMESPACE file.
Package in Depends field not imported from: ‘gtools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

make_template: no visible global function definition for ‘invalid’
Undefined global functions or variables:
  invalid
Non-standard files/directories found at top level:
  ‘getsp.class’ ‘getsp.java’ ‘version’
.getJavaGDObject: no visible global function definition for ‘.jmkref’
.javaGD.copy.device: no visible global function definition for
  ‘dev.cur’
.javaGD.copy.device: no visible binding for global variable ‘pdf’
.javaGD.copy.device: no visible global function definition for
  ‘dev.set’
.javaGD.copy.device: no visible global function definition for
  ‘dev.copy’
.javaGD.copy.device: no visible global function definition for ‘par’
.javaGD.copy.device: no visible global function definition for
  ‘dev.off’
.javaGD.get.size: no visible global function definition for ‘dev.cur’
.javaGD.resize: no visible global function definition for ‘dev.cur’
JavaGD: no visible global function definition for ‘.jinit’
Undefined global functions or variables:
  .jinit .jmkref dev.copy dev.cur dev.off dev.set par pdf
Consider adding
  importFrom("grDevices", "dev.copy", "dev.cur", "dev.off", "dev.set",
             "pdf")
  importFrom("graphics", "par")
to your NAMESPACE file.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
getSysinfo: no visible global function definition for ‘sessionInfo’
getVecInfo: no visible global function definition for ‘sd’
isSeriesConstant: no visible global function definition for ‘median’
labelMargins: no visible global function definition for ‘mtext’
plotBG: no visible global function definition for ‘plot’
plotBG: no visible global function definition for ‘polygon’
plotBG: no visible global function definition for ‘par’
plotColorScale: no visible global function definition for ‘par’
plotColorScale: no visible global function definition for ‘text’
plotImageRotated: no visible global function definition for
  ‘heat.colors’
plotImageRotated: no visible global function definition for ‘par’
plotImageRotated: no visible global function definition for ‘plot’
plotImageRotated: no visible global function definition for ‘image’
plotImageRotated: no visible global function definition for ‘axis’
plotNLines: no visible global function definition for ‘par’
plotNLines: no visible global function definition for ‘plot’
plotNLines: no visible global function definition for ‘mtext’
plotNLines: no visible global function definition for ‘axis’
plotNLines: no visible global function definition for ‘points’
plotNLines: no visible global function definition for ‘sd’
userCoords: no visible global function definition for ‘par’
Undefined global functions or variables:
  axis heat.colors image median mtext par plot points polygon sd
  sessionInfo text
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "axis", "image", "mtext", "par", "plot",
             "points", "polygon", "text")
  importFrom("stats", "median", "sd")
  importFrom("utils", "sessionInfo")
to your NAMESPACE file.
'library' or 'require' call to ‘igraph’ which was already attached by Depends.
  Please remove these calls from your code.
Found the following apparent S3 methods exported but not registered:
  plot.jgl print.jgl
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
JGL: no visible global function definition for ‘cov’
admm.iters: no visible global function definition for ‘cov’
admm.iters.unconnected: no visible global function definition for ‘var’
plot.jgl: no visible global function definition for ‘plot’
Undefined global functions or variables:
  cov plot var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "cov", "var")
to your NAMESPACE file.
Rd file 'JGL.Rd':
  \usage lines wider than 90 characters:
     JGL(Y,penalty="fused",lambda1,lambda2,rho=1,weights="equal",penalize.diagonal=FALSE,maxiter=500,tol=1e-5,warm=NULL,return.whole.theta=F ... [TRUNCATED]

These lines will be truncated in the PDF manual.
powerLongSurv: no visible global function definition for ‘qnorm’
powerLongSurv: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
JBTest: no visible global function definition for ‘pchisq’
generateSignificance: no visible global function definition for ‘pnorm’
packages: no visible global function definition for ‘install.packages’
shift: no visible global function definition for ‘tail’
shift: no visible global function definition for ‘head’
splitBy: no visible global function definition for ‘head’
Undefined global functions or variables:
  head install.packages pchisq pnorm tail
Consider adding
  importFrom("stats", "pchisq", "pnorm")
  importFrom("utils", "head", "install.packages", "tail")
to your NAMESPACE file.
RE.ADT: no visible global function definition for ‘sd’
RE.ADT: no visible global function definition for ‘pnorm’
RE.Johnson: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm sd
Consider adding
  importFrom("stats", "pnorm", "sd")
to your NAMESPACE file.
binteg: no visible global function definition for ‘contourLines’
binteg: no visible global function definition for ‘approx’
binteg: no visible global function definition for ‘par’
plot1: no visible global function definition for ‘plot’
plot1: no visible global function definition for ‘par’
plot1: no visible global function definition for ‘rect’
plot1: no visible global function definition for ‘axis’
plot1: no visible global function definition for ‘contour’
plot1: no visible global function definition for ‘contourLines’
plot1: no visible binding for global variable ‘approx’
plot1: no visible global function definition for ‘lines’
plot1: no visible global function definition for ‘text’
plot2: no visible global function definition for ‘plot’
plot2: no visible global function definition for ‘abline’
plot2: no visible global function definition for ‘lines’
plot2: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline approx axis contour contourLines legend lines par plot rect
  text
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "abline", "axis", "contour", "legend", "lines",
             "par", "plot", "rect", "text")
  importFrom("stats", "approx")
to your NAMESPACE file.
Found the following significant warnings:
  jomo1clmmC.c:105:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo1clmmhrC.c:107:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo2clmmC.c:128:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo2clmmhrC.c:132:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomooprobitC.c:84:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/jomo.Rcheck/00install.out’ for details.
Packages in Depends field not imported from:
  ‘Rsolnp’ ‘dglm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
sonarCSV: no visible global function definition for ‘read.csv’
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
File ‘jsonlite/libs/jsonlite.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
qtls: no visible global function definition for ‘quantile’
qtls: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm quantile
Consider adding
  importFrom("stats", "pnorm", "quantile")
to your NAMESPACE file.
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
expression_up : <anonymous>: no visible global function definition for
  ‘quantile’
expression_up : <anonymous>: no visible global function definition for
  ‘IQR’
expression_up : <anonymous>: no visible global function definition for
  ‘median’
expression_up : <anonymous>: no visible global function definition for
  ‘sd’
plot_up: no visible global function definition for ‘plot’
plot_up: no visible global function definition for ‘text’
Undefined global functions or variables:
  IQR median plot quantile sd text
Consider adding
  importFrom("graphics", "plot", "text")
  importFrom("stats", "IQR", "median", "quantile", "sd")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  print.CI3Cats print.CI4Cats print.CI5Cats print.CIBinary
  print.FixedN3Cats print.FixedN4Cats print.FixedN5Cats
  print.FixedNBinary print.Power3Cats print.Power4Cats print.Power5Cats
  print.PowerBinary summary.CI3Cats summary.CI4Cats summary.CI5Cats
  summary.CIBinary summary.FixedN3Cats summary.FixedN4Cats
  summary.FixedN5Cats summary.FixedNBinary summary.Power3Cats
  summary.Power4Cats summary.Power5Cats summary.PowerBinary
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
.hichi: no visible global function definition for ‘pchisq’
.powchi: no visible global function definition for ‘qchisq’
CI3Cats: no visible global function definition for ‘qchisq’
CI4Cats: no visible global function definition for ‘qchisq’
CI5Cats: no visible global function definition for ‘qchisq’
CIBinary: no visible global function definition for ‘qchisq’
FixedN3Cats: no visible global function definition for ‘qchisq’
FixedN4Cats: no visible global function definition for ‘qchisq’
FixedN5Cats: no visible global function definition for ‘qchisq’
FixedNBinary: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  pchisq qchisq
Consider adding
  importFrom("stats", "pchisq", "qchisq")
to your NAMESPACE file.
KappaV: no visible global function definition for ‘over’
KappaV: no visible global function definition for ‘layout’
KappaV: no visible global function definition for ‘terrain.colors’
KappaV: no visible global function definition for ‘as’
Undefined global functions or variables:
  as layout over terrain.colors
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "layout")
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
gimli.17929hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.25269hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.3210hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.12113hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.20276hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.26632hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.30847hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.7633hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.19838hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.30520hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.5051hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
ikcirt.fun.mss.eta: no visible global function definition for ‘var’
ikcirt.fun.mss.eta: no visible global function definition for ‘pnorm’
ikcirt.fun.mss.lambda: no visible global function definition for ‘var’
ikcirt.fun.mss.lambda: no visible global function definition for
  ‘pnorm’
ikcirt.fun.mss.mu: no visible global function definition for ‘pnorm’
kcirt.fitEE: no visible binding for global variable ‘sd’
kcirt.fitEE: no visible global function definition for ‘var’
kcirt.fitEE: no visible global function definition for ‘cor’
kcirt.fitMSS: no visible global function definition for ‘var’
kcirt.fitMSS: no visible global function definition for ‘pnorm’
kcirt.fitMSS: no visible global function definition for ‘sfInit’
kcirt.fitMSS: no visible global function definition for ‘sfExport’
kcirt.fitMSS: no visible global function definition for ‘rnorm’
kcirt.fitMSS: no visible global function definition for
  ‘txtProgressBar’
kcirt.fitMSS: no visible global function definition for ‘sfIsRunning’
kcirt.fitMSS: no visible global function definition for ‘sfStop’
kcirt.fitMSS: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor pnorm rnorm sd sfExport sfInit sfIsRunning sfStop txtProgressBar
  var
Consider adding
  importFrom("stats", "cor", "pnorm", "rnorm", "sd", "var")
  importFrom("utils", "txtProgressBar")
to your NAMESPACE file.
as.matrix.multiPhylo : tip2tip: no visible global function definition
  for ‘cophenetic’
bw.nn : <anonymous>: no visible global function definition for
  ‘quantile’
dist.diss: no visible binding for global variable ‘median’
dist.diss: no visible global function definition for ‘dist’
hist.kdetrees: no visible binding for global variable ‘density’
kdetrees : cutoff: no visible global function definition for ‘quantile’
kdetrees.complete: no visible global function definition for ‘plot’
kdetrees.complete: no visible global function definition for ‘hist’
kdetrees.complete: no visible global function definition for
  ‘write.csv’
plot.kdetrees: no visible binding for global variable ‘density’
Undefined global functions or variables:
  cophenetic density dist hist median plot quantile write.csv
Consider adding
  importFrom("graphics", "hist", "plot")
  importFrom("stats", "cophenetic", "density", "dist", "median",
             "quantile")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
SeasonalMannKendall: no visible global function definition for ‘is.ts’
SeasonalMannKendall: no visible global function definition for
  ‘frequency’
SeasonalMannKendall: no visible global function definition for ‘cycle’
SeasonalMannKendall: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  cycle frequency is.ts pnorm
Consider adding
  importFrom("stats", "cycle", "frequency", "is.ts", "pnorm")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
Checking should be performed on sources prepared by ‘R CMD build’.
Packages in Depends field not imported from:
  ‘chron’ ‘date’ ‘evir’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ALbw: no visible global function definition for ‘sd’
ALbw: no visible global function definition for ‘quantile’
CVbw: no visible global function definition for ‘quantile’
PBbw: no visible global function definition for ‘sd’
PBbw: no visible global function definition for ‘IQR’
kernel_function: no visible global function definition for ‘dnorm’
kernel_function_distribution: no visible global function definition for
  ‘pnorm’
simp_int: no visible global function definition for ‘approx’
Undefined global functions or variables:
  IQR approx dnorm pnorm quantile sd
Consider adding
  importFrom("stats", "IQR", "approx", "dnorm", "pnorm", "quantile",
             "sd")
to your NAMESPACE file.
Found the following significant warnings:
  CV.cpp:67:8: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  CV.cpp:73:8: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  smoother3.cpp:108:4: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  smoother3.cpp:120:4: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/KernSmoothIRT.Rcheck/00install.out’ for details.
kissmigDummyS: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
distrct.analysis : <anonymous> : <anonymous>: no visible global
  function definition for ‘cor’
grand.table: no visible global function definition for ‘write.csv2’
grand.table: no visible global function definition for ‘write.csv’
klausur: no visible global function definition for ‘sd’
klausur: no visible global function definition for ‘na.omit’
klausur.gen.marks : suggestion : <anonymous>: no visible global
  function definition for ‘qnorm’
klausur.mufo: no visible global function definition for ‘sd’
klausur.report: no visible global function definition for ‘dev.off’
klausur.report : tabellenbau: no visible global function definition for
  ‘capture.output’
plot,klausuR-missing: no visible global function definition for
  ‘na.omit’
plot,klausuR-missing: no visible global function definition for ‘sd’
plot,klausuR-missing : <anonymous>: no visible global function
  definition for ‘dnorm’
Undefined global functions or variables:
  capture.output cor dev.off dnorm na.omit qnorm sd write.csv
  write.csv2
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("stats", "cor", "dnorm", "na.omit", "qnorm", "sd")
  importFrom("utils", "capture.output", "write.csv", "write.csv2")
to your NAMESPACE file.
klin.solve : <anonymous>: no visible global function definition for
  ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
comp.npci: no visible global function definition for ‘qnorm’
epband.fun: no visible global function definition for ‘data’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.90’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.95’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.99’
hall.wellner.fun: no visible global function definition for ‘data’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.90’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.95’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.99’
lrt.confints: no visible global function definition for ‘qchisq’
rothman.fun: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  critical.value.hall.90 critical.value.hall.95 critical.value.hall.99
  critical.value.nair.90 critical.value.nair.95 critical.value.nair.99
  data qchisq qnorm
Consider adding
  importFrom("stats", "qchisq", "qnorm")
  importFrom("utils", "data")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘km.ci/R/epband.fun.R’:
  data(critical.value.nair.90, critical.value.nair.95, critical.value.nair.99)
File ‘km.ci/R/hall.wellner.fun.R’:
  data(critical.value.hall.90, critical.value.hall.95, critical.value.hall.99)
See section ‘Good practice’ in ‘?data’.
noe.compute.pv: no visible global function definition for ‘punif’
Undefined global functions or variables:
  punif
Consider adding
  importFrom("stats", "punif")
to your NAMESPACE file.
dscore: no visible global function definition for ‘glm’
dscore: no visible binding for global variable ‘binomial’
dscore: no visible global function definition for ‘pnorm’
pearson.group: no visible global function definition for ‘cor’
spearman.group: no visible global function definition for ‘cor’
sscore: no visible global function definition for ‘glm’
sscore: no visible binding for global variable ‘binomial’
sscore: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  binomial cor glm pnorm
Consider adding
  importFrom("stats", "binomial", "cor", "glm", "pnorm")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from ‘kmlcov’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
C_zero : <anonymous>: no visible global function definition for ‘runif’
get_extra_centroid_index: no visible global function definition for
  ‘head’
get_within_cluster_ss: no visible global function definition for
  ‘aggregate’
kmod: no visible global function definition for ‘head’
kmod: no visible global function definition for ‘tail’
Undefined global functions or variables:
  aggregate head runif tail
Consider adding
  importFrom("stats", "aggregate", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
knncat: no visible global function definition for ‘quantile’
plot.knncat: no visible global function definition for ‘plot’
plot.knncat: no visible global function definition for ‘box’
plot.knncat: no visible global function definition for ‘axis’
plot.knncat: no visible global function definition for ‘text’
Undefined global functions or variables:
  axis box plot quantile text
Consider adding
  importFrom("graphics", "axis", "box", "plot", "text")
  importFrom("stats", "quantile")
to your NAMESPACE file.
Package in Depends field not imported from: ‘cluster’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dataFiller : central.value: no visible global function definition for
  ‘median’
dataFiller: no visible global function definition for ‘daisy’
dataFiller: no visible global function definition for ‘complete.cases’
knnMCN: no visible global function definition for ‘cov’
knnVCN: no visible global function definition for ‘dist’
Undefined global functions or variables:
  complete.cases cov daisy dist median
Consider adding
  importFrom("stats", "complete.cases", "cov", "dist", "median")
to your NAMESPACE file.
Rd file 'knnMCN.Rd':
  \examples lines wider than 100 characters:
                 ") ", "you have selected is bigger than the capacity of one class in your training data set", 
             stop("\nWarnings:\nsample variance-covariance matrix is singular,\nand larger class sample capacity is required ,\nor you can t ... [TRUNCATED]
                     stop("\nWarnings:\nsample variance-covariance matrix is singular,\nand larger class sample capacity is required ,\nor y ... [TRUNCATED]

Rd file 'knnVCN.Rd':
  \examples lines wider than 100 characters:
                 ") ", "you have selected is bigger than the capacity of one class in your training data set", 

These lines will be truncated in the PDF manual.
benchmark.patchwork.copula : <anonymous> : <anonymous>: no visible
  global function definition for ‘rbeta’
benchmark.patchwork.copula : <anonymous> : <anonymous>: no visible
  global function definition for ‘runif’
calculate.power : <anonymous>: no visible binding for global variable
  ‘quantile’
generate.benchmark.data: no visible global function definition for
  ‘runif’
generate.benchmark.data: no visible global function definition for
  ‘rnorm’
generate.benchmark.data: no visible global function definition for
  ‘rbinom’
generate.patchwork.copula: no visible global function definition for
  ‘rbeta’
generate.patchwork.copula: no visible global function definition for
  ‘runif’
novelTest.chisq: no visible global function definition for ‘pchisq’
novelTest.chisq4nn: no visible global function definition for ‘pchisq’
optimise.copula.mi : <anonymous>: no visible global function definition
  for ‘optimize’
power.plot: no visible global function definition for ‘plot’
power.plot: no visible global function definition for ‘axis’
power.plot : <anonymous>: no visible global function definition for
  ‘points’
power.plot: no visible global function definition for ‘legend’
roc.plot: no visible global function definition for ‘colorRampPalette’
roc.plot : <anonymous>: no visible global function definition for
  ‘plot’
roc.plot : <anonymous> : <anonymous>: no visible global function
  definition for ‘points’
run.tests : <anonymous> : <anonymous>: no visible global function
  definition for ‘runif’
Undefined global functions or variables:
  axis colorRampPalette legend optimize pchisq plot points quantile
  rbeta rbinom rnorm runif
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "legend", "plot", "points")
  importFrom("stats", "optimize", "pchisq", "quantile", "rbeta",
             "rbinom", "rnorm", "runif")
to your NAMESPACE file.
assign_clustpp: no visible global function definition for ‘kmeans’
kpod: no visible global function definition for ‘kmeans’
makeData: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  kmeans rnorm
Consider adding
  importFrom("stats", "kmeans", "rnorm")
to your NAMESPACE file.
image.kriging: no visible global function definition for ‘heat.colors’
image.kriging: no visible global function definition for ‘image’
kriging: no visible global function definition for ‘lm’
plot.kriging: no visible global function definition for ‘plot’
plot.kriging: no visible global function definition for ‘curve’
Undefined global functions or variables:
  curve heat.colors image lm plot
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "curve", "image", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
kselection: no visible global function definition for ‘txtProgressBar’
kselection: no visible global function definition for
  ‘setTxtProgressBar’
plot.Kselection: no visible global function definition for ‘plot’
plot.Kselection: no visible global function definition for ‘lines’
plot.Kselection: no visible global function definition for ‘legend’
Undefined global functions or variables:
  legend lines plot setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘BB’ ‘nleqslv’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
ktsolve: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following hidden files and directories:
  .Rbuildindex.10034
  .Rbuildindex.31551
  .Rbuildindex.31678
  .Rbuildindex.9995
  inst/doc/.fr-hy2VZf
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Package in Depends field not imported from: ‘Biobase’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'ROC.graphic.ktsp.Rd':
  \usage lines wider than 90 characters:
     ROC.graphic.ktsp(roc, m = 1, boxplot = TRUE, AUC = TRUE, auc.x = 0.55, auc.y = 0.25, box.col = "yellow", line.col = "red", multiple.col ... [TRUNCATED]

Rd file 'ROC.offset.Rd':
  \usage lines wider than 90 characters:
     ROC.offset(dat, grp, n = 200, healthy = NULL, seed = NULL, para1 = 200, para2 = 1, mult.cutoff = FALSE, length = 40, display = FALSE, m ... [TRUNCATED]

Rd file 'ROC.voting.Rd':
  \usage lines wider than 90 characters:
     ROC.voting(dat, grp, n = 200, healthy = NULL, seed = NULL, para1 = 200, para2 = 1, length = 40, display = FALSE, med = FALSE)

Rd file 'bootstrap.ktsp.Rd':
  \usage lines wider than 90 characters:
     bootstrap.ktsp(dat, grp, k = NULL, seed = NULL, n = 500, length = 40, display = FALSE, med = FALSE)

Rd file 'cv.Rd':
  \usage lines wider than 90 characters:
     cv(dat, grp, cross = 5, display = FALSE, length = 40, seed = NULL, med = FALSE, healthy = NULL)

Rd file 'cv2.Rd':
  \usage lines wider than 90 characters:
     cv2(indice, dat, grp, cross = 5, display = FALSE, length = 40, seed = NULL, med = FALSE, healthy = NULL)

Rd file 'ktspcalc.Rd':
  \usage lines wider than 90 characters:
     ktspcalc(dat, grp, k = NULL, cross = 5, performance = FALSE, healthy = NULL, seed = NULL, display = TRUE, length = 40, med = FALSE)

Rd file 'ktspcalc2.Rd':
  \usage lines wider than 90 characters:
     ktspcalc2(indice, dat, grp, length = 40, cross =5, display = display, med = FALSE, performance = FALSE, seed = NULL, healthy = NULL)

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

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

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
'library' or 'require' call to ‘XML’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
auc: no visible global function definition for ‘approx’
kulife.colors: no visible global function definition for ‘palette’
rootonorm: no visible global function definition for ‘sd’
rootonorm: no visible global function definition for ‘hist’
rootonorm: no visible global function definition for ‘pnorm’
rootonorm: no visible global function definition for ‘dnorm’
rootonorm: no visible global function definition for ‘plot’
rootonorm: no visible global function definition for ‘rect’
rootonorm: no visible global function definition for ‘lines’
rootonorm: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline approx dnorm hist lines palette plot pnorm rect sd
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "abline", "hist", "lines", "plot", "rect")
  importFrom("stats", "approx", "dnorm", "pnorm", "sd")
to your NAMESPACE file.
compareModelResults: no visible global function definition for
  ‘reshape’
erf: no visible global function definition for ‘pnorm’
getModelComparisonTable: no visible global function definition for
  ‘read.csv’
hantushSstar: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate pnorm read.csv reshape
Consider adding
  importFrom("stats", "integrate", "pnorm", "reshape")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘readme.txt’
kztp: warning in rowMeans(kztp, dim = 2): partial argument match of
  ‘dim’ to ‘dims’
Found the following hidden files and directories:
  .Rapp.history
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
extended.figures: no visible global function definition for ‘par’
extended.figures: no visible global function definition for ‘runif’
extended.figures : figure2: no visible global function definition for
  ‘hist’
extended.figures : figure2: no visible global function definition for
  ‘axis’
extended.figures : figure3 : <anonymous>: no visible global function
  definition for ‘median’
extended.figures : figure3: no visible global function definition for
  ‘barplot’
Undefined global functions or variables:
  axis barplot hist median par runif
Consider adding
  importFrom("graphics", "axis", "barplot", "hist", "par")
  importFrom("stats", "median", "runif")
to your NAMESPACE file.
LDuncan.aov : prob: no visible global function definition for ‘qtukey’
LDuncan.aov: no visible global function definition for ‘qtukey’
LScottKnott.aov : sk: no visible global function definition for
  ‘pchisq’
LScottKnott.aov: no visible global function definition for ‘read.table’
LTukey.aov: no visible global function definition for ‘qtukey’
Undefined global functions or variables:
  pchisq qtukey read.table
Consider adding
  importFrom("stats", "pchisq", "qtukey")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘GPArotation’ ‘mice’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
angoff: no visible global function definition for ‘cov2cor’
angoff: no visible global function definition for ‘runif’
cov.lambda4: no visible global function definition for ‘cov2cor’
cov.lambda4: no visible global function definition for ‘median’
guttman: no visible global function definition for ‘cov2cor’
impute.cov: no visible global function definition for ‘cov’
impute.cov: no visible global function definition for ‘complete’
impute.cov: no visible global function definition for ‘mice’
kristof: no visible global function definition for ‘cov2cor’
kristof: no visible global function definition for ‘runif’
lambda1: no visible global function definition for ‘cov2cor’
lambda2: no visible global function definition for ‘cov2cor’
lambda3: no visible global function definition for ‘cov2cor’
lambda3: no visible binding for global variable ‘sd’
lambda5: no visible global function definition for ‘cov2cor’
lambda6: no visible global function definition for ‘cov2cor’
omega.tot: no visible global function definition for ‘cov2cor’
omega.tot: no visible global function definition for ‘factanal’
quant.lambda4: no visible global function definition for ‘cov2cor’
quant.lambda4: no visible global function definition for ‘runif’
quant.lambda4: no visible global function definition for ‘quantile’
raju: no visible global function definition for ‘cov2cor’
raju: no visible global function definition for ‘runif’
user.lambda4: no visible global function definition for ‘runif’
user.lambda4: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  complete cov cov2cor factanal median mice quantile runif sd
Consider adding
  importFrom("stats", "cov", "cov2cor", "factanal", "median", "quantile",
             "runif", "sd")
to your NAMESPACE file.
Found the following significant warnings:
  W_gamma_Cpp.cpp:14:39: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/LambertW.Rcheck/00install.out’ for details.
getGO: no visible global function definition for ‘new’
getGO: no visible global function definition for ‘getGeneric’
graph.kd: no visible global function definition for ‘as’
Undefined global functions or variables:
  as getGeneric new
Consider adding
  importFrom("methods", "as", "getGeneric", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Kern.FUN: no visible global function definition for ‘dnorm’
Prob.Covariate.ShortEvent: no visible global function definition for
  ‘bw.nrd’
optimize.mse.BW: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  bw.nrd dnorm optimize
Consider adding
  importFrom("stats", "bw.nrd", "dnorm", "optimize")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘rgdal’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
BSL: no visible global function definition for ‘read.asciigrid’
BSL: no visible global function definition for ‘quantile’
PIF: no visible global function definition for ‘read.asciigrid’
PIF: no visible global function definition for ‘quantile’
RCS: no visible global function definition for ‘quantile’
clouds: no visible global function definition for ‘read.asciigrid’
geoshift: no visible global function definition for ‘bbox’
histmatch: no visible global function definition for ‘hist’
minnaert: no visible global function definition for ‘coefficients’
minnaert: no visible global function definition for ‘lm’
minnaert: no visible global function definition for ‘predict’
topocorr: no visible global function definition for ‘lm’
topocorr: no visible global function definition for ‘coefficients’
Undefined global functions or variables:
  bbox coefficients hist lm predict quantile read.asciigrid
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "coefficients", "lm", "predict", "quantile")
to your NAMESPACE file.
'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.
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.
betabreaker: no visible global function definition for ‘predict’
coef.lars: no visible global function definition for ‘predict’
cv.lars: no visible global function definition for ‘predict’
cv.lars: no visible binding for global variable ‘var’
error.bars: no visible global function definition for ‘segments’
plot.lars: no visible global function definition for ‘plot’
plot.lars: no visible global function definition for ‘matplot’
plot.lars: no visible global function definition for ‘title’
plot.lars: no visible global function definition for ‘abline’
plot.lars: no visible global function definition for ‘axis’
plotCVLars: no visible global function definition for ‘plot’
predict.lars: no visible global function definition for ‘approx’
Undefined global functions or variables:
  abline approx axis matplot plot predict segments title var
Consider adding
  importFrom("graphics", "abline", "axis", "matplot", "plot", "segments",
             "title")
  importFrom("stats", "approx", "predict", "var")
to your NAMESPACE file.
Rd file 'cv.lars.Rd':
  \usage lines wider than 90 characters:
         trace = FALSE, plot.it = TRUE, se = TRUE,type = c("lasso", "lar", "forward.stagewise", "stepwise"),

Rd file 'lars.Rd':
  \usage lines wider than 90 characters:
         trace = FALSE, normalize = TRUE, intercept = TRUE, Gram, eps = .Machine$double.eps, max.steps, use.Gram = TRUE)

Rd file 'plot.lars.Rd':
  \usage lines wider than 90 characters:
     plot(x, xvar= c("norm", "df", "arc.length", "step"), breaks = TRUE, plottype = c("coefficients", 

These lines will be truncated in the PDF manual.
Found the following apparent S3 methods exported but not registered:
  merge.formula
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
gl1ce: no visible binding for global variable ‘gaussian’
gl1ce: no visible global function definition for ‘glm.control’
gl1ce: no visible global function definition for ‘model.extract’
gl1ce: no visible global function definition for ‘terms’
gl1ce: no visible global function definition for ‘model.matrix’
gl1ce: no visible binding for global variable ‘sd’
l1ce: no visible global function definition for ‘model.extract’
l1ce: no visible global function definition for ‘terms’
l1ce: no visible global function definition for ‘model.matrix’
l1ce: no visible binding for global variable ‘sd’
merge.formula: no visible global function definition for ‘as.formula’
plot.l1celist: no visible global function definition for ‘matplot’
plot.l1celist: no visible global function definition for ‘rug’
predict.l1ce: no visible global function definition for ‘model.matrix’
print.summary.gl1ce: no visible binding for global variable ‘quantile’
print.summary.gl1ce: no visible global function definition for
  ‘quantile’
print.summary.l1ce: no visible binding for global variable ‘quantile’
print.summary.l1ce: no visible global function definition for
  ‘quantile’
residuals.l1ce: no visible global function definition for
  ‘residuals.glm’
summary.l1ce: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as.formula gaussian glm.control matplot model.extract model.matrix
  pnorm quantile residuals.glm rug sd terms
Consider adding
  importFrom("graphics", "matplot", "rug")
  importFrom("stats", "as.formula", "gaussian", "glm.control",
             "model.extract", "model.matrix", "pnorm", "quantile",
             "residuals.glm", "sd", "terms")
to your NAMESPACE file.
glassoscore: no visible global function definition for ‘var’
glassoscore: no visible global function definition for ‘pchisq’
lassoscore: no visible global function definition for ‘txtProgressBar’
lassoscore: no visible global function definition for
  ‘setTxtProgressBar’
lassoscore: no visible global function definition for ‘pchisq’
plot.glassoscore: no visible global function definition for ‘legend’
plot.lassoscore: no visible global function definition for ‘legend’
plot.mbscore: no visible global function definition for ‘legend’
qqpval: no visible global function definition for ‘ppoints’
qqpval: no visible global function definition for ‘qbeta’
qqpval: no visible global function definition for ‘points’
qqpval: no visible global function definition for ‘plot’
qqpval: no visible global function definition for ‘abline’
qqpval: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  abline legend pchisq plot points polygon ppoints qbeta
  setTxtProgressBar txtProgressBar var
Consider adding
  importFrom("graphics", "abline", "legend", "plot", "points", "polygon")
  importFrom("stats", "pchisq", "ppoints", "qbeta", "var")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Rd file 'lassoshooting.Rd':
  \usage lines wider than 90 characters:
     lassoshooting(X=NULL, y=NULL, lambda, XtX=NULL, Xty=NULL, thr=1.0e-6, maxit=1e4, nopenalize=NULL, penaltyweight=NULL, trace=0, ...)

These lines will be truncated in the PDF manual.
Found the following calls to attach():
File ‘lazyData/R/requireData.R’:
  attach(NULL, pos = pos, name = searchDataName)
See section ‘Good practice’ in ‘?attach’.
lbfgs: no visible global function definition for ‘hasArg’
Undefined global functions or variables:
  hasArg
Consider adding
  importFrom("methods", "hasArg")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  NLLabsel.cpp:69:11: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/LBSPR.Rcheck/00install.out’ for details.
LCA: no visible global function definition for ‘dist’
LCA: no visible global function definition for ‘combn’
LCA: no visible global function definition for ‘p.adjust’
LCA: no visible global function definition for ‘pchisq’
LCA : <anonymous>: no visible global function definition for ‘pchisq’
LCD: no visible global function definition for ‘ecdf’
estimateB: no visible global function definition for ‘median’
evaluateDiffSignificance: no visible global function definition for
  ‘ecdf’
fitPTLmodel: no visible global function definition for ‘lm’
getPTLparams: no visible global function definition for ‘nls’
getPTLparams: no visible global function definition for ‘coef’
predictPTLparams: no visible global function definition for
  ‘predict.lm’
Undefined global functions or variables:
  coef combn dist ecdf lm median nls p.adjust pchisq predict.lm
Consider adding
  importFrom("stats", "coef", "dist", "ecdf", "lm", "median", "nls",
             "p.adjust", "pchisq", "predict.lm")
  importFrom("utils", "combn")
to your NAMESPACE file.
cclcda.default: no visible global function definition for ‘as.formula’
cclcda.default: no visible global function definition for ‘chisq.test’
cclcda.formula: no visible global function definition for ‘model.frame’
cclcda2.default: no visible global function definition for ‘runif’
cclcda2.default: no visible global function definition for ‘chisq.test’
cclcda2.formula: no visible global function definition for
  ‘model.frame’
lcda.default: no visible global function definition for ‘as.formula’
lcda.formula: no visible global function definition for ‘model.frame’
Undefined global functions or variables:
  as.formula chisq.test model.frame runif
Consider adding
  importFrom("stats", "as.formula", "chisq.test", "model.frame", "runif")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘LDOD.Rproj’
multistart : <anonymous>: no visible global function definition for
  ‘runif’
plot.FreD.x: no visible global function definition for ‘modifyList’
plot.FreD.x: no visible global function definition for ‘abline’
plot.FreD.x: no visible global function definition for ‘points’
Undefined global functions or variables:
  abline modifyList points runif
Consider adding
  importFrom("graphics", "abline", "points")
  importFrom("stats", "runif")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
ARConfIntEst: no visible global function definition for ‘sd’
PTLinkFunc: no visible global function definition for ‘pnorm’
PTLinkFunc: no visible global function definition for ‘qnorm’
PTMultiPeriodPD: no visible global function definition for ‘uniroot’
PTOnePeriodPD : f: no visible global function definition for ‘pbinom’
PTOnePeriodPD: no visible global function definition for ‘uniroot’
QMMGetRLogitPD: no visible global function definition for ‘ecdf’
QMMPDlinkFunc: no visible global function definition for ‘qnorm’
QMMPlot: no visible global function definition for ‘plot’
QMMPlot: no visible global function definition for ‘lines’
QMMPlot: no visible global function definition for ‘legend’
VDBCalibratePD: no visible global function definition for ‘ecdf’
VDBGetK: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  ecdf legend lines pbinom plot pnorm qnorm sd uniroot
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "ecdf", "pbinom", "pnorm", "qnorm", "sd",
             "uniroot")
to your NAMESPACE file.
prepare_Rd: HWE2sided.Rd:15-16: Dropping empty section \details
prepare_Rd: HWE2sided.table.Rd:17-18: Dropping empty section \details
prepare_Rd: LD2sided.pvals.Rd:13-14: Dropping empty section \details
BEAPFrOG: no visible global function definition for ‘jags.model’
BEAPFrOG: no visible global function definition for ‘coda.samples’
LEAPFrOG_EM: no visible global function definition for ‘write.table’
LEAPFrOG_EM: no visible global function definition for ‘constrOptim’
LEAPFrOG_plot: no visible global function definition for ‘par’
LEAPFrOG_plot: no visible global function definition for ‘barplot’
LEAPFrOG_plot: no visible global function definition for ‘legend’
constrOptim2: no visible global function definition for ‘optim’
Undefined global functions or variables:
  barplot coda.samples constrOptim jags.model legend optim par
  write.table
Consider adding
  importFrom("graphics", "barplot", "legend", "par")
  importFrom("stats", "constrOptim", "optim")
  importFrom("utils", "write.table")
to your NAMESPACE file.
AlternateSVD: no visible binding for global variable ‘sd’
IPOD: no visible global function definition for ‘mad’
IPOD: no visible global function definition for ‘pnorm’
Pvalue: no visible global function definition for ‘pf’
ROCplot: no visible global function definition for ‘png’
ROCplot: no visible global function definition for ‘matplot’
ROCplot: no visible global function definition for ‘legend’
ROCplot: no visible global function definition for ‘dev.off’
leapp: no visible global function definition for ‘png’
leapp: no visible global function definition for ‘plot’
leapp: no visible global function definition for ‘dev.off’
ridge: no visible global function definition for ‘sd’
ridge: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dev.off legend mad matplot pf plot png pnorm sd
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "matplot", "plot")
  importFrom("stats", "mad", "pf", "pnorm", "sd")
to your NAMESPACE file.
File ‘leaps/libs/leaps.so’:
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Object: ‘leaps.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Fmntd.a : Fmntd.a.sub: no visible global function definition for
  ‘weighted.mean’
Fmpd : Fmpd.sub: no visible global function definition for ‘as.dist’
Fmpd.a : Fmpd.a.sub: no visible global function definition for
  ‘weighted.mean’
Fsntd : Fsntd.sub: no visible global function definition for ‘sd’
com.trait.moments : skewness: no visible global function definition for
  ‘var’
com.trait.moments : kurtosis: no visible global function definition for
  ‘var’
com.trait.moments : sd.funk: no visible global function definition for
  ‘sd’
com.trait.weighted : weight.mean.funk: no visible global function
  definition for ‘weighted.mean’
Undefined global functions or variables:
  as.dist sd var weighted.mean
Consider adding
  importFrom("stats", "as.dist", "sd", "var", "weighted.mean")
to your NAMESPACE file.
'library' or 'require' call to ‘snow’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Depends: includes the non-default packages:
  'sn', 'moments', 'BB', 'Bolstad2', 'optimx', 'Rmpfr'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Non-standard files/directories found at top level:
  ‘LIHNPSD-manual.pdf’ ‘PSD-Paper.pdf’ ‘Rplots.pdf’
Packages in Depends field not imported from:
  ‘BB’ ‘Bolstad2’ ‘Rmpfr’ ‘moments’ ‘optimx’ ‘sn’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'LIHNPSD-package.Rd':
  \examples lines wider than 100 characters:
       dist <- list( sigma= 0.004625, alpha= 0.292645, gamma= 0.482744, beta= -0.154049, location= 0.002968 )

Rd file 'LIHNPSD_standardfit_fn.Rd':
  \usage lines wider than 90 characters:
     LIHNPSD_standardfit_fn(psd, data_stats, hist, plotqq = 1, weights = list(), merge_tails = c(0, 0), debug = 0)

Rd file 'prepare.Rd':
  \examples lines wider than 100 characters:
       dist <- list( sigma= 0.004625, alpha= 0.292645, gamma= 0.482744, beta= -0.154049, location= 0.002968 )

Rd file 'rawmean.Rd':
  \examples lines wider than 100 characters:
       dist <- list( sigma= 0.004625, alpha= 0.292645, gamma= 0.482744, beta= -0.154049, location= 0.002968 )

These lines will be truncated in the PDF manual.
plotBox: no visible global function definition for ‘sd’
plotBox: no visible global function definition for ‘rect’
plotBox: no visible global function definition for ‘qnorm’
plotBox: no visible global function definition for ‘segments’
plotInit: no visible global function definition for ‘plot’
plotInit: no visible global function definition for ‘runif’
plotInit: no visible global function definition for ‘mtext’
plotInit: no visible global function definition for ‘segments’
plotStack: no visible global function definition for ‘points’
Undefined global functions or variables:
  mtext plot points qnorm rect runif sd segments
Consider adding
  importFrom("graphics", "mtext", "plot", "points", "rect", "segments")
  importFrom("stats", "qnorm", "runif", "sd")
to your NAMESPACE file.
Plotranges.double: no visible global function definition for ‘strwidth’
Plotranges.double: no visible global function definition for
  ‘strheight’
Plotranges.double: no visible global function definition for ‘plot.new’
Plotranges.double: no visible global function definition for ‘par’
Plotranges.double: no visible global function definition for
  ‘plot.window’
Plotranges.double: no visible global function definition for ‘mtext’
Plotranges.double: no visible global function definition for ‘abline’
Plotranges.double: no visible global function definition for ‘points’
Plotranges.double: no visible global function definition for ‘segments’
Plotranges.double: no visible global function definition for ‘text’
Plotranges.double: no visible global function definition for ‘axis’
Plotranges.double: no visible global function definition for ‘box’
Plotranges.double: no visible global function definition for ‘title’
Undefined global functions or variables:
  abline axis box mtext par plot.new plot.window points segments
  strheight strwidth text title
Consider adding
  importFrom("graphics", "abline", "axis", "box", "mtext", "par",
             "plot.new", "plot.window", "points", "segments",
             "strheight", "strwidth", "text", "title")
to your NAMESPACE file.
class.calib: no visible global function definition for ‘lm’
class.calib: no visible global function definition for ‘coef’
class.calib: no visible global function definition for ‘qt’
hoad.calib: no visible global function definition for ‘lm’
hoad.calib: no visible global function definition for ‘anova’
hoad.calib: no visible global function definition for ‘qt’
hoad.calib: no visible global function definition for ‘rnorm’
huntlam.calib: no visible global function definition for ‘lm’
huntlam.calib: no visible global function definition for ‘anova’
huntlam.calib: no visible global function definition for ‘rnorm’
huntlam.calib: no visible global function definition for ‘qnorm’
inver.calib: no visible global function definition for ‘lm’
inver.calib: no visible global function definition for ‘coef’
inver.calib: no visible global function definition for ‘anova’
inver.calib: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  anova coef lm qnorm qt rnorm
Consider adding
  importFrom("stats", "anova", "coef", "lm", "qnorm", "qt", "rnorm")
to your NAMESPACE file.
Found the following significant warnings:
  auxFun.cpp:16:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/linearQ.Rcheck/00install.out’ for details.
gcomb: no visible global function definition for ‘complete.cases’
linkim: no visible global function definition for ‘runif’
missing.dist: no visible global function definition for
  ‘complete.cases’
pgdata1: no visible global function definition for ‘barplot’
pgdata1: no visible global function definition for ‘layout’
pgdata1: no visible global function definition for ‘par’
pgdata1: no visible global function definition for ‘rainbow’
singim: no visible global function definition for ‘complete.cases’
singim: no visible global function definition for ‘runif’
Undefined global functions or variables:
  barplot complete.cases layout par rainbow runif
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "barplot", "layout", "par")
  importFrom("stats", "complete.cases", "runif")
to your NAMESPACE file.
gen.lms: no visible global function definition for ‘na.omit’
plot.idf: no visible global function definition for ‘plot’
plot.idf: no visible global function definition for ‘mtext’
plot.idf: no visible global function definition for ‘points’
plot.idf: no visible global function definition for ‘segments’
plot.idf: no visible global function definition for ‘ftable’
plot.idf: no visible global function definition for ‘image’
plot.idf: no visible global function definition for ‘gray’
plot.idf: no visible global function definition for ‘abline’
plot.s.linlir: no visible global function definition for ‘plot’
plot.s.linlir: no visible global function definition for ‘mtext’
plot.s.linlir: no visible global function definition for ‘polygon’
plot.s.linlir: no visible global function definition for ‘points’
plot.s.linlir: no visible global function definition for ‘curve’
s.linlir: no visible global function definition for ‘na.omit’
s.linlir: no visible global function definition for ‘dbinom’
s.linlir: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  abline curve dbinom ftable gray image mtext na.omit pchisq plot
  points polygon segments
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "curve", "image", "mtext", "plot",
             "points", "polygon", "segments")
  importFrom("stats", "dbinom", "ftable", "na.omit", "pchisq")
to your NAMESPACE file.
Rd file 'idf.Rd':
  \usage lines wider than 90 characters:
     plot(x, y=NULL, ..., var = NULL, typ="hist", k.x = 1, k.y = 1, inf.margin=10, p.cex=1, col.lev=15, plot.grid=FALSE, x.adj = 0.5, x.padj ... [TRUNCATED]
  \examples lines wider than 100 characters:
     plot(pm.idf, typ="draft", k.x=10, k.y=20, p.cex=0.35, x.adj=0.5, x.padj=4, y.las=0, y.adj=0.5, y.padj=-4, x.lab="temperature", y.lab="p ... [TRUNCATED]

Rd file 's.linlir.Rd':
  \usage lines wider than 90 characters:
     plot(x, y=NULL, ..., typ, para.typ="polygon", b.grid=500, nb.func=1000, seed.func=NULL, pl.lrm=TRUE, pl.band=FALSE, lrm.col="blue", pl. ... [TRUNCATED]
  \examples lines wider than 100 characters:
     plot(test, typ="lrm", lrm.col="red", pl.band=TRUE, pl.dat=TRUE, pl.dat.typ="draft",k.x=10, k.y=10, y.las=1, y.adj=6)

These lines will be truncated in the PDF manual.
Non-standard file/directory found at top level:
  ‘pkg.Rproj’
'library' or 'require' call to ‘lpSolve’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘lpSolve’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
solveLP: no visible global function definition for ‘lp’
Undefined global functions or variables:
  lp
Non-standard file/directory found at top level:
  ‘package.R’
last: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
getMatrix : <anonymous>: no visible global function definition for
  ‘read.table’
Undefined global functions or variables:
  read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
'library' or 'require' call to ‘scatterplot3d’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘rgl’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Rd file 'lle.Rd':
  \examples lines wider than 100 characters:
             plot( results$id, main="intrinsic dimension", type="l", xlab=expression(x[i]), ylab="id", lwd=2 )

These lines will be truncated in the PDF manual.
lm.beta: no visible global function definition for ‘coef’
lm.beta: no visible global function definition for ‘model.matrix’
lm.beta: no visible global function definition for ‘model.frame’
Undefined global functions or variables:
  coef model.frame model.matrix
Consider adding
  importFrom("stats", "coef", "model.frame", "model.matrix")
to your NAMESPACE file.
lmec: warning in qr.Q(qrZ, compl = TRUE): partial argument match of
  ‘compl’ to ‘complete’
lmec: warning in qr.Q(qra, compl = TRUE): partial argument match of
  ‘compl’ to ‘complete’
lmec: no visible global function definition for ‘lm’
lmec: no visible global function definition for ‘pnorm’
lmec: no visible global function definition for ‘dnorm’
lmec : vtrnorm2: no visible global function definition for ‘runif’
lmec : vtrnorm2: no visible global function definition for ‘qnorm’
lmec : vtrnorm2: no visible global function definition for ‘pnorm’
lmec: no visible global function definition for ‘rnorm’
lmec: no visible global function definition for ‘ar’
Undefined global functions or variables:
  ar dnorm lm pnorm qnorm rnorm runif
Consider adding
  importFrom("stats", "ar", "dnorm", "lm", "pnorm", "qnorm", "rnorm",
             "runif")
to your NAMESPACE file.
Rd file 'lmec-package.Rd':
  \examples lines wider than 100 characters:
     X<- cbind((UTIdata$Fup==0)+0, (UTIdata$Fup==1)+0, (UTIdata$Fup==3)+0, (UTIdata$Fup==6)+0, (UTIdata$Fup==9)+0, (UTIdata$Fup==12)+0, (UTI ... [TRUNCATED]

Rd file 'lmec.Rd':
  \usage lines wider than 90 characters:
     lmec(yL, cens, X, Z, cluster, maxstep = 200, varstruct = "unstructured", init, method = "ML", epsstop = 0.001, abspmv = 0.001, mcmc0 =  ... [TRUNCATED]
  \examples lines wider than 100 characters:
     X = cbind((UTIdata$Fup==0)+0, (UTIdata$Fup==1)+0, (UTIdata$Fup==3)+0, (UTIdata$Fup==6)+0, (UTIdata$Fup==9)+0, (UTIdata$Fup==12)+0, (UTI ... [TRUNCATED]

These lines will be truncated in the PDF manual.
mq.diagnostics : mq_missinggenotype_plot: no visible global function
  definition for ‘plot.missing’
Undefined global functions or variables:
  plot.missing
Package in Depends field not imported from: ‘nlme’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
approx.Z : <anonymous>: no visible global function definition for
  ‘approx’
smspline: no visible global function definition for ‘model.frame’
Undefined global functions or variables:
  approx model.frame
Consider adding
  importFrom("stats", "approx", "model.frame")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘emulator’ ‘methods’ ‘miscTools’ ‘penalized’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'plot.lmmlasso.Rd':
  \examples lines wider than 100 characters:
     fit <- lmmlasso(x=classroomStudy$X,y=classroomStudy$y,z=classroomStudy$Z,grp=classroomStudy$grp,lambda=15,pdMat="pdIdent")

These lines will be truncated in the PDF manual.
AnalyticalOptim: no visible global function definition for ‘optim’
LLConstructor : LL: no visible global function definition for ‘dpois’
MixtureDensity: no visible global function definition for ‘glm’
MixtureDensity : f_hat: no visible global function definition for
  ‘predict’
NullDensity : f0: no visible global function definition for ‘dpois’
Undefined global functions or variables:
  dpois glm optim predict
Consider adding
  importFrom("stats", "dpois", "glm", "optim", "predict")
to your NAMESPACE file.
'library' or 'require' call to ‘akima’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Missing or unexported objects:
  ‘lattice::render.3d.trellis’ ‘lattice::render.contour.trellis’
available.loglevels: no visible global function definition for
  ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
Package in Depends field not imported from: ‘logcondens’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  updateOptions.environment
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Logger: no visible global function definition for ‘new’
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
EstimateProbability: no visible global function definition for
  ‘predict’
LOGICOIL: no visible binding for global variable ‘pssm’
LOGICOIL: no visible binding for global variable ‘LOGICOILfit’
LOGICOIL: no visible binding for global variable ‘Model_Parameters’
plot_LOGICOIL: no visible global function definition for ‘png’
plot_LOGICOIL: no visible global function definition for ‘par’
plot_LOGICOIL: no visible global function definition for ‘plot’
plot_LOGICOIL: no visible global function definition for ‘lines’
plot_LOGICOIL: no visible global function definition for ‘axis’
plot_LOGICOIL: no visible global function definition for ‘mtext’
plot_LOGICOIL: no visible global function definition for ‘legend’
plot_LOGICOIL: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  LOGICOILfit Model_Parameters axis dev.off legend lines mtext par plot
  png predict pssm
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "axis", "legend", "lines", "mtext", "par",
             "plot")
  importFrom("stats", "predict")
to your NAMESPACE file.
test_compute_gradient: no visible global function definition for
  ‘rnorm’
test_compute_probabilities: no visible global function definition for
  ‘rnorm’
test_logitchoice: no visible global function definition for ‘rnorm’
test_solver: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
LogitNet.weight: no visible global function definition for ‘lowess’
LogitNet.weight: no visible global function definition for ‘median’
Undefined global functions or variables:
  lowess median
Consider adding
  importFrom("stats", "lowess", "median")
to your NAMESPACE file.
rloglognorm: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
LogrankA: no visible global function definition for ‘is.Surv’
LogrankA: no visible global function definition for ‘na.omit’
LogrankA: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  is.Surv na.omit pchisq
Consider adding
  importFrom("stats", "na.omit", "pchisq")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  plot.lsp summary.lsp summary.randlsp
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
lsp: no visible global function definition for ‘var’
plot.lsp: no visible global function definition for ‘plot’
plot.lsp: no visible global function definition for ‘lines’
plot.lsp: no visible global function definition for ‘abline’
randlsp: no visible global function definition for ‘is.ts’
randlsp: no visible global function definition for ‘par’
randlsp: no visible global function definition for ‘hist’
randlsp: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline hist is.ts lines par plot var
Consider adding
  importFrom("graphics", "abline", "hist", "lines", "par", "plot")
  importFrom("stats", "is.ts", "var")
to your NAMESPACE file.
fplot: no visible global function definition for ‘rnorm’
fplot: no visible global function definition for ‘plot’
fplot: no visible global function definition for ‘segments’
fplot: no visible global function definition for ‘points’
fplot: no visible global function definition for ‘text’
fplot.foodweb: no visible global function definition for ‘plot’
fplot.foodweb: no visible global function definition for ‘segments’
fplot.foodweb: no visible global function definition for ‘points’
fplot.foodweb: no visible global function definition for ‘text’
gplot: no visible global function definition for ‘runif’
groupplot: no visible global function definition for ‘rnorm’
groupplot: no visible global function definition for ‘plot’
groupplot: no visible global function definition for ‘segments’
groupplot: no visible global function definition for ‘points’
groupplot: no visible global function definition for ‘text’
groupplot.foodweb: no visible global function definition for ‘rnorm’
groupplot.foodweb: no visible global function definition for ‘plot’
groupplot.foodweb: no visible global function definition for ‘segments’
groupplot.foodweb: no visible global function definition for ‘points’
groupplot.foodweb: no visible global function definition for ‘text’
Undefined global functions or variables:
  plot points rnorm runif segments text
Consider adding
  importFrom("graphics", "plot", "points", "segments", "text")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Rd file 'fplot.Rd':
  \usage lines wider than 90 characters:
     fplot(gemat,type="both",metric="jaccard",addlabels=FALSE,scaled=TRUE,weighted=TRUE,pch=20,bg=1,pcex=3,pcol=4,lty=1,lcol=8,tfont=12,tcol ... [TRUNCATED]

Rd file 'fplot.foodweb.Rd':
  \usage lines wider than 90 characters:
     fplot.foodweb(gemat,ranks,addlabels=FALSE,scaled=TRUE,weighted=TRUE,pch=20,bg=1,pcex=3,pcol=4,lty=1,lcol=8,tfont=12,tcol=1)

Rd file 'groupplot.Rd':
  \usage lines wider than 90 characters:
     groupplot(gemat, groups, type = "both", metric = "jaccard", addlabels = FALSE, scaled = TRUE, pch = 20, bg = 1, pcex = 3, pcol = 4, lty ... [TRUNCATED]

Rd file 'groupplot.foodweb.Rd':
  \usage lines wider than 90 characters:
     groupplot.foodweb(gemat, ranks, groups, addlabels = FALSE, scaled = TRUE, pch = 20, bg = 1, pcex = 3, pcol = 4, lty = 1, lcol = 8, tfon ... [TRUNCATED]
  \examples lines wider than 100 characters:
     groupplot.foodweb(gemat=mat,ranks=rlist,groups=glist,pch=pch,lcol=lcol) #other parameters are set in default

These lines will be truncated in the PDF manual.
amendColumns: no visible global function definition for ‘setNames’
fillColumns: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  print.lpcfdrobj print.lpcobj print.tfdrobj
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
EstimateTFDR: no visible global function definition for ‘quantile’
GetSoftThresh: no visible global function definition for ‘lm’
LPC: no visible global function definition for ‘lm’
PlotFDRs: no visible global function definition for ‘quantile’
PlotFDRs: no visible global function definition for ‘plot’
PlotFDRs: no visible global function definition for ‘points’
PlotFDRs: no visible global function definition for ‘legend’
PredictiveAdvantage: no visible global function definition for ‘par’
PredictiveAdvantage: no visible global function definition for ‘plot’
PredictiveAdvantage: no visible global function definition for ‘points’
PredictiveAdvantage: no visible global function definition for ‘legend’
Undefined global functions or variables:
  legend lm par plot points quantile
Consider adding
  importFrom("graphics", "legend", "par", "plot", "points")
  importFrom("stats", "lm", "quantile")
to your NAMESPACE file.
lpint : <anonymous>: no visible global function definition for
  ‘integrate’
lpint: no visible global function definition for ‘integrate’
lpint : lpint : <anonymous>: no visible global function definition for
  ‘integrate’
lplikint : lplikint.fun : <anonymous>: no visible global function
  definition for ‘integrate’
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
'library' or 'require' call to ‘Rsymphony’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
mipSolve.Rsymphony: no visible global function definition for
  ‘Rsymphony_solve_LP’
Undefined global functions or variables:
  Rsymphony_solve_LP
learnPattern.default: no visible global function definition for ‘runif’
plot.learnPattern: no visible global function definition for ‘matplot’
plotMDS: no visible global function definition for ‘par’
plotMDS: no visible global function definition for ‘rainbow’
plotMDS: no visible global function definition for ‘plot’
plotMDS: no visible global function definition for ‘pairs’
visualizePattern: no visible global function definition for ‘par’
visualizePattern: no visible global function definition for ‘plot’
visualizePattern: no visible global function definition for ‘points’
visualizePattern: no visible global function definition for ‘legend’
Undefined global functions or variables:
  legend matplot pairs par plot points rainbow runif
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend", "matplot", "pairs", "par", "plot",
             "points")
  importFrom("stats", "runif")
to your NAMESPACE file.
LP.comoment: no visible global function definition for ‘cor’
LP.comoment: no visible global function definition for ‘cov’
LP.moment: no visible global function definition for ‘cor’
LPTrans: no visible global function definition for ‘ecdf’
VAR: no visible global function definition for ‘embed’
VAR: no visible global function definition for ‘lm’
Undefined global functions or variables:
  cor cov ecdf embed lm
Consider adding
  importFrom("stats", "cor", "cov", "ecdf", "embed", "lm")
to your NAMESPACE file.
associate: no visible global function definition for ‘cor’
textmatrix: no visible global function definition for ‘xtabs’
textvector: no visible global function definition for ‘data’
Undefined global functions or variables:
  cor data xtabs
Consider adding
  importFrom("stats", "cor", "xtabs")
  importFrom("utils", "data")
to your NAMESPACE file.
Lsdv.formula: no visible global function definition for ‘model.frame’
Lsdv.formula: no visible global function definition for ‘model.matrix’
Lsdv.formula: no visible global function definition for
  ‘model.response’
lsdv: no visible global function definition for ‘pf’
summary.Lsdv: no visible global function definition for ‘coef’
summary.Lsdv: no visible global function definition for ‘pt’
Undefined global functions or variables:
  coef model.frame model.matrix model.response pf pt
Consider adding
  importFrom("stats", "coef", "model.frame", "model.matrix",
             "model.response", "pf", "pt")
to your NAMESPACE file.
legend.lshorth: no visible global function definition for ‘legend’
legend.lshorth: no visible global function definition for ‘strwidth’
legend.lshorth: no visible global function definition for ‘text’
plot.lshorth: no visible global function definition for ‘plot.new’
plot.lshorth: no visible global function definition for ‘plot.window’
plot.lshorth: no visible global function definition for ‘axis’
plot.lshorth: no visible global function definition for ‘title’
plot.lshorth: no visible global function definition for ‘box’
plot.lshorth: no visible global function definition for ‘lines’
plot.lshorth: no visible global function definition for ‘legend’
plot.lshorth: no visible global function definition for ‘strwidth’
plot.lshorth: no visible global function definition for ‘text’
Undefined global functions or variables:
  axis box legend lines plot.new plot.window strwidth text title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "lines", "plot.new",
             "plot.window", "strwidth", "text", "title")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  print.lss
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
lss: no visible binding for global variable ‘na.exclude’
lss: no visible global function definition for ‘model.extract’
lss: no visible binding for global variable ‘response’
lss: no visible global function definition for ‘model.matrix’
lss: no visible global function definition for ‘rexp’
lss: no visible global function definition for ‘pnorm’
lss.betag: no visible global function definition for ‘l1fit’
Undefined global functions or variables:
  l1fit model.extract model.matrix na.exclude pnorm response rexp
Consider adding
  importFrom("stats", "model.extract", "model.matrix", "na.exclude",
             "pnorm", "rexp")
to your NAMESPACE file.
Rd file 'lss.Rd':
  \usage lines wider than 90 characters:
     lss(formula, data, subset, trace = FALSE, mcsize = 500, maxiter = 10, tolerance = 0.001, gehanonly = FALSE, cov = FALSE, na.action = na ... [TRUNCATED]
  \examples lines wider than 100 characters:
     fit1<-lss(cbind(log10(time),status) ~ age + t5,data=stan,subset=!is.na(t5), mcsize=100,trace=TRUE,gehanonly=FALSE,maxiter=10,tolerance= ... [TRUNCATED]
     fit2<-lss(cbind(log10(time),status) ~ age + I(age^2),data=stan,subset=!is.na(t5)&time>=100,mcsize=5,trace=TRUE, gehanonly=FALSE,cov=TRU ... [TRUNCATED]

These lines will be truncated in the PDF manual.
OC : Lnapprox: no visible global function definition for ‘pnorm’
OC : Lnapprox: no visible global function definition for ‘qnorm’
OC : Lt: no visible global function definition for ‘pt’
OC : Lt: no visible global function definition for ‘qnorm’
OC : OC_emwa2: no visible global function definition for ‘pnorm’
OC : OC_emwa2: no visible global function definition for ‘qnorm’
OC: no visible global function definition for ‘pnorm’
OC: no visible global function definition for ‘qnorm’
cmBE : LAtHy: no visible global function definition for ‘phyper’
cmBE: no visible global function definition for ‘uniroot’
planAOQL : Gderivacex: no visible global function definition for
  ‘pnorm’
planAOQL : Mnk: no visible global function definition for ‘uniroot’
planAOQL : k0AOQL : delta: no visible global function definition for
  ‘pnorm’
planAOQL : alpha0: no visible global function definition for ‘pnorm’
planAOQL : alpha0: no visible global function definition for ‘qnorm’
planAOQL : fMSmodq2: no visible global function definition for
  ‘optimize’
planAOQL : kAOQL: no visible global function definition for ‘uniroot’
planLTPD : nAPPROXL : k0L : g: no visible global function definition
  for ‘qnorm’
planLTPD : nAPPROXL : k0L : h: no visible global function definition
  for ‘qnorm’
planLTPD : nAPPROXL : k0L: no visible global function definition for
  ‘qnorm’
planLTPD : nAPPROXL : alpha0: no visible global function definition for
  ‘pnorm’
planLTPD : nAPPROXL : alpha0: no visible global function definition for
  ‘qnorm’
planLTPD : nAPPROXL: no visible global function definition for
  ‘uniroot’
planLTPD : kEWMA: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  optimize phyper pnorm pt qnorm uniroot
Consider adding
  importFrom("stats", "optimize", "phyper", "pnorm", "pt", "qnorm",
             "uniroot")
to your NAMESPACE file.
fit.LTR: no visible global function definition for ‘lm’
Undefined global functions or variables:
  lm
Consider adding
  importFrom("stats", "lm")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘robustbase’
  Please remove these calls from your code.
ltsbase: no visible global function definition for ‘lm’
ltsbase: no visible global function definition for ‘lines’
ltsbase: no visible global function definition for ‘legend’
Undefined global functions or variables:
  legend lines lm
Consider adding
  importFrom("graphics", "legend", "lines")
  importFrom("stats", "lm")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘genetics’ ‘survival’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘genetics’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  summary.luca
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
get.Z.HWP: no visible global function definition for ‘is.genotype’
get.Z.HWP: no visible global function definition for ‘allele.count’
get.Z.dep: no visible global function definition for ‘model.matrix’
get.Z.dep: no visible global function definition for ‘formula’
get.Z.saturated: no visible global function definition for ‘formula’
get.Z.saturated: no visible global function definition for
  ‘model.matrix’
get.lambda: no visible global function definition for ‘is.genotype’
get.lambda: no visible global function definition for ‘model.matrix’
get.lambda: no visible global function definition for ‘heterozygote’
luca: no visible global function definition for ‘is.genotype’
luca: no visible global function definition for ‘genotype’
luca: no visible global function definition for ‘Surv’
luca: no visible global function definition for ‘coxph.fit’
luca: no visible global function definition for ‘coxph.control’
summary.luca: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  Surv allele.count coxph.control coxph.fit formula genotype
  heterozygote is.genotype model.matrix pchisq
Consider adding
  importFrom("stats", "formula", "model.matrix", "pchisq")
to your NAMESPACE file.
terrestrial.season: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
generate.clonal.data : pcr.rpareto.func: no visible global function
  definition for ‘runif’
generate.clonal.data : get.readcount.given.cellcount: no visible global
  function definition for ‘rlnorm’
generate.clonal.data: no visible global function definition for
  ‘rmultinom’
generate.clonal.data: no visible global function definition for ‘rpois’
infer.clonality: no visible global function definition for ‘cov’
infer.clonality: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  capture.output cov rlnorm rmultinom rpois runif
Consider adding
  importFrom("stats", "cov", "rlnorm", "rmultinom", "rpois", "runif")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
project.M3.1.to.M3.2: no visible global function definition for
  ‘coordinates<-’
project.M3.1.to.M3.2: no visible global function definition for
  ‘proj4string<-’
project.M3.1.to.M3.2: no visible global function definition for ‘CRS’
project.M3.1.to.M3.2: no visible global function definition for
  ‘spTransform’
project.M3.1.to.M3.2: no visible global function definition for
  ‘coordinates’
Undefined global functions or variables:
  CRS coordinates coordinates<- proj4string<- spTransform
maboost.default: no visible global function definition for
  ‘flush.console’
maboost.default: no visible binding for global variable ‘na.pass’
maboost.default : predict.type: no visible global function definition
  for ‘predict’
maboost.formula: no visible global function definition for
  ‘model.extract’
maboost.machine.bin: no visible global function definition for ‘runif’
maboost.machine.bin: no visible binding for global variable ‘na.pass’
maboost.machine.multi: no visible global function definition for
  ‘runif’
maboost.machine.multi: no visible binding for global variable ‘na.pass’
projsplx_k: no visible global function definition for ‘tail’
varplot.maboost: no visible global function definition for ‘dotchart’
Undefined global functions or variables:
  dotchart flush.console model.extract na.pass predict runif tail
Consider adding
  importFrom("graphics", "dotchart")
  importFrom("stats", "model.extract", "na.pass", "predict", "runif")
  importFrom("utils", "flush.console", "tail")
to your NAMESPACE file.
logistic_z: no visible global function definition for ‘glm’
logistic_z: no visible binding for global variable ‘binomial’
logistic_z: no visible global function definition for ‘predict’
plsrf_x: no visible global function definition for ‘qnorm’
plsrf_x: no visible global function definition for ‘predict’
plsrf_x_pv: no visible global function definition for ‘qnorm’
plsrf_x_pv: no visible global function definition for ‘predict’
plsrf_xz: no visible global function definition for ‘qnorm’
plsrf_xz: no visible global function definition for ‘predict’
plsrf_xz_pv: no visible global function definition for ‘qnorm’
plsrf_xz_pv: no visible global function definition for ‘predict’
rf_z: no visible global function definition for ‘qnorm’
rf_z: no visible global function definition for ‘predict’
simuldata_list: no visible global function definition for ‘rnorm’
simuldatacluster_list: no visible global function definition for
  ‘rnorm’
svm_x: no visible global function definition for ‘predict’
Undefined global functions or variables:
  binomial glm predict qnorm rnorm
Consider adding
  importFrom("stats", "binomial", "glm", "predict", "qnorm", "rnorm")
to your NAMESPACE file.
Package suggested but not available for checking: ‘R2wd’
'library' or 'require' calls in package code:
  ‘R2wd’ ‘ggplot2’ ‘metafor’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package required but not available: ‘lumi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package in Depends field not imported from: ‘rJava’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
MalletLDA: no visible global function definition for ‘.jnew’
mallet.doc.topics: no visible global function definition for
  ‘.jevalArray’
mallet.import: no visible global function definition for ‘J’
mallet.import: no visible global function definition for ‘.jnew’
mallet.import: no visible global function definition for ‘.jcast’
mallet.subset.topic.words: no visible global function definition for
  ‘.jevalArray’
mallet.topic.hclust: no visible global function definition for ‘hclust’
mallet.topic.hclust: no visible global function definition for ‘dist’
mallet.topic.words: no visible global function definition for
  ‘.jevalArray’
mallet.word.freqs: no visible global function definition for
  ‘.jevalArray’
Undefined global functions or variables:
  .jcast .jevalArray .jnew J dist hclust
Consider adding
  importFrom("stats", "dist", "hclust")
to your NAMESPACE file.
mp_corpus: no visible binding for global variable ‘annotations’
print.ManifestoAvailability: no visible binding for global variable
  ‘annotations’
Undefined global functions or variables:
  annotations
Registration problems:
  Evaluating ‘getNativeSymbolInfo("rs_activeManipulator", PACKAGE = "")’ during check gives error
‘no such symbol rs_activeManipulator’:
   .Call(getNativeSymbolInfo("rs_activeManipulator", PACKAGE = ""))
  Evaluating ‘getNativeSymbolInfo("rs_createUUID", PACKAGE = "")’ during check gives error
‘no such symbol rs_createUUID’:
   .Call(getNativeSymbolInfo("rs_createUUID", PACKAGE = ""))
  Evaluating ‘getNativeSymbolInfo("rs_ensureManipulatorSaved", PACKAGE = "")’ during check gives error
‘no such symbol rs_ensureManipulatorSaved’:
   .Call(getNativeSymbolInfo("rs_ensureManipulatorSaved", PACKAGE = ""))
  Evaluating ‘getNativeSymbolInfo("rs_executeAndAttachManipulator", PACKAGE = "")’ during check gives error
‘no such symbol rs_executeAndAttachManipulator’:
   .Call(getNativeSymbolInfo("rs_executeAndAttachManipulator", PACKAGE = ""), 
       manipulator)
  Evaluating ‘getNativeSymbolInfo("rs_hasActiveManipulator", PACKAGE = "")’ during check gives error
‘no such symbol rs_hasActiveManipulator’:
   .Call(getNativeSymbolInfo("rs_hasActiveManipulator", PACKAGE = ""))
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
cf1.sample: no visible global function definition for ‘rexp’
cf1.sample: no visible global function definition for ‘rmultinom’
dherlang : <anonymous> : <anonymous>: no visible global function
  definition for ‘dgamma’
erhmm.param.kmeans: no visible global function definition for ‘kmeans’
erhmm.param.kmeans: no visible global function definition for ‘var’
erhmm.param.kmeans: no visible global function definition for ‘runif’
gmmpp.param.kmeans: no visible global function definition for ‘kmeans’
gmmpp.param.kmeans: no visible global function definition for ‘runif’
herlang.param.kmeans: no visible global function definition for
  ‘kmeans’
herlang.param.kmeans: no visible global function definition for ‘var’
map.param.kmeans: no visible global function definition for ‘kmeans’
map.param.kmeans: no visible global function definition for ‘runif’
ph.param.random: no visible global function definition for ‘runif’
ph.sample: no visible global function definition for ‘rmultinom’
ph.sample: no visible global function definition for ‘rexp’
pherlang : <anonymous> : <anonymous>: no visible global function
  definition for ‘pgamma’
rherlang: no visible global function definition for ‘rmultinom’
rherlang : <anonymous>: no visible global function definition for
  ‘rgamma’
Undefined global functions or variables:
  dgamma kmeans pgamma rexp rgamma rmultinom runif var
Consider adding
  importFrom("stats", "dgamma", "kmeans", "pgamma", "rexp", "rgamma",
             "rmultinom", "runif", "var")
to your NAMESPACE file.
'library' or 'require' call to ‘mgcv’ which was already attached by Depends.
  Please remove these calls from your code.
ageprofile: no visible global function definition for ‘model.frame’
ageprofile: no visible binding for global variable ‘poisson’
ageprofile: no visible global function definition for ‘predict.gam’
ageprofile: no visible global function definition for ‘as.formula’
ageprofile: no visible global function definition for ‘summary.gam’
ageprofile: no visible global function definition for ‘contrasts<-’
ageprofile: no visible global function definition for ‘anova.gam’
plotap: no visible global function definition for ‘dev.new’
plotap: no visible global function definition for ‘plot’
plotap: no visible global function definition for ‘lines’
plotap: no visible global function definition for ‘points’
plotap: no visible global function definition for ‘legend’
splitter: no visible global function definition for ‘reshape’
tabm: no visible global function definition for ‘coef’
tabm: no visible global function definition for ‘AIC’
Undefined global functions or variables:
  AIC anova.gam as.formula coef contrasts<- dev.new legend lines
  model.frame plot points poisson predict.gam reshape summary.gam
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("stats", "AIC", "as.formula", "coef", "contrasts<-",
             "model.frame", "poisson", "reshape")
to your NAMESPACE file.
calcStats: no visible global function definition for ‘as.formula’
calcStats: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  as.formula na.omit
Consider adding
  importFrom("stats", "as.formula", "na.omit")
to your NAMESPACE file.
plot.topics: no visible global function definition for ‘hist’
plot.topics: no visible global function definition for ‘grey’
plot.topics: no visible global function definition for ‘plot’
plot.topics: no visible global function definition for ‘par’
plot.topics: no visible global function definition for ‘image’
plot.topics: no visible global function definition for ‘axis’
plot.topics: no visible global function definition for ‘points’
plot.topics: no visible global function definition for ‘text’
rdir: no visible global function definition for ‘rgamma’
summary.topics: no visible global function definition for ‘pchisq’
tpxResids: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  axis grey hist image par pchisq plot points rgamma text
Consider adding
  importFrom("grDevices", "grey")
  importFrom("graphics", "axis", "hist", "image", "par", "plot",
             "points", "text")
  importFrom("stats", "pchisq", "rgamma")
to your NAMESPACE file.
'library' or 'require' call to ‘MARSS’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘MARSS:::is.diagonal’
  See the note in ?`:::` about the use of this operator.
Found the following apparent S3 methods exported but not registered:
  plot.MAR
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
'library' or 'require' calls in package code:
  ‘gsl’ ‘taRifx’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  aa.account aa.default as.data.frame.bond
  as.data.frame.history.account as.data.frame.portfolio.bond
  as.history.account.sum.account cashflow.account cashflow.bond
  cashflow.cash cashflow.default cashflow.portfolio.bond
  count.history.account duration.account duration.bond duration.cash
  duration.default duration.history.account duration.portfolio.bond
  duration.sum.account fv.bond fv.cash fv.default issueTime.bond
  issueTime.default issueTime.portfolio.bond matTime.bond
  matTime.default matTime.portfolio.bond mktTime.account
  mktTime.default mktTime.history.account mktTime.market
  plot.history.account plot.history.market plot.sum.account
  plot.sum.vasicek.discrete plot.vasicek.discrete print.account
  print.bond print.cash print.history.account print.history.market
  print.market print.market.bond print.portfolio.bond print.sum.account
  print.sum.bond print.sum.market.bond print.sum.portfolio.bond
  pv.account pv.bond pv.cash pv.default pv.history.account
  pv.portfolio.bond rebalance.account rebalance.default summary.account
  summary.bond summary.market summary.market.bond
  summary.portfolio.bond summary.vasicek.discrete
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
negbin.rel.clust: no visible global function definition for ‘kmeans’
negbin.rel.clust: no visible global function definition for ‘matplot’
negbin.rel.pca: no visible global function definition for ‘princomp’
negbin.rel.pca: no visible global function definition for ‘biplot’
pois.rel.clust: no visible global function definition for ‘kmeans’
pois.rel.clust: no visible global function definition for ‘matplot’
pois.rel.pca: no visible global function definition for ‘princomp’
pois.rel.pca: no visible global function definition for ‘biplot’
sim.negbin: no visible global function definition for ‘rnbinom’
sim.pois: no visible global function definition for ‘rpois’
wt.rel.negbin: no visible global function definition for ‘var’
wt.rel.negbin: no visible global function definition for ‘optimize’
wt.rel.negbin: no visible global function definition for ‘integrate’
wt.rel.pois: no visible global function definition for ‘optimize’
wt.rel.pois: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  biplot integrate kmeans matplot optimize princomp rnbinom rpois var
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "biplot", "integrate", "kmeans", "optimize",
             "princomp", "rnbinom", "rpois", "var")
to your NAMESPACE file.
marqLevAlg: no visible global function definition for ‘flush.console’
print.marqLevAlg: no visible global function definition for ‘qnorm’
print.marqLevAlg: no visible global function definition for ‘pchisq’
summary.marqLevAlg: no visible global function definition for ‘qnorm’
summary.marqLevAlg: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  flush.console pchisq qnorm
Consider adding
  importFrom("stats", "pchisq", "qnorm")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
mAr.pca: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Running examples in ‘MARSS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: augment.marssMLE
> ### Title: Return the model predicted values, residuals, and optionally
> ###   confidence intervals
> ### Aliases: augment.marssMLE augment_dfa augment_marss augmentmarxss
> 
> ### ** Examples
> 
>   dat <- t(harborSeal)
>   dat <- dat[c(2,11,12),]
>   MLEobj <- MARSS(dat, model=list(Z=factor(c("WA","OR","OR"))))
Success! abstol and log-log tests passed at 37 iterations.
Alert: conv.test.slope.tol is 0.5.
Test with smaller values (<0.1) to ensure convergence.

MARSS fit is
Estimation method: kem 
Convergence test: conv.test.slope.tol = 0.5, abstol = 0.001
Estimation converged in 37 iterations. 
Log-likelihood: 13.72233 
AIC: -11.44465   AICc: -8.918339   
 
                Estimate
A.OR.SouthCoast  0.49280
R.diag           0.02509
U.WA             0.06171
U.OR             0.03686
Q.(WA,WA)        0.01082
Q.(OR,OR)        0.00439
x0.WA            7.41712
x0.OR            6.56460
Initial states (x0) defined at t=0

Standard errors have not been calculated. 
Use MARSSparamCIs to compute CIs and bias estimates.

> 
> library(broom)
> library(ggplot2)
> theme_set(theme_bw())
> 
> # Make a plot of the observations and model fits
> d <- augment(MLEobj, interval="confidence")
Error: No augment method for objects of class marssMLE
Execution halted
mata.wald: no visible global function definition for ‘uniroot’
tailarea.t: no visible global function definition for ‘pt’
tailarea.z: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm pt uniroot
Consider adding
  importFrom("stats", "pnorm", "pt", "uniroot")
to your NAMESPACE file.
Found the following possibly unsafe calls:
File ‘matlab/R/zzz.R’:
  unlockBinding("savedTime", .MatlabNamespaceEnv)

colorbar : colorbar.EO: no visible global function definition for ‘par’
colorbar : colorbar.EO: no visible global function definition for
  ‘axis’
colorbar : colorbar.EO: no visible global function definition for
  ‘axTicks’
colorbar : colorbar.EO: no visible global function definition for ‘box’
colorbar : colorbar.NO: no visible global function definition for
  ‘axis’
colorbar : colorbar.NO: no visible global function definition for
  ‘axTicks’
colorbar : colorbar.NO: no visible global function definition for ‘box’
imagesc : pretty.axp: no visible global function definition for ‘par’
imagesc: no visible global function definition for ‘axis’
imagesc: no visible global function definition for ‘box’
jet.colors: no visible global function definition for ‘rgb’
multiline.plot.colors : get.gca.colororder: no visible global function
  definition for ‘rgb’
std: no visible global function definition for ‘sd’
Undefined global functions or variables:
  axTicks axis box par rgb sd
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axTicks", "axis", "box", "par")
  importFrom("stats", "sd")
to your NAMESPACE file.
'library' or 'require' call to ‘bigmemory’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
MAT: no visible global function definition for ‘dev.new’
MAT: no visible global function definition for ‘plot’
MAT: no visible global function definition for ‘points’
MAT: no visible global function definition for ‘abline’
MAT: no visible global function definition for ‘text’
MAT: no visible global function definition for ‘legend’
MAT: no visible global function definition for ‘lines’
MAT: no visible global function definition for ‘par’
MAT: no visible global function definition for ‘barplot’
MAT: no visible global function definition for ‘cor’
print.MAT: no visible global function definition for ‘sd’
print.MAT: no visible global function definition for ‘cor’
simM3PL: no visible global function definition for ‘rnorm’
simM3PL: no visible global function definition for ‘runif’
Undefined global functions or variables:
  abline barplot cor dev.new legend lines par plot points rnorm runif
  sd text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "barplot", "legend", "lines", "par",
             "plot", "points", "text")
  importFrom("stats", "cor", "rnorm", "runif", "sd")
to your NAMESPACE file.
Rd file 'mat.dissim.Rd':
  \usage lines wider than 90 characters:
     mat.dissim(inFossil, inModern, llMod = c(), modTaxa = c(), llFoss = c(), fosTaxa = c(), numAnalogs = 1, counts = T, sitenames = 1:lengt ... [TRUNCATED]

Rd file 'mat.fossavg.Rd':
  \usage lines wider than 90 characters:
     mat.fossavg(dObj, modEnvCol, fossEnvCol = 0, fossCols = 0, cutoff = 0, distance = -1, wmethod = "none", numanalogs = length(dObj$positi ... [TRUNCATED]

Rd file 'mat.jumprecon.Rd':
  \usage lines wider than 90 characters:
     mat.jumprecon(dObj, modEnvCol, fossEnvCol, cutoff = 0, alpha = NULL, distance = -1, numanalogs = length(dObj$position[, 1]))

Rd file 'mat.mc.Rd':
  \usage lines wider than 90 characters:
     mat.mc(inModern, modTaxa = c(NULL, NULL), probs = c(0.05, 0.025, 0.01, 0.001), freqint = seq(0, 2, 0.02), sampleSize = length(inModern[ ... [TRUNCATED]

Rd file 'mat.roc.Rd':
  \usage lines wider than 90 characters:
     mat.roc(inModern, modTaxa = c(), colClasses = NULL, numAnalogs = 2, rocEvalSeq = seq(0, 2, 0.05), counts = F, aucmethod = "trap")

Rd file 'mat.roc.allpair.Rd':
  \usage lines wider than 90 characters:
     mat.roc.allpair(inModern, modTaxa = c(), colClasses = NULL, numAnalogs = 2, rocEvalSeq = seq(0, 2, 0.05), counts = F, aucmethod = "trap ... [TRUNCATED]

These lines will be truncated in the PDF manual.
GSTplot : <anonymous>: no visible global function definition for
  ‘t.test’
GSTplot: no visible global function definition for ‘rt’
GSTplot: no visible global function definition for ‘layout’
GSTplot: no visible global function definition for ‘par’
GSTplot: no visible global function definition for ‘plot’
GSTplot: no visible global function definition for ‘text’
GSTplot: no visible global function definition for ‘lines’
GSTplot: no visible global function definition for ‘polygon’
GSTplot: no visible global function definition for ‘abline’
GSTplot: no visible global function definition for ‘ecdf’
GSTplot: no visible global function definition for ‘knots’
GSTplot : <anonymous>: no visible global function definition for ‘aov’
GSTplot: no visible global function definition for ‘qf’
MAVTn : <anonymous>: no visible global function definition for ‘aov’
MAVTn: no visible global function definition for ‘p.adjust’
MAVTn: no visible global function definition for ‘plot’
MAVTn: no visible global function definition for ‘par’
MAVTn: no visible global function definition for ‘abline’
MAVTn: no visible global function definition for ‘legend’
MAVTn: no visible global function definition for ‘locator’
Tols : olsf: no visible global function definition for ‘t.test’
Tols: no visible global function definition for ‘cor’
Undefined global functions or variables:
  abline aov cor ecdf knots layout legend lines locator p.adjust par
  plot polygon qf rt t.test text
Consider adding
  importFrom("graphics", "abline", "layout", "legend", "lines",
             "locator", "par", "plot", "polygon", "text")
  importFrom("stats", "aov", "cor", "ecdf", "knots", "p.adjust", "qf",
             "rt", "t.test")
to your NAMESPACE file.
Package in Depends field not imported from: ‘mnormt’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
catt.test: no visible global function definition for ‘pnorm’
fnorm2: no visible global function definition for ‘sadmvn’
fnorm3: no visible global function definition for ‘sadmvn’
Undefined global functions or variables:
  pnorm sadmvn
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
tune.maxent: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
File ‘maxent/libs/maxent.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘sgd.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
MI.2: no visible global function definition for ‘xtabs’
RNASeq.Data: no visible binding for global variable ‘quantile’
loc.node: no visible global function definition for ‘head’
loc.node: no visible global function definition for ‘tail’
plotHybrid.Tree: no visible global function definition for ‘par’
plotHybrid.Tree: no visible global function definition for ‘plot’
plotHybrid.Tree: no visible global function definition for ‘text’
plotHybrid.Tree: no visible global function definition for ‘image’
plotHybrid.Tree: no visible global function definition for ‘grey’
plotHybrid.Tree: no visible global function definition for
  ‘heat.colors’
plotHybrid.Tree: no visible global function definition for ‘head’
plotHybrid.Tree: no visible global function definition for ‘segments’
plotbr: no visible global function definition for ‘segments’
Undefined global functions or variables:
  grey head heat.colors image par plot quantile segments tail text
  xtabs
Consider adding
  importFrom("grDevices", "grey", "heat.colors")
  importFrom("graphics", "image", "par", "plot", "segments", "text")
  importFrom("stats", "quantile", "xtabs")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
cfull: no visible global function definition for ‘combn’
cl: no visible global function definition for ‘combn’
cn: no visible global function definition for ‘combn’
crep: no visible global function definition for ‘combn’
crich: no visible global function definition for ‘combn’
ct: no visible global function definition for ‘combn’
mjaccard: no visible global function definition for ‘combn’
ml: no visible global function definition for ‘combn’
mn: no visible global function definition for ‘combn’
mrep: no visible global function definition for ‘combn’
mrich: no visible global function definition for ‘combn’
msorensen: no visible global function definition for ‘combn’
mt: no visible global function definition for ‘combn’
wnodf: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  confint.mblm summary.mblm
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
confint.mblm: no visible global function definition for ‘wilcox.test’
mblm: no visible global function definition for ‘terms’
mblm: no visible global function definition for ‘median’
mblm: no visible global function definition for ‘lm’
summary.mblm: no visible global function definition for ‘mad’
summary.mblm: no visible global function definition for ‘wilcox.test’
summary.mblm: no visible global function definition for ‘coef’
Undefined global functions or variables:
  coef lm mad median terms wilcox.test
Consider adding
  importFrom("stats", "coef", "lm", "mad", "median", "terms",
             "wilcox.test")
to your NAMESPACE file.
Package in Depends field not imported from: ‘logistf’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
mbmdr : NextModel: no visible global function definition for
  ‘read.table’
mbmdr : OffsetFit: no visible global function definition for ‘glm’
mbmdr : Regresion: no visible global function definition for ‘logistf’
mbmdr : Regresion: no visible global function definition for ‘glm’
mbmdr: no visible global function definition for ‘write.table’
mbmdr.PermTest: no visible global function definition for ‘read.table’
mbmdr.PermTest: no visible global function definition for ‘qnorm’
print.mbmdr: no visible global function definition for ‘read.table’
summary.mbmdr: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  glm logistf qnorm read.table write.table
Consider adding
  importFrom("stats", "glm", "qnorm")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Rd file 'VegTypeChanges.Rd':
  \examples lines wider than 100 characters:
     ## vegChanges = VegTypeChanges(ncdf.th <- system.file("netcdf", "WW2100_HadGEM2-ES85_year_sample.nc", PACKAGE = "MC2toPath")path, base. ... [TRUNCATED]

These lines will be truncated in the PDF manual.
laugreen: no visible global function definition for ‘combn’
laugreen: no visible global function definition for ‘lp’
maxpear: no visible global function definition for ‘hclust’
maxpear: no visible global function definition for ‘as.dist’
maxpear : <anonymous>: no visible global function definition for
  ‘cutree’
medv: no visible global function definition for ‘cutree’
medv: no visible global function definition for ‘hclust’
medv: no visible global function definition for ‘as.dist’
minbinder: no visible global function definition for ‘hclust’
minbinder: no visible global function definition for ‘as.dist’
minbinder : <anonymous>: no visible global function definition for
  ‘cutree’
relabel : min.perm.labels: no visible global function definition for
  ‘lp.transport’
Undefined global functions or variables:
  as.dist combn cutree hclust lp lp.transport
Consider adding
  importFrom("stats", "as.dist", "cutree", "hclust")
  importFrom("utils", "combn")
to your NAMESPACE file.
getbetap.A: no visible global function definition for ‘pbeta’
getbetap.A: no visible global function definition for ‘cor.test’
Undefined global functions or variables:
  cor.test pbeta
Consider adding
  importFrom("stats", "cor.test", "pbeta")
to your NAMESPACE file.
mcgibbsit: no visible global function definition for ‘is.mcmc.list’
mcgibbsit: no visible global function definition for ‘start’
mcgibbsit: no visible global function definition for ‘end’
mcgibbsit: no visible global function definition for ‘thin’
mcgibbsit: no visible global function definition for ‘nvar’
mcgibbsit: no visible global function definition for ‘mcmc’
mcgibbsit: no visible global function definition for ‘mcmc.list’
mcgibbsit: no visible global function definition for ‘varnames’
mcgibbsit: no visible global function definition for ‘qnorm’
mcgibbsit: no visible global function definition for ‘niter’
mcgibbsit: no visible global function definition for ‘quantile’
mcgibbsit : to.table: no visible global function definition for
  ‘window’
mcgibbsit: no visible global function definition for ‘var’
read.mcmc: no visible global function definition for ‘mcmc.list’
read.mcmc: no visible global function definition for ‘mcmc’
Undefined global functions or variables:
  end is.mcmc.list mcmc mcmc.list niter nvar qnorm quantile start thin
  var varnames window
Consider adding
  importFrom("stats", "end", "qnorm", "quantile", "start", "var",
             "window")
to your NAMESPACE file.
call_localoptim: no visible global function definition for ‘optim’
call_localoptim: no visible global function definition for ‘nlminb’
call_localoptim: no visible global function definition for
  ‘txtProgressBar’
call_localoptim: no visible global function definition for
  ‘setTxtProgressBar’
call_localoptim : <anonymous>: no visible global function definition
  for ‘optim’
call_localoptim : <anonymous>: no visible global function definition
  for ‘nlminb’
multiStartoptim: no visible global function definition for ‘median’
Undefined global functions or variables:
  median nlminb optim setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "median", "nlminb", "optim")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
mcheatmaps : coscolorFun: no visible global function definition for
  ‘rgb’
mcheatmaps : halfcmat: no visible global function definition for
  ‘order.dendrogram’
mcheatmaps : fullcmat: no visible global function definition for
  ‘order.dendrogram’
mcheatmaps : calculateDendrogram: no visible global function definition
  for ‘hclust’
mcheatmaps : calculateDendrogram: no visible global function definition
  for ‘as.dist’
mcheatmaps : calculateDendrogram: no visible global function definition
  for ‘sd’
mcheatmaps : calculateDendrogram: no visible global function definition
  for ‘cophenetic’
mcheatmaps : printDiag: no visible global function definition for
  ‘order.dendrogram’
mcheatmaps: no visible global function definition for ‘strwidth’
mcheatmaps: no visible global function definition for ‘pdf’
mcheatmaps: no visible global function definition for ‘plot.new’
mcheatmaps: no visible global function definition for ‘as.dendrogram’
mcheatmaps: no visible global function definition for ‘reorder’
mcheatmaps: no visible global function definition for ‘par’
mcheatmaps: no visible global function definition for ‘plot’
mcheatmaps: no visible global function definition for
  ‘order.dendrogram’
mcheatmaps: no visible global function definition for ‘heat.colors’
mcheatmaps: no visible global function definition for ‘terrain.colors’
mcheatmaps: no visible global function definition for ‘as.dist’
mcheatmaps: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  as.dendrogram as.dist cophenetic dev.off hclust heat.colors
  order.dendrogram par pdf plot plot.new reorder rgb sd strwidth
  terrain.colors
Consider adding
  importFrom("grDevices", "dev.off", "heat.colors", "pdf", "rgb",
             "terrain.colors")
  importFrom("graphics", "par", "plot", "plot.new", "strwidth")
  importFrom("stats", "as.dendrogram", "as.dist", "cophenetic", "hclust",
             "order.dendrogram", "reorder", "sd")
to your NAMESPACE file.
lik_locfit: no visible global function definition for ‘predict’
mcll_coeff: no visible global function definition for ‘optim’
mcll_est: no visible global function definition for ‘cov’
mcll_est: no visible global function definition for ‘optim’
mcll_se: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov optim predict
Consider adding
  importFrom("stats", "cov", "optim", "predict")
to your NAMESPACE file.
Found the following significant warnings:

  Warning: 'cBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
do.linear.conjoint: no visible global function definition for
  ‘as.formula’
do.linear.conjoint: no visible global function definition for ‘lm’
do.linear.conjoint: no visible global function definition for
  ‘coefficients’
is.close.to.orthogonal: no visible global function definition for ‘cor’
mc.add.to.design: no visible global function definition for ‘combn’
mc.good.designs: no visible global function definition for ‘combn’
Undefined global functions or variables:
  as.formula coefficients combn cor lm
Consider adding
  importFrom("stats", "as.formula", "coefficients", "cor", "lm")
  importFrom("utils", "combn")
to your NAMESPACE file.
'library' or 'require' call to ‘scatterplot3d’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.nsga2: no visible global function definition for ‘plot’
plot.nsga2: no visible global function definition for ‘lines’
plot.nsga2: no visible global function definition for ‘pairs’
plot.nsga2.collection: no visible global function definition for
  ‘devAskNewPage’
plot.nsga2.collection: no visible binding for global variable ‘plot’
Undefined global functions or variables:
  devAskNewPage lines pairs plot
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "lines", "pairs", "plot")
to your NAMESPACE file.
src/Makevars: incorrect macro SHLIB_OPENMP_CFLAGS included in PKG_CXXFLAGS
  src/Makevars.win: incorrect macro SHLIB_OPENMP_CFLAGS included in PKG_CXXFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
Package in Depends field not imported from: ‘metafor’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  print.PermMeta
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘coda’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘MASS’ ‘coda’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Depends: includes the non-default packages:
  'lattice', 'locfit', 'maptools', 'quantreg', 'RANN', 'SparseM'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' call to ‘lattice’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘RColorBrewer’ ‘car’ ‘spatstat’ ‘spdep’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘RANN’ ‘maptools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  anova.mdm
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
anova.mdm : <anonymous>: no visible global function definition for
  ‘formula’
anova.mdm : <anonymous>: no visible global function definition for
  ‘deviance’
anova.mdm: no visible global function definition for ‘pchisq’
entropy.plot: no visible global function definition for ‘plot’
entropy.plot: no visible global function definition for ‘axis’
entropy.plot: no visible global function definition for ‘box’
entropy.plot: no visible global function definition for ‘segments’
entropy.plot: no visible global function definition for ‘points’
mdm: no visible global function definition for ‘model.matrix’
mdm: no visible global function definition for ‘model.response’
mdm: no visible global function definition for ‘model.weights’
mdm: no visible global function definition for ‘model.offset’
mdm: no visible binding for global variable ‘weighted.mean’
mdm: no visible global function definition for ‘.getXlevels’
simdata: no visible global function definition for ‘rainbow’
simdata: no visible global function definition for ‘runif’
simdata: no visible global function definition for ‘rpois’
simdata: no visible global function definition for ‘rnorm’
simdata: no visible global function definition for ‘matplot’
simdata: no visible global function definition for ‘rug’
Undefined global functions or variables:
  .getXlevels axis box deviance formula matplot model.matrix
  model.offset model.response model.weights pchisq plot points rainbow
  rnorm rpois rug runif segments weighted.mean
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "box", "matplot", "plot", "points",
             "rug", "segments")
  importFrom("stats", ".getXlevels", "deviance", "formula",
             "model.matrix", "model.offset", "model.response",
             "model.weights", "pchisq", "rnorm", "rpois", "runif",
             "weighted.mean")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘AUTHORS’
Authors information should be in file inst/AUTHORS
conf.interval: no visible global function definition for ‘pbinom’
conf.statement: no visible global function definition for ‘pbinom’
Undefined global functions or variables:
  pbinom
Consider adding
  importFrom("stats", "pbinom")
to your NAMESPACE file.
Depends: includes the non-default packages:
  'seqinr', 'pcaMethods', 'Matrix', 'ROCR', 'Hmisc', 'KernSmooth',
  'seqLogo'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  ‘Hmisc’ ‘KernSmooth’ ‘Matrix’ ‘ROCR’ ‘methods’ ‘pcaMethods’ ‘seqLogo’
  ‘seqinr’
  Please remove these calls from your code.
Rd file 'MEET.Rd':
  \usage lines wider than 90 characters:
     MEET(TF,nameTF, seqin, alg, method, mode, org, vector, num_motif, len_motif, direction, threshold, order, model,position, mv, gapopen,  ... [TRUNCATED]

Rd file 'MIread.Rd':
  \examples lines wider than 100 characters:
     test<-MIread(training.set=iicc[["a1"]]$Transcriptionfactor, val.set=iicc[["a1"]]$Transcriptionfactor[1,],iicc=model)

Rd file 'align.muscle.Rd':
  \usage lines wider than 90 characters:
     align.muscle(filein , fileout = "Sq.fa", gapopen = gapopen, maxiters = maxiters, gapextend = gapextend, call)

These lines will be truncated in the PDF manual.
.df: no visible global function definition for ‘logLik’
coef_simple: no visible global function definition for ‘coef’
fitall: no visible binding for global variable ‘as.formula’
fitbest: no visible binding for global variable ‘as.formula’
lmboot: no visible global function definition for ‘lm’
residuals.ensemble : <anonymous>: no visible global function definition
  for ‘resid’
residuals.ensemble : <anonymous>: no visible global function definition
  for ‘rstudent’
residuals.ensemble : <anonymous>: no visible global function definition
  for ‘fitted’
residuals.ensemble : <anonymous>: no visible global function definition
  for ‘influence.measures’
stdcoef: no visible global function definition for ‘coef’
stdcoef: no visible global function definition for ‘update’
summary.ensemble : <anonymous>: no visible global function definition
  for ‘logLik’
summary.ensemble : <anonymous>: no visible global function definition
  for ‘AIC’
summary.ensemble : <anonymous>: no visible global function definition
  for ‘fitted’
summary.resid_ensemble: no visible binding for global variable
  ‘rstudent’
summary.resid_ensemble: no visible global function definition for ‘sd’
summary.variable_ensemble: no visible global function definition for
  ‘sd’
Undefined global functions or variables:
  AIC as.formula coef fitted influence.measures lm logLik resid
  rstudent sd update
Consider adding
  importFrom("stats", "AIC", "as.formula", "coef", "fitted",
             "influence.measures", "lm", "logLik", "resid", "rstudent",
             "sd", "update")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘adegenet’ ‘geosphere’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  print.mgLandscape
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
workspace_management : tellme: no visible global function definition
  for ‘file.edit’
workspace_management: no visible global function definition for
  ‘object.size’
Undefined global functions or variables:
  file.edit object.size
Consider adding
  importFrom("utils", "file.edit", "object.size")
to your NAMESPACE file.
dometa: no visible global function definition for ‘qchisq’
dometa: no visible global function definition for ‘median’
dometa: no visible global function definition for ‘pchisq’
forestplot: no visible global function definition for ‘pchisq’
forestplot: no visible global function definition for ‘qnorm’
forestplot: no visible global function definition for ‘plot’
forestplot: no visible global function definition for ‘points’
forestplot: no visible global function definition for ‘text’
metagwa.files: no visible global function definition for ‘read.csv’
metagwa.files: no visible global function definition for ‘write.csv’
metagwa.tables: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  median pchisq plot points qchisq qnorm read.csv text write.csv
Consider adding
  importFrom("graphics", "plot", "points", "text")
  importFrom("stats", "median", "pchisq", "qchisq", "qnorm")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
Rd file 'ht.Rd':
  \usage lines wider than 90 characters:
     ht(x, Rowv = NULL, Colv = if (symm) "Rowv" else NULL, distfun = dist, hclustfun = hclust, reorderfun = function(d, w) reorder(d, w), ad ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Packages required but not available: 'biomformat', 'phyloseq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages in Depends field not imported from:
  ‘gsl’ ‘rmeta’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
metacor.DSL: no visible global function definition for ‘qnorm’
metacor.DSL: no visible global function definition for ‘pnorm’
metacor.DSL: no visible global function definition for ‘metaplot’
metacor.OP: no visible global function definition for ‘hyperg_2F1’
metacor.OP: no visible global function definition for ‘qnorm’
metacor.OP: no visible global function definition for ‘pnorm’
metacor.OP: no visible global function definition for ‘metaplot’
Undefined global functions or variables:
  hyperg_2F1 metaplot pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
bcgVaccineData: no visible global function definition for ‘data’
bcgVaccineData: no visible global function definition for ‘qnorm’
hConfidence: no visible global function definition for ‘qchisq’
intervalEstimates_OneSgnf : crt: no visible global function definition
  for ‘qt’
intervalEstimates_OneSgnf: no visible binding for global variable
  ‘qnorm’
metagenGeneralised: no visible binding for global variable ‘quantile’
performancePointH : property: no visible global function definition for
  ‘var’
performancePointR : property: no visible global function definition for
  ‘var’
pfunc : pfun: no visible global function definition for ‘uniroot’
pivotalStream: no visible global function definition for ‘rchisq’
pivotalStream : <anonymous>: no visible global function definition for
  ‘rchisq’
pivotalStream: no visible global function definition for ‘rnorm’
rBinomGauss: no visible global function definition for ‘rnorm’
rBinomGauss: no visible global function definition for ‘rbinom’
rD: no visible global function definition for ‘rchisq’
rY: no visible global function definition for ‘rnorm’
render: no visible global function definition for ‘pdf’
render: no visible global function definition for ‘dev.off’
renderSVG: no visible global function definition for ‘svg’
renderSVG: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  data dev.off pdf qchisq qnorm qt quantile rbinom rchisq rnorm svg
  uniroot var
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "svg")
  importFrom("stats", "qchisq", "qnorm", "qt", "quantile", "rbinom",
             "rchisq", "rnorm", "uniroot", "var")
  importFrom("utils", "data")
to your NAMESPACE file.
EScombination: no visible global function definition for ‘model.matrix’
EScombination: no visible global function definition for ‘p.adjust’
EScombination: no visible global function definition for ‘pt’
EScombination.paired: no visible global function definition for
  ‘p.adjust’
EScombination.paired: no visible global function definition for ‘pt’
calcfit2Diffrep: no visible global function definition for
  ‘model.matrix’
directEScombi: no visible global function definition for ‘pnorm’
directEScombi: no visible global function definition for ‘p.adjust’
directpvalcombi : fstatmeta: no visible global function definition for
  ‘qnorm’
directpvalcombi: no visible global function definition for ‘pnorm’
directpvalcombi: no visible global function definition for ‘p.adjust’
pvalcombination: no visible global function definition for
  ‘model.matrix’
pvalcombination: no visible global function definition for ‘p.adjust’
pvalcombination: no visible global function definition for ‘pt’
pvalcombination.paired: no visible global function definition for
  ‘p.adjust’
pvalcombination.paired: no visible global function definition for ‘pt’
Undefined global functions or variables:
  model.matrix p.adjust pnorm pt qnorm
Consider adding
  importFrom("stats", "model.matrix", "p.adjust", "pnorm", "pt", "qnorm")
to your NAMESPACE file.
gimli.5277hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.10882hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.18398hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.25494hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.20822hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.27164hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.5396hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.15442hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.21908hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
MAPE: no visible global function definition for ‘is’
MAPE: no visible global function definition for ‘new’
Undefined global functions or variables:
  is new
Consider adding
  importFrom("methods", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package suggested but not available for checking: ‘doSMP’
Package in Depends field not imported from: ‘foreach’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  ‘pcaPP:::l1median_HoCr’ ‘pcaPP:::l1median_VaZh’
  See the note in ?`:::` about the use of this operator.
prepare_Rd: DropDupGenes.Rd:29-31: Dropping empty section \details
prepare_Rd: DropDupGenes.Rd:41-43: Dropping empty section \note
prepare_Rd: DropDupGenes.Rd:47-49: Dropping empty section \seealso
prepare_Rd: MetaPCA-package.Rd:29-30: Dropping empty section \seealso
prepare_Rd: MetaPCA.Rd:76-78: Dropping empty section \details
prepare_Rd: MetaPCA.Rd:88-90: Dropping empty section \note
prepare_Rd: MetaPCA.Rd:94-96: Dropping empty section \seealso
prepare_Rd: PlotPC2D.Rd:80-82: Dropping empty section \details
prepare_Rd: PlotPC2D.Rd:92-94: Dropping empty section \note
prepare_Rd: PlotPC2D.Rd:98-100: Dropping empty section \seealso
prepare_Rd: PreprocessMetaAnalysis.Rd:39-41: Dropping empty section \details
prepare_Rd: PreprocessMetaAnalysis.Rd:51-53: Dropping empty section \note
prepare_Rd: PreprocessMetaAnalysis.Rd:57-59: Dropping empty section \seealso
prepare_Rd: requireAll.Rd:19-21: Dropping empty section \details
prepare_Rd: requireAll.Rd:31-33: Dropping empty section \note
prepare_Rd: requireAll.Rd:25-27: Dropping empty section \references
prepare_Rd: requireAll.Rd:37-39: Dropping empty section \seealso
'library' or 'require' call to ‘survival’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘foreach’ ‘iterators’ ‘proto’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  plot.proto print.proto
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
fishercomb: no visible global function definition for ‘pchisq’
fishercomb: no visible global function definition for ‘p.adjust’
invnorm : <anonymous>: no visible global function definition for
  ‘qnorm’
invnorm: no visible global function definition for ‘pnorm’
invnorm: no visible global function definition for ‘p.adjust’
sim.function : <anonymous>: no visible global function definition for
  ‘rnorm’
sim.function : <anonymous>: no visible global function definition for
  ‘rnbinom’
Undefined global functions or variables:
  p.adjust pchisq pnorm qnorm rnbinom rnorm
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "pnorm", "qnorm", "rnbinom",
             "rnorm")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  print.metatest summary.metatest
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
estim: no visible global function definition for ‘var’
metareg: no visible global function definition for ‘pchisq’
metareg: no visible global function definition for ‘pnorm’
metareg: no visible global function definition for ‘pt’
metatest: no visible global function definition for ‘model.matrix’
metatest: no visible global function definition for ‘model.response’
permute: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  model.matrix model.response pchisq pnorm pt rbinom var
Consider adding
  importFrom("stats", "model.matrix", "model.response", "pchisq",
             "pnorm", "pt", "rbinom", "var")
to your NAMESPACE file.
fit.bivar: no visible binding for global variable ‘binomial’
summary.fit.bivar: no visible global function definition for ‘qt’
summary.fit.bivar: no visible global function definition for ‘pt’
Undefined global functions or variables:
  binomial pt qt
Consider adding
  importFrom("stats", "binomial", "pt", "qt")
to your NAMESPACE file.
crosssection: no visible global function definition for
  ‘colorRampPalette’
crosssection: no visible global function definition for
  ‘filled.contour’
crosssection: no visible global function definition for ‘axis’
crosssection: no visible global function definition for ‘par’
crosssection: no visible global function definition for ‘contour’
temperatures: no visible binding for global variable ‘time’
Undefined global functions or variables:
  axis colorRampPalette contour filled.contour par time
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "contour", "filled.contour", "par")
  importFrom("stats", "time")
to your NAMESPACE file.
'library' or 'require' call to ‘nlme’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘BRugs’ ‘R2WinBUGS’ ‘coda’ ‘rjags’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘nlme’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘nlme:::VarCorr’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘VC.est.fixed’ ‘VC.est.random’
Found the following apparent S3 methods exported but not registered:
  plot.VarComp
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
getdata: no visible global function definition for ‘read.csv’
plotdata: no visible global function definition for ‘head’
Undefined global functions or variables:
  head read.csv
Consider adding
  importFrom("utils", "head", "read.csv")
to your NAMESPACE file.
RUVRand: no visible global function definition for ‘barplot’
RUVRand: no visible global function definition for ‘prcomp’
RuvRandIter: no visible global function definition for ‘kmeans’
RuvRandIter: no visible global function definition for ‘barplot’
RuvRandIter: no visible global function definition for ‘prcomp’
opt: no visible global function definition for ‘optim’
printdata: no visible global function definition for ‘head’
Undefined global functions or variables:
  barplot head kmeans optim prcomp
Consider adding
  importFrom("graphics", "barplot")
  importFrom("stats", "kmeans", "optim", "prcomp")
  importFrom("utils", "head")
to your NAMESPACE file.
Found the following significant warnings:
  binomial-twostage.cpp:78:4: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  binomial-twostage.cpp:280:4: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/mets.Rcheck/00install.out’ for details.
Packages in Depends field not imported from:
  ‘MASS’ ‘abind’ ‘pls’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
show,mewTyp: no visible global function definition for ‘head’
Undefined global functions or variables:
  head
Consider adding
  importFrom("utils", "head")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  print.KPlus1.statis.compromise print.KPlus1.statis.innerproduct
  print.KPlus1.statis.overview print.KPlus1.statis.table
  print.covstatis.compromise print.covstatis.innerproduct
  print.covstatis.overview print.covstatis.table
  print.distatis.compromise print.distatis.innerproduct
  print.distatis.overview print.distatis.table
  print.doact.statis.compromise print.doact.statis.innerproduct
  print.doact.statis.table print.mexPosition.Output print.mpANISOSTATIS
  print.mpCOVSTATIS print.mpDISTATIS print.mpDOACT.STATIS
  print.mpGraphs print.mpKPlus1STATIS print.mpSTATIS
  print.statis.compromise print.statis.innerproduct
  print.statis.overview print.statis.table
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-16

Killed
Found the following apparent S3 methods exported but not registered:
  print.betamfx print.betaor print.logitmfx print.logitor
  print.negbinirr print.negbinmfx print.poissonirr print.poissonmfx
  print.probitmfx
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
maglm: no visible global function definition for ‘combn’
maglm: no visible global function definition for ‘glm’
maglm: no visible global function definition for ‘logLik’
mamglm: no visible global function definition for ‘combn’
mamglm: no visible global function definition for ‘logLik’
ses.maglm: no visible global function definition for ‘rnorm’
ses.maglm: no visible binding for global variable ‘sd’
ses.mamglm: no visible global function definition for ‘rnorm’
ses.mamglm: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  combn glm logLik rnorm sd
Consider adding
  importFrom("stats", "glm", "logLik", "rnorm", "sd")
  importFrom("utils", "combn")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘corpcor’ ‘evd’ ‘fields’ ‘numDeriv’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Non-standard file/directory found at top level:
  ‘Rplots.pdf’
Found the following apparent S3 methods exported but not registered:
  barmap.default boxmap.default dotmap.default histmap.default
  linemap.default map.default piemap.default plot.barmap plot.boxmap
  plot.dotmap plot.histmap plot.linemap plot.map plot.piemap
  plot.scattermap print.barmap print.boxmap print.dotmap print.histmap
  print.linemap print.map print.piemap print.scattermap
  scattermap.default summary.barmap summary.boxmap summary.dotmap
  summary.histmap summary.linemap summary.map summary.piemap
  summary.scattermap
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'map.Rd':
  \examples lines wider than 100 characters:
     graph=map(source,layer=layer,attribute='PlantPop',type="points",label="Plant population",col="green")

These lines will be truncated in the PDF manual.
'library' or 'require' call to ‘RJSONIO’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.onAttach: no visible global function definition for ‘packageVersion’
.onAttach: no visible binding for global variable ‘.MGRAST’
build.MGRAST: no visible binding for global variable ‘.MGRAST’
build.MGRAST: no visible global function definition for ‘fromJSON’
call.MGRAST: no visible binding for global variable ‘.MGRAST’
call.MGRAST: no visible global function definition for ‘download.file’
call.MGRAST: no visible global function definition for ‘isValidJSON’
call.MGRAST: no visible global function definition for ‘fromJSON’
doc.MGRAST: no visible binding for global variable ‘.MGRAST’
doc.MGRAST: no visible global function definition for ‘str’
load.MGRAST: no visible binding for global variable ‘.MGRAST’
parse.MGRAST: no visible binding for global variable ‘.MGRAST’
this.package: no visible binding for global variable ‘.MGRAST’
Undefined global functions or variables:
  .MGRAST download.file fromJSON isValidJSON packageVersion str
Consider adding
  importFrom("utils", "download.file", "packageVersion", "str")
to your NAMESPACE file.
calc_z_var: no visible binding for global variable ‘median’
diffScore: no visible global function definition for ‘new’
diffScore: no visible global function definition for ‘model.matrix’
logNORMcdf: no visible global function definition for ‘pnorm’
mGSZ.adj.mean.std: no visible binding for global variable ‘sd’
pick.data.cols: no visible binding for global variable ‘var’
plotProfile: no visible binding for global variable ‘quantile’
plotProfile: no visible global function definition for ‘plot’
plotProfile: no visible global function definition for ‘lines’
plotProfile: no visible global function definition for ‘legend’
Undefined global functions or variables:
  legend lines median model.matrix new plot pnorm quantile sd var
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("methods", "new")
  importFrom("stats", "median", "model.matrix", "pnorm", "quantile",
             "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
BCI: no visible global function definition for ‘quantile’
Metro_Hastings: no visible global function definition for ‘optim’
Metro_Hastings: no visible global function definition for ‘runif’
Metro_Hastings: no visible global function definition for ‘var’
plotMH: no visible global function definition for ‘hist’
plotMH: no visible global function definition for ‘plot’
plotMH: no visible global function definition for ‘frame’
plotMH: no visible global function definition for ‘text’
Undefined global functions or variables:
  frame hist optim plot quantile runif text var
Consider adding
  importFrom("graphics", "frame", "hist", "plot", "text")
  importFrom("stats", "optim", "quantile", "runif", "var")
to your NAMESPACE file.
.snqProfitImposeConvexityStEr: no visible global function definition
  for ‘runif’
predict.snqProfitEst: no visible global function definition for
  ‘model.matrix’
predict.snqProfitEst: no visible global function definition for ‘qt’
predict.snqProfitEst: no visible global function definition for
  ‘df.residual’
predict.snqProfitEst: no visible global function definition for
  ‘residuals’
snqProfitCoef: no visible global function definition for ‘pt’
snqProfitEla: no visible global function definition for ‘pt’
snqProfitEst: no visible global function definition for ‘as.formula’
snqProfitEst: no visible global function definition for ‘coef’
snqProfitEst: no visible global function definition for ‘vcov’
snqProfitEst: no visible global function definition for ‘fitted’
snqProfitEst: no visible global function definition for ‘df.residual’
snqProfitImposeConvexity: no visible global function definition for
  ‘optim’
snqProfitSystem: no visible global function definition for ‘as.formula’
Undefined global functions or variables:
  as.formula coef df.residual fitted model.matrix optim pt qt residuals
  runif vcov
Consider adding
  importFrom("stats", "as.formula", "coef", "df.residual", "fitted",
             "model.matrix", "optim", "pt", "qt", "residuals", "runif",
             "vcov")
to your NAMESPACE file.
src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_LIBS but not in PKG_CXXFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
Package suggested but not available for checking: ‘microcontax.data’
Package unavailable to check Rd xrefs: ‘microcontax.data’
runMicrosamplingDesignApp: warning in dev_package_deps(pkg =
  system.file(package = "microsamplingDesign"), dependencies =
  "Suggests"): partial argument match of ‘pkg’ to ‘pkgdir’
Non-standard file/directory found at top level:
  ‘MicroStrategyR-Ex.R’
'library' or 'require' call to ‘gWidgetsRGtk2’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘gWidgetsRGtk2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages in Depends field not imported from:
  ‘SDMTools’ ‘raster’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
MigClim.genClust: no visible global function definition for ‘raster’
MigClim.migrate: no visible global function definition for ‘raster’
MigClim.migrate: no visible global function definition for
  ‘dataframe2asc’
MigClim.migrate: no visible global function definition for
  ‘writeRaster’
MigClim.migrate: no visible global function definition for ‘cellStats’
MigClim.migrate: no visible global function definition for ‘read.table’
MigClim.migrate: no visible global function definition for
  ‘write.table’
MigClim.plot: no visible global function definition for ‘raster’
MigClim.plot: no visible global function definition for ‘rainbow’
MigClim.plot: no visible global function definition for ‘jpeg’
MigClim.plot: no visible global function definition for ‘ymax’
MigClim.plot: no visible global function definition for ‘ymin’
MigClim.plot: no visible global function definition for ‘xmax’
MigClim.plot: no visible global function definition for ‘xmin’
MigClim.plot: no visible global function definition for ‘image’
MigClim.plot: no visible global function definition for ‘dev.off’
MigClim.plot: no visible global function definition for ‘png’
MigClim.plot: no visible global function definition for ‘dev.new’
MigClim.plot: no visible global function definition for ‘plot’
Undefined global functions or variables:
  cellStats dataframe2asc dev.new dev.off image jpeg plot png rainbow
  raster read.table write.table writeRaster xmax xmin ymax ymin
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "jpeg", "png", "rainbow")
  importFrom("graphics", "image", "plot")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
File ‘MigClim/libs/MigClim.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Objects: ‘genclust.o’, ‘migrate.o’, ‘src_cell.o’, ‘validate.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Objects: ‘genclust.o’, ‘migrate.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
migration.cv.in : <anonymous>: no visible global function definition
  for ‘sd’
migration.cv.out : <anonymous>: no visible global function definition
  for ‘sd’
migration.field.diagram: no visible global function definition for
  ‘plot’
migration.field.diagram: no visible global function definition for
  ‘lines’
migration.field.diagram: no visible global function definition for
  ‘text’
migration.field.diagram: no visible global function definition for
  ‘polygon’
migration.field.diagram: no visible global function definition for ‘lm’
migration.field.diagram: no visible global function definition for
  ‘predict’
migration.field.diagram: no visible global function definition for
  ‘points’
migration.field.diagram: no visible global function definition for
  ‘resid’
migration.field.diagram: no visible global function definition for
  ‘coef’
migration.field.diagram: no visible global function definition for
  ‘mtext’
migration.field.diagram: no visible global function definition for
  ‘density’
migration.field.diagram: no visible global function definition for
  ‘rug’
migration.gini.col : <anonymous>: no visible global function definition
  for ‘dist’
migration.gini.in : <anonymous>: no visible global function definition
  for ‘dist’
migration.gini.out : <anonymous>: no visible global function definition
  for ‘dist’
migration.gini.row : <anonymous>: no visible global function definition
  for ‘dist’
migration.gini.total: no visible global function definition for ‘dist’
Undefined global functions or variables:
  coef density dist lines lm mtext plot points polygon predict resid
  rug sd text
Consider adding
  importFrom("graphics", "lines", "mtext", "plot", "points", "polygon",
             "rug", "text")
  importFrom("stats", "coef", "density", "dist", "lm", "predict",
             "resid", "sd")
to your NAMESPACE file.
.default_model: no visible global function definition for ‘is’
.guess_type: no visible global function definition for ‘is.ts’
.parse_trans: no visible binding for global variable ‘qnorm’
do_get_data_from_disk: no visible global function definition for
  ‘read.csv’
do_get_data_from_mi: no visible global function definition for ‘data’
do_get_data_from_r : <anonymous>: no visible global function definition
  for ‘is’
do_parametric_eval : <anonymous>: no visible global function definition
  for ‘dev.off’
do_parametric_eval : <anonymous>: no visible global function definition
  for ‘title’
do_var_options : varHandler2: no visible global function definition for
  ‘is’
do_var_options : varHandler3: no visible global function definition for
  ‘getClass’
do_var_options : varHandler3: no visible global function definition for
  ‘is’
do_var_options : changeHandler: no visible global function definition
  for ‘is’
do_var_options : <anonymous>: no visible global function definition for
  ‘title’
do_var_options: no visible global function definition for ‘getClass’
do_var_options: no visible global function definition for ‘is’
helpHandler: no visible global function definition for ‘browseURL’
is.method_in_mi: no visible global function definition for
  ‘selectMethod’
is.method_in_mi: no visible global function definition for ‘signature’
Undefined global functions or variables:
  browseURL data dev.off getClass is is.ts qnorm read.csv selectMethod
  signature title
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("graphics", "title")
  importFrom("methods", "getClass", "is", "selectMethod", "signature")
  importFrom("stats", "is.ts", "qnorm")
  importFrom("utils", "browseURL", "data", "read.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
nat_hist: no visible global function definition for ‘data’
nat_hist: no visible binding for global variable ‘current.other’
t_mal: no visible global function definition for ‘uniroot’
t_prog: no visible global function definition for ‘rlnorm’
tdeath_lung: no visible global function definition for ‘data’
tdeath_lung: no visible binding for global variable ‘ci.lung’
tdeath_lung: no visible binding for global variable ‘current.other’
tdeath_lung: no visible binding for global variable ‘former.other’
tdeath_lung: no visible binding for global variable ‘never.other’
tdeath_other: no visible global function definition for ‘data’
tdeath_other: no visible binding for global variable ‘ci.lung’
tdeath_other: no visible binding for global variable ‘current.other’
tdeath_other: no visible binding for global variable ‘former.other’
tdeath_other: no visible binding for global variable ‘never.other’
Undefined global functions or variables:
  ci.lung current.other data former.other never.other rlnorm uniroot
Consider adding
  importFrom("stats", "rlnorm", "uniroot")
  importFrom("utils", "data")
to your NAMESPACE file.
MImix.default: no visible binding for global variable ‘coef’
MImix.default: no visible binding for global variable ‘vcov’
MImix.one: no visible global function definition for ‘qnorm’
MImix.one: no visible global function definition for ‘uniroot’
mixcdf.target: no visible global function definition for ‘pnorm’
print.MImixresult: no visible global function definition for ‘coef’
print.MImixresult: no visible global function definition for ‘vcov’
summary.MImixresult: no visible global function definition for ‘coef’
summary.MImixresult: no visible global function definition for ‘vcov’
summary.MImixresult: no visible global function definition for ‘qt’
Undefined global functions or variables:
  coef pnorm qnorm qt uniroot vcov
Consider adding
  importFrom("stats", "coef", "pnorm", "qnorm", "qt", "uniroot", "vcov")
to your NAMESPACE file.
Rd file 'MImix.Rd':
  \usage lines wider than 90 characters:
     MImix(results,variances,weights = 1/length(results), percentiles = c(0.025, 0.5, 0.975), ...) 

These lines will be truncated in the PDF manual.
miney : plot.initial.matrix: no visible global function definition for
  ‘plot’
miney : plot.initial.matrix: no visible global function definition for
  ‘rect’
miney : plot.known.matrix: no visible global function definition for
  ‘plot’
miney : plot.known.matrix: no visible global function definition for
  ‘rect’
miney : plot.known.matrix: no visible global function definition for
  ‘text’
miney: no visible global function definition for ‘locator’
miney: no visible global function definition for ‘rect’
miney: no visible global function definition for ‘title’
Undefined global functions or variables:
  locator plot rect text title
Consider adding
  importFrom("graphics", "locator", "plot", "rect", "text", "title")
to your NAMESPACE file.
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but not in PKG_CFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
rminimax: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘parallel’ ‘snowfall’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  summary.minPtest
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
read_design: no visible global function definition for ‘model.frame’
read_design: no visible global function definition for ‘read.table’
read_design: no visible global function definition for ‘model.matrix’
read_response: no visible global function definition for ‘read.table’
update_beta: no visible global function definition for ‘update’
update_beta: no visible global function definition for ‘glm’
update_beta: no visible global function definition for ‘poisson’
Undefined global functions or variables:
  glm model.frame model.matrix poisson read.table update
Consider adding
  importFrom("stats", "glm", "model.frame", "model.matrix", "poisson",
             "update")
  importFrom("utils", "read.table")
to your NAMESPACE file.
minxent.multiple: no visible global function definition for ‘cov.wt’
minxent.single: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  cov.wt optimize
Consider adding
  importFrom("stats", "cov.wt", "optimize")
to your NAMESPACE file.
Rd file 'minxent.multiple.Rd':
  \examples lines wider than 100 characters:
     minxent.multiple(q=q,G=G,eta=eta,c(0,0)) #estimates of lagrangian multipliers and MinxEnt distribution

Rd file 'minxent.single.Rd':
  \examples lines wider than 100 characters:
     minxent.single(q=q,G=G,eta=eta,c(0)) # estimate of lagrangian multipliers and Kullback minimimum cross entropy distribution

These lines will be truncated in the PDF manual.
cdf.pval: no visible global function definition for ‘median’
cdf.pval: no visible binding for global variable ‘ecdf’
find_hits: no visible global function definition for ‘na.omit’
mad.scores: no visible global function definition for ‘as.formula’
mad.scores: no visible binding for global variable ‘median’
mad.scores: no visible binding for global variable ‘mad’
rm.outliers: no visible global function definition for ‘as.formula’
rm.outliers: no visible binding for global variable ‘median’
rm.outliers: no visible binding for global variable ‘mad’
Undefined global functions or variables:
  as.formula ecdf mad median na.omit
Consider adding
  importFrom("stats", "as.formula", "ecdf", "mad", "median", "na.omit")
to your NAMESPACE file.

Found the following calls to attach():
File ‘MIPHENO/R/cdf.pval.R’:
  attach(sample.cdf)
See section ‘Good practice’ in ‘?attach’.
.FCLoess: no visible global function definition for ‘loess’
.FCLoessM: no visible global function definition for ‘loess’
.FCLoessM: no visible global function definition for ‘median’
.Import.Luminex: no visible global function definition for ‘read.csv’
.Intra.Me: no visible global function definition for ‘sd’
.Intra.Me: no visible global function definition for ‘quantile’
.Intra.Me: no visible global function definition for ‘qchisq’
.Intra.Median: no visible global function definition for ‘median’
.boxplot.rtprofile: no visible global function definition for ‘boxplot’
.denplot: no visible global function definition for ‘plot’
.denplot: no visible global function definition for ‘density’
.denplot: no visible global function definition for ‘abline’
.normalize.Luminex: no visible global function definition for ‘sd’
.normalize.qrtpcr: no visible global function definition for ‘density’
.validate.default: no visible global function definition for ‘t.test’
Undefined global functions or variables:
  abline boxplot density loess median plot qchisq quantile read.csv sd
  t.test
Consider adding
  importFrom("graphics", "abline", "boxplot", "plot")
  importFrom("stats", "density", "loess", "median", "qchisq", "quantile",
             "sd", "t.test")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
fisher.combination: no visible global function definition for ‘pchisq’
gs.test: no visible global function definition for ‘ks.test’
gs.test: no visible global function definition for ‘wilcox.test’
gs.test: no visible global function definition for ‘fisher.test’
inverse.normal.combination: no visible global function definition for
  ‘qnorm’
inverse.normal.combination: no visible global function definition for
  ‘pnorm’
limma.one.sided: no visible global function definition for ‘pt’
Undefined global functions or variables:
  fisher.test ks.test pchisq pnorm pt qnorm wilcox.test
Consider adding
  importFrom("stats", "fisher.test", "ks.test", "pchisq", "pnorm", "pt",
             "qnorm", "wilcox.test")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘rgl’ ‘tkrplot’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘canonicalizeAndMergeScene’ ‘colorScene’ ‘t2ve’ ‘vertexNormals’
  ‘vertexTriangles’
Found the following significant warnings:
  simcensor.cpp:91:16: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:91:41: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:95:17: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/missDeaths.Rcheck/00install.out’ for details.
missForest: no visible global function definition for ‘predict’
missForest: no visible global function definition for ‘idiv’
missForest: no visible global function definition for ‘var’
nrmse: no visible global function definition for ‘var’
Undefined global functions or variables:
  idiv predict var
Consider adding
  importFrom("stats", "predict", "var")
to your NAMESPACE file.
AndersonDarling: no visible global function definition for ‘spline’
Hawkins: no visible global function definition for ‘cov’
Hawkins: no visible global function definition for ‘pf’
Impute: no visible global function definition for ‘cov’
Mimpute: no visible global function definition for ‘rnorm’
SimNey: no visible global function definition for ‘runif’
TestMCARNormality: no visible global function definition for ‘cov’
TestMCARNormality: no visible global function definition for ‘pchisq’
TestUNey: no visible global function definition for ‘pchisq’
boxplot.testhomosc: no visible global function definition for ‘par’
boxplot.testhomosc: no visible global function definition for ‘title’
boxplot.testhomosc: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline cov par pchisq pf rnorm runif spline title
Consider adding
  importFrom("graphics", "abline", "par", "title")
  importFrom("stats", "cov", "pchisq", "pf", "rnorm", "runif", "spline")
to your NAMESPACE file.
'library' or 'require' call to ‘CompQuadForm’ which was already attached by Depends.
  Please remove these calls from your code.
linear.test: no visible global function definition for ‘lm’
linear.test: no visible global function definition for ‘pchisq’
linear.weight.test: no visible global function definition for ‘lm’
linear.weight.test: no visible global function definition for ‘dbeta’
linear.weight.test: no visible global function definition for ‘pchisq’
logit.test: no visible global function definition for ‘glm’
logit.test: no visible global function definition for ‘binomial’
logit.test: no visible binding for global variable ‘logit’
logit.test: no visible global function definition for ‘pchisq’
logit.weight.test: no visible global function definition for ‘glm’
logit.weight.test: no visible global function definition for ‘binomial’
logit.weight.test: no visible binding for global variable ‘logit’
logit.weight.test: no visible global function definition for ‘dbeta’
logit.weight.test: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  binomial dbeta glm lm logit pchisq
Consider adding
  importFrom("stats", "binomial", "dbeta", "glm", "lm", "pchisq")
to your NAMESPACE file.
MIcombine.default: no visible binding for global variable ‘vcov’
MIcombine.default: no visible binding for global variable ‘coef’
MIcombine.default: no visible global function definition for ‘var’
MIcombine.imputationResultList: no visible binding for global variable
  ‘vcov’
MIcombine.imputationResultList: no visible binding for global variable
  ‘coef’
close.DBimputationList: no visible global function definition for ‘is’
getvars: no visible global function definition for ‘is’
print.MIresult: no visible global function definition for ‘coef’
print.MIresult: no visible global function definition for ‘vcov’
summary.MIresult: no visible global function definition for ‘coef’
summary.MIresult: no visible global function definition for ‘vcov’
summary.MIresult: no visible global function definition for ‘qt’
Undefined global functions or variables:
  coef is qt var vcov
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "coef", "qt", "var", "vcov")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
gimli.29798hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Packages in Depends field not imported from:
  ‘MASS’ ‘RODBC’ ‘tcltk’ ‘tcltk2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fit.mixtNB: no visible global function definition for ‘dnbinom’
fit.mixtNB: no visible global function definition for ‘nlminb’
wald.test: no visible global function definition for ‘pnorm’
wald.test: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  dnbinom nlminb p.adjust pnorm
Consider adding
  importFrom("stats", "dnbinom", "nlminb", "p.adjust", "pnorm")
to your NAMESPACE file.
computeContourValues: no visible global function definition for
  ‘na.omit’
deselectNonMovementSteps : coOccurProb: no visible global function
  definition for ‘dnorm’
deselectNonMovementSteps: no visible global function definition for
  ‘pnorm’
estVarMKDE: no visible global function definition for ‘na.omit’
estVarMKDE: no visible global function definition for ‘qnorm’
estVarMKDE: no visible global function definition for ‘optimize’
plotMKDE: no visible global function definition for ‘rainbow’
Undefined global functions or variables:
  dnorm na.omit optimize pnorm qnorm rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("stats", "dnorm", "na.omit", "optimize", "pnorm", "qnorm")
to your NAMESPACE file.
mkle: no visible global function definition for ‘sd’
mkle: no visible global function definition for ‘density’
mkle: no visible global function definition for ‘optimize’
mkle.ci: no visible global function definition for ‘sd’
mkle.ci: no visible binding for global variable ‘var’
mkle.ci: no visible global function definition for ‘quantile’
mkle.ci: no visible global function definition for ‘qnorm’
opt.bw: no visible global function definition for ‘sd’
opt.bw : mse: no visible global function definition for ‘var’
opt.bw: no visible global function definition for ‘optimize’
opt.bw: no visible global function definition for ‘var’
Undefined global functions or variables:
  density optimize qnorm quantile sd var
Consider adding
  importFrom("stats", "density", "optimize", "qnorm", "quantile", "sd",
             "var")
to your NAMESPACE file.
mkssd: no visible global function definition for ‘txtProgressBar’
mkssd: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘Data-Administration.R’
'library' or 'require' calls in package code:
  ‘cairoDevice’ ‘gplots’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  ‘MASS:::lda.default’ ‘MASS:::qda.default’
  ‘e1071:::naiveBayes.default’ ‘e1071:::svm.default’
  ‘randomForest:::randomForest.default’
  See the note in ?`:::` about the use of this operator.
confusionBarplot: no visible global function definition for ‘par’
confusionBarplot: no visible global function definition for ‘barplot’
confusionBarplot: no visible global function definition for ‘lines’
confusionBarplot: no visible global function definition for ‘text’
confusionBarplot: no visible global function definition for ‘legend’
confusionBarplot: no visible global function definition for ‘axis’
confusionDendrogram: no visible global function definition for ‘plot’
confusionImage: no visible global function definition for ‘par’
confusionImage: no visible global function definition for ‘image’
confusionImage: no visible global function definition for ‘text’
confusionImage: no visible global function definition for ‘abline’
confusionImage: no visible global function definition for ‘axis’
confusionImage: no visible global function definition for ‘plot’
confusionImage: no visible global function definition for ‘mtext’
confusionStars: no visible global function definition for ‘par’
confusionStars: no visible global function definition for ‘stars’
confusionStars: no visible global function definition for ‘rect’
plot.mlearning: no visible global function definition for ‘plot’
Undefined global functions or variables:
  abline axis barplot image legend lines mtext par plot rect stars text
Consider adding
  importFrom("graphics", "abline", "axis", "barplot", "image", "legend",
             "lines", "mtext", "par", "plot", "rect", "stars", "text")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘CONTENTS’
dftest: no visible global function definition for ‘slot’
mctest: no visible global function definition for ‘rnorm’
mleurDiag: no visible global function definition for ‘acf’
mleurDiag: no visible global function definition for ‘pchisq’
mleurDiag: no visible global function definition for ‘par’
mleurDiag: no visible global function definition for ‘boxplot’
mleurDiag: no visible global function definition for ‘shapiroTest’
mleurDiag: no visible global function definition for ‘title’
mleurDiag: no visible global function definition for ‘abline’
mleurDiag: no visible global function definition for ‘lines’
simar1: no visible global function definition for ‘rnorm’
simar1: no visible global function definition for ‘rt’
simar1: no visible global function definition for ‘convolve’
Undefined global functions or variables:
  abline acf boxplot convolve lines par pchisq rnorm rt shapiroTest
  slot title
Consider adding
  importFrom("graphics", "abline", "boxplot", "lines", "par", "title")
  importFrom("methods", "slot")
  importFrom("stats", "acf", "convolve", "pchisq", "rnorm", "rt")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Non-standard file/directory found at top level:
  ‘CHANGELOG.txt’
Packages in Depends field not imported from:
  ‘methods’ ‘seqinr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CheckStability: no visible global function definition for ‘cor’
CheckStability: no visible global function definition for ‘var’
PriorNormPCA: no visible global function definition for ‘barplot’
SortModes: no visible global function definition for ‘rnorm’
mlicaMAIN: no visible global function definition for ‘runif’
Undefined global functions or variables:
  barplot cor rnorm runif var
Consider adding
  importFrom("graphics", "barplot")
  importFrom("stats", "cor", "rnorm", "runif", "var")
to your NAMESPACE file.
Rd file 'SortModes.Rd':
  \examples lines wider than 100 characters:
             # A) Computation of relative data power. Store values in vector of size H=ncp. Could use different criterion here.

Rd file 'mlica.rd':
  \examples lines wider than 100 characters:
                 print("Consider either increasing the threshold for pca eigenvalues to perform ICA on a smaller subspace or increasing maxi ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Packages suggested but not available for checking:
  'minfi', 'wateRmelon', 'IlluminaHumanMethylation450kmanifest'
Error in re-building vignettes:
  ...
Quitting from lines 73-77 (vignette.Rmd) 
Error: processing vignette ‘vignette.Rmd’ failed with diagnostics:
there is no package called 'minfi'
Execution halted
Packages in Depends field not imported from:
  ‘BMA’ ‘abind’ ‘maxLik’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
listGenoToTable: no visible binding for global variable ‘dummy’
Undefined global functions or variables:
  dummy

Found the following assignments to the global environment:
File ‘mlPhaser/R/mlPhaser.R’:
  assign("validHaploGroups", c(get("validHaploGroups", globalenv()), 
    groupStoreList), globalenv())
  assign("validHaploGroups", list(), globalenv())
Rd file 'phaseReport.Rd':
  \examples lines wider than 100 characters:
     phaseReport(my.genotypes,haplotypes, haploFreqs, outFormat="all")       # outFormat="all" is the default

These lines will be truncated in the PDF manual.
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/MM2Sdata.Rnw’
(Is a VignetteBuilder field missing?)
File which contains pragma(s) suppressing diagnostics:
  ‘src/lemon/core.h’
mmm2: no visible global function definition for ‘model.frame’
mmm2: no visible global function definition for ‘model.matrix’
mmm2: no visible global function definition for ‘model.response’
mmm2: no visible global function definition for ‘as.formula’
Undefined global functions or variables:
  as.formula model.frame model.matrix model.response
Consider adding
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response")
to your NAMESPACE file.
mmm: no visible global function definition for ‘model.frame’
mmm: no visible global function definition for ‘model.matrix’
mmm: no visible global function definition for ‘model.response’
mmm: no visible global function definition for ‘as.formula’
mmm: no visible global function definition for ‘gee’
Undefined global functions or variables:
  as.formula gee model.frame model.matrix model.response
Consider adding
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response")
to your NAMESPACE file.
get.score: no visible global function definition for ‘sd’
get.score: no visible global function definition for ‘coef’
get.score: no visible global function definition for ‘as’
get.score.main: no visible global function definition for ‘sd’
get.score.main: no visible global function definition for ‘coef’
get.subgroup: no visible global function definition for ‘sd’
sample.tte: no visible global function definition for ‘runif’
Undefined global functions or variables:
  as coef runif sd
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "coef", "runif", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
sadmvng: no visible global function definition for ‘cov2cor’
sadmvng: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  cov2cor pnorm
Consider adding
  importFrom("stats", "cov2cor", "pnorm")
to your NAMESPACE file.
bin.by.date: no visible binding for global variable ‘quantile’
bin.by.date: no visible global function definition for ‘na.omit’
biplot: no visible global function definition for ‘na.omit’
biplot.character: no visible global function definition for ‘runif’
biplot.character: no visible global function definition for ‘opts’
biplot.character: no visible global function definition for
  ‘theme_blank’
distributionplot: no visible global function definition for ‘na.omit’
distributionplot.character: no visible global function definition for
  ‘head’
distributionplot.factor: no visible global function definition for
  ‘opts’
distributionplot.factor: no visible global function definition for
  ‘theme_text’
mapmobility: no visible global function definition for ‘lines’
responseplot: no visible global function definition for ‘na.omit’
scatterplot: no visible global function definition for ‘na.omit’
scatterplot: no visible global function definition for ‘opts’
scatterplot: no visible global function definition for ‘theme_text’
sharedtimeplot: no visible global function definition for ‘na.omit’
timeplot: no visible global function definition for ‘na.omit’
timeplot: no visible global function definition for ‘opts’
timeplot.character: no visible global function definition for ‘runif’
timeplot.character: no visible global function definition for ‘rnorm’
timeplot.character: no visible binding for global variable ‘text’
userplot: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  head lines na.omit opts quantile rnorm runif text theme_blank
  theme_text
Consider adding
  importFrom("graphics", "lines", "text")
  importFrom("stats", "na.omit", "quantile", "rnorm", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
'library' or 'require' call to ‘SparseM’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘glmnet’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘date’ ‘raster’ ‘rgdal’ ‘sfsmisc’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘date’ ‘raster’ ‘rgdal’ ‘sfsmisc’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.clustOrder: no visible global function definition for ‘hclust’
.clustOrder: no visible global function definition for ‘as.dist’
consensusMEDissimilarity: no visible global function definition for
  ‘cor’
mergeCloseModules: no visible global function definition for ‘cor’
mergeCloseModules: no visible global function definition for ‘hclust’
mergeCloseModules: no visible global function definition for ‘as.dist’
moduleEigengenes: no visible global function definition for ‘cor’
moduleEigengenes: no visible global function definition for ‘cov’
moduleNumber: no visible global function definition for ‘cutree’
orderMEs: no visible global function definition for ‘cor’
orderMEs: no visible global function definition for ‘as.dist’
plotHclustColors: no visible global function definition for ‘barplot’
plotHclustColors: no visible global function definition for ‘strwidth’
plotHclustColors: no visible global function definition for ‘rect’
plotHclustColors: no visible global function definition for ‘text’
plotHclustColors: no visible global function definition for ‘lines’
Undefined global functions or variables:
  as.dist barplot cor cov cutree hclust lines rect strwidth text
Consider adding
  importFrom("graphics", "barplot", "lines", "rect", "strwidth", "text")
  importFrom("stats", "as.dist", "cor", "cov", "cutree", "hclust")
to your NAMESPACE file.
agostino.test: no visible global function definition for
  ‘complete.cases’
agostino.test: no visible global function definition for ‘pnorm’
anscombe.test: no visible global function definition for
  ‘complete.cases’
anscombe.test: no visible global function definition for ‘pnorm’
bonett.test: no visible global function definition for ‘complete.cases’
bonett.test: no visible global function definition for ‘pnorm’
jarque.test: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  complete.cases pchisq pnorm
Consider adding
  importFrom("stats", "complete.cases", "pchisq", "pnorm")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from ‘mondate’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
.date.to.mondate: no visible global function definition for ‘new’
as.character.mondate: no visible global function definition for ‘slot’
Arith,array-mondate: no visible global function definition for
  ‘callGeneric’
Arith,mondate-array: no visible global function definition for
  ‘callGeneric’
Arith,mondate-mondate: no visible global function definition for
  ‘callGeneric’
Arith,mondate-numeric: no visible global function definition for
  ‘callGeneric’
Arith,numeric-mondate: no visible global function definition for
  ‘callGeneric’
Compare,mondate-ANY: no visible global function definition for
  ‘callGeneric’
Compare,mondate-ANY: no visible global function definition for
  ‘getDataPart’
Summary,mondate: no visible global function definition for
  ‘callGeneric’
[,mondate: no visible global function definition for ‘callNextMethod’
[,mondate: no visible global function definition for ‘new’
array,mondate: no visible global function definition for
  ‘callNextMethod’
as.numeric,mondate: no visible global function definition for ‘slot’
c,mondate: no visible global function definition for ‘new’
c,mondate: no visible binding for global variable ‘getDataPart’
c,mondate: no visible global function definition for ‘getDataPart’
matrix,mondate: no visible global function definition for
  ‘callNextMethod’
mondate,Date: no visible global function definition for ‘new’
mondate,POSIXt: no visible global function definition for ‘new’
mondate,missing: no visible global function definition for ‘new’
mondate,mondate: no visible global function definition for ‘new’
mondate,numeric: no visible global function definition for ‘new’
Undefined global functions or variables:
  callGeneric callNextMethod getDataPart new slot
Consider adding
  importFrom("methods", "callGeneric", "callNextMethod", "getDataPart",
             "new", "slot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Missing or unexported objects:
  ‘dplyr::base_agg’ ‘dplyr::base_scalar’ ‘dplyr::build_sql’
  ‘dplyr::is.ident’ ‘dplyr::sql_infix’ ‘dplyr::sql_prefix’
  ‘dplyr::sql_translator’ ‘dplyr::sql_variant’ ‘dplyr::src_sql’
  ‘dplyr::tbl_sql’
Found the following apparent S3 methods exported but not registered:
  format.dms format.jd format.time plot.apos plot.rst print.eqc
  print.jd print.time
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.apos: no visible global function definition for ‘plot’
plot.apos: no visible global function definition for ‘abline’
plot.apos: no visible global function definition for ‘text’
plot.rst: no visible global function definition for ‘matplot’
plot.rst: no visible global function definition for ‘abline’
plot.rst: no visible global function definition for ‘text’
track : background: no visible global function definition for ‘par’
track : background: no visible global function definition for ‘plot’
track : background: no visible global function definition for ‘axTicks’
track : background: no visible global function definition for ‘abline’
track : background: no visible global function definition for ‘box’
track : tracks: no visible global function definition for ‘lines’
track : magselect: no visible global function definition for ‘na.omit’
track : add.stars: no visible global function definition for ‘points’
track : addlab.eqc: no visible global function definition for ‘points’
track : addlab.eqc: no visible global function definition for ‘text’
track : add.planet: no visible global function definition for ‘text’
track : add.planet: no visible global function definition for ‘points’
track : add.ecliptic: no visible global function definition for ‘lines’
track : add.brightlab: no visible global function definition for ‘text’
track: no visible global function definition for ‘par’
track: no visible binding for global variable ‘axis’
track: no visible global function definition for ‘title’
Undefined global functions or variables:
  abline axTicks axis box lines matplot na.omit par plot points text
  title
Consider adding
  importFrom("graphics", "abline", "axTicks", "axis", "box", "lines",
             "matplot", "par", "plot", "points", "text", "title")
  importFrom("stats", "na.omit")
to your NAMESPACE file.
mopsocd : initialize_pop: no visible global function definition for
  ‘runif’
mopsocd : compute_velocity: no visible global function definition for
  ‘runif’
mopsocd : mutate: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
checkTH: no visible global function definition for ‘pchisq’
getOrderPval: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
ametrine : <anonymous>: no visible global function definition for
  ‘approx’
ametrine: no visible global function definition for ‘rgb’
isolum : <anonymous>: no visible global function definition for
  ‘approx’
isolum: no visible global function definition for ‘rgb’
morgenstemning : <anonymous>: no visible global function definition for
  ‘approx’
morgenstemning: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  approx rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "approx")
to your NAMESPACE file.
cor.gen: no visible global function definition for ‘rnorm’
cor.gen: no visible global function definition for ‘resid’
cor.gen: no visible global function definition for ‘lm’
cor.gen: no visible binding for global variable ‘sd’
cor.gen: no visible global function definition for ‘cor’
cor.gen: no visible global function definition for ‘write.table’
stat.gen: no visible global function definition for ‘rexp’
stat.gen: no visible global function definition for ‘rnorm’
stat.gen: no visible binding for global variable ‘sd’
stat.gen: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  cor lm resid rexp rnorm sd write.table
Consider adding
  importFrom("stats", "cor", "lm", "resid", "rexp", "rnorm", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Rd file 'cor.gen.Rd':
  \usage lines wider than 90 characters:
     cor.gen(num.subj, x.mean, x.sd, y.mean, y.sd, correlation, data.dec = 2, x.name = "Variable X", y.name = "Variable Y")

Rd file 'stat.gen.Rd':
  \usage lines wider than 90 characters:
     stat.gen(num.subj, target.mean, target.sd, data.dec = 2, neg.data = TRUE, x.name = "Variable X")

These lines will be truncated in the PDF manual.
Mort1Dsmooth: no visible global function definition for ‘time’
Mort1Dsmooth: no visible global function definition for ‘glm’
Mort1Dsmooth: no visible binding for global variable ‘poisson’
Mort1Dsmooth_optimize: no visible global function definition for
  ‘median’
Mort2Dsmooth: no visible global function definition for ‘glm’
Mort2Dsmooth: no visible binding for global variable ‘poisson’
Mort2Dsmooth: no visible global function definition for ‘median’
Mort2Dsmooth_optimize: no visible global function definition for
  ‘median’
plot.HMDdata: no visible global function definition for ‘plot’
plot.Mort1Dsmooth: no visible global function definition for ‘matplot’
plot.Mort2Dsmooth: no visible global function definition for ‘quantile’
predict.Mort1Dsmooth: no visible global function definition for ‘glm’
predict.Mort1Dsmooth: no visible binding for global variable ‘poisson’
predict.Mort2Dsmooth: no visible global function definition for ‘glm’
predict.Mort2Dsmooth: no visible binding for global variable ‘poisson’
print.summary.Mort1Dsmooth: no visible global function definition for
  ‘quantile’
print.summary.Mort2Dsmooth: no visible global function definition for
  ‘quantile’
Undefined global functions or variables:
  glm matplot median plot poisson quantile time
Consider adding
  importFrom("graphics", "matplot", "plot")
  importFrom("stats", "glm", "median", "poisson", "quantile", "time")
to your NAMESPACE file.
Running examples in ‘MoTBFs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MoTBFs_Learning
> ### Title: Learning MoTBFs in a Network
> ### Aliases: MoTBFs_Learning
> 
> ### ** Examples
> 
> ## Dataset Ecoli
> require(MoTBFs)
> data(ecoli)
> data <- ecoli[,-c(1)] ## remove variable sequence
> 
> ## Directed acyclic graph
> dag <- LearningHC(data)
> 
> ## Learning BN
> intervals <- 3
> potential <- "MOP"
> P1 <- MoTBFs_Learning(graph = dag, data = data, POTENTIAL_TYPE=potential,
+ maxParam = 5)
Error in conditionalMethod(data, Parents, Child, numIntervals, POTENTIAL_TYPE,  : 
  argument "numIntervals" is missing, with no default
Calls: MoTBFs_Learning ... learn.tree.Intervals -> quantileIntervals -> sapply -> lapply
Execution halted
getmouseDV: no visible global function definition for ‘tail’
interpltraj: no visible global function definition for ‘approx’
trim1: no visible global function definition for ‘tail’
Undefined global functions or variables:
  approx tail
Consider adding
  importFrom("stats", "approx")
  importFrom("utils", "tail")
to your NAMESPACE file.
Package suggested but not available for checking: ‘corpus.useR.2008.abstracts’
Error in re-building vignettes:
  ...
Warning: package 'corpus.useR.2008.abstracts' is not available (for R Under development)

Error: processing vignette ‘movMF.Rnw’ failed with diagnostics:
 chunk 3 (label = corpus-package) 
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'corpus.useR.2008.abstracts'
Execution halted
Non-standard file/directory found at top level:
  ‘mpa-Ex.R’
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘mpa/R/zzz.R’:
  .First.lib calls:
    cat("\n mpa: CoWords Method")
    cat("\n ")
    cat("\n Universidad Nacional de Colombia")
    cat("\n ")
    cat("\n Elaborado por: Daniel Rodriguez <dhrodriguezt@unal.edu.co>")
    cat("\n                Campo Elias Pardo <cepardot@unal.edu.co>")
    cat("\n For help: ?mpa   \n\n")

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

diagram.mpa: no visible global function definition for ‘plot’
diagram.mpa: no visible global function definition for ‘abline’
diagram.mpa: no visible global function definition for ‘text’
plotmpa: no visible global function definition for ‘plot’
Undefined global functions or variables:
  abline plot text
Consider adding
  importFrom("graphics", "abline", "plot", "text")
to your NAMESPACE file.
mpcv: no visible binding for global variable ‘median’
mpcv: no visible global function definition for ‘cov’
mpcv: no visible global function definition for ‘dist’
plot.mpcv: no visible binding for global variable ‘median’
plot.mpcv: no visible global function definition for ‘par’
plot.mpcv: no visible global function definition for ‘plot’
plot.mpcv: no visible global function definition for ‘rect’
plot.mpcv: no visible global function definition for ‘lines’
plot.mpcv: no visible global function definition for ‘points’
plot.mpcv: no visible global function definition for ‘legend’
Undefined global functions or variables:
  cov dist legend lines median par plot points rect
Consider adding
  importFrom("graphics", "legend", "lines", "par", "plot", "points",
             "rect")
  importFrom("stats", "cov", "dist", "median")
to your NAMESPACE file.
GetExampleData: no visible binding for global variable ‘MPINetData’
Getenvir: no visible binding for global variable ‘MPINetData’
getPSS: no visible global function definition for ‘lines’
performpcls: no visible global function definition for ‘binomial’
Undefined global functions or variables:
  MPINetData binomial lines
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "binomial")
to your NAMESPACE file.
'library' or 'require' call to ‘MASS’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘KernSmooth’ ‘MASS’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
export.summary.mpm: warning in complex(real = x$Rows[, FdimsR[1]], imag
  = x$Rows[, FdimsR[2]]): partial argument match of ‘imag’ to
  ‘imaginary’
export.summary.mpm: warning in complex(real = x$Columns[, FdimsC[1]],
  imag = x$Columns[, FdimsC[2]]): partial argument match of ‘imag’ to
  ‘imaginary’
.onAttach: no visible global function definition for
  ‘packageDescription’
export.summary.mpm: no visible global function definition for
  ‘write.table’
mpm: no visible binding for global variable ‘median’
plot.mpm: no visible global function definition for ‘rainbow’
plot.mpm: no visible global function definition for ‘quantile’
plot.mpm: no visible global function definition for ‘par’
plot.mpm: no visible global function definition for ‘points’
plot.mpm: no visible global function definition for ‘smoothScatter’
plot.mpm: no visible global function definition for ‘colorRampPalette’
plot.mpm: no visible global function definition for ‘symbols’
plot.mpm: no visible global function definition for ‘text’
plot.mpm: no visible global function definition for ‘lines’
plot.mpm: no visible global function definition for ‘box’
Undefined global functions or variables:
  box colorRampPalette lines median packageDescription par points
  quantile rainbow smoothScatter symbols text write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
  importFrom("graphics", "box", "lines", "par", "points",
             "smoothScatter", "symbols", "text")
  importFrom("stats", "median", "quantile")
  importFrom("utils", "packageDescription", "write.table")
to your NAMESPACE file.
place: no visible global function definition for ‘points’
plot,mproc: no visible binding for global variable ‘rainbow’
plot,mproc: no visible global function definition for ‘plot.default’
plot,mproc: no visible global function definition for ‘axis’
plot,mproc: no visible global function definition for ‘points’
Undefined global functions or variables:
  axis plot.default points rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "plot.default", "points")
to your NAMESPACE file.
ppersp: no visible global function definition for ‘colorRampPalette’
Undefined global functions or variables:
  colorRampPalette
Consider adding
  importFrom("grDevices", "colorRampPalette")
to your NAMESPACE file.
densityfn: no visible global function definition for ‘dnbinom’
densityfn: no visible global function definition for ‘dpois’
densityfn: no visible global function definition for ‘dgeom’
form.add: no visible global function definition for ‘formula’
mreg: no visible global function definition for ‘model.frame’
mreg: no visible global function definition for ‘model.response’
mreg: no visible global function definition for ‘model.matrix’
mreg: no visible global function definition for ‘model.offset’
mreg: no visible global function definition for ‘nlm’
paper: no visible global function definition for ‘model.matrix’
randfn: no visible global function definition for ‘rnbinom’
randfn: no visible global function definition for ‘rpois’
randfn: no visible global function definition for ‘rgeom’
randfn: no visible global function definition for ‘rbinom’
summary.mreg: no visible global function definition for ‘pnorm’
summary.mreg: no visible global function definition for ‘printCoefmat’
Undefined global functions or variables:
  dgeom dnbinom dpois formula model.frame model.matrix model.offset
  model.response nlm pnorm printCoefmat rbinom rgeom rnbinom rpois
Consider adding
  importFrom("stats", "dgeom", "dnbinom", "dpois", "formula",
             "model.frame", "model.matrix", "model.offset",
             "model.response", "nlm", "pnorm", "printCoefmat", "rbinom",
             "rgeom", "rnbinom", "rpois")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  summary.MRSP
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Packages in Depends field not imported from:
  ‘mvtnorm’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
MRsurvival: no visible global function definition for ‘rmvnorm’
MRsurvival: no visible global function definition for ‘optim’
MRsurvival : <anonymous>: no visible global function definition for
  ‘quantile’
Undefined global functions or variables:
  optim quantile rmvnorm
Consider adding
  importFrom("stats", "optim", "quantile")
to your NAMESPACE file.
MRwarp: no visible global function definition for ‘dev.new’
MRwarp: no visible global function definition for ‘plot’
MRwarp: no visible global function definition for ‘lines’
MRwarp: no visible global function definition for ‘points’
MRwarp: no visible global function definition for ‘hist’
Undefined global functions or variables:
  dev.new hist lines plot points
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "hist", "lines", "plot", "points")
to your NAMESPACE file.
File ‘MRwarping/libs/MRwarping.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘interfaceRC_warp.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
msap: no visible global function definition for ‘packageVersion’
msap: no visible global function definition for ‘read.csv’
msap: no visible global function definition for ‘write.csv’
msap: no visible global function definition for ‘sd’
msap: no visible global function definition for ‘wilcox.test’
msap: no visible global function definition for ‘dist’
msap: no visible global function definition for ‘rainbow’
msap: no visible global function definition for ‘png’
msap: no visible global function definition for ‘legend’
msap: no visible global function definition for ‘dev.off’
pcoa: no visible global function definition for ‘cmdscale’
pcoa: no visible global function definition for ‘png’
pcoa: no visible global function definition for ‘par’
pcoa: no visible global function definition for ‘plot’
pcoa: no visible global function definition for ‘rainbow’
pcoa: no visible global function definition for ‘points’
pcoa: no visible global function definition for ‘dev.off’
pcoa: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  cmdscale dev.off dist legend packageVersion par plot png points
  rainbow read.csv sd wilcox.test write.csv
Consider adding
  importFrom("grDevices", "dev.off", "png", "rainbow")
  importFrom("graphics", "legend", "par", "plot", "points")
  importFrom("stats", "cmdscale", "dist", "sd", "wilcox.test")
  importFrom("utils", "packageVersion", "read.csv", "write.csv")
to your NAMESPACE file.
cv.msda: no visible global function definition for ‘predict’
formatoutput: no visible global function definition for ‘new’
msda.prep: no visible global function definition for ‘cov’
plot.msda: no visible global function definition for ‘par’
plot.msda: no visible global function definition for ‘matplot’
plot.msda: no visible global function definition for ‘rainbow’
plot.msda: no visible global function definition for ‘approx’
plot.msda: no visible global function definition for ‘axis’
predict.msda: no visible binding for global variable ‘sd’
predict.msda: no visible global function definition for ‘predict’
zeromat: no visible global function definition for ‘new’
Undefined global functions or variables:
  approx axis cov matplot new par predict rainbow sd
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "matplot", "par")
  importFrom("methods", "new")
  importFrom("stats", "approx", "cov", "predict", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Non-standard file/directory found at top level:
  ‘sample’
csv2list: no visible global function definition for ‘read.csv’
kgml_i: no visible global function definition for ‘xmlTreeParse’
kgml_i: no visible global function definition for ‘xmlRoot’
kgml_i: no visible global function definition for ‘xmlAttrs’
list2xml: no visible global function definition for ‘xmlNode’
list2xml: no visible global function definition for ‘append.xmlNode’
msea_ora: no visible global function definition for ‘fisher.test’
msea_ora: no visible global function definition for ‘p.adjust’
msea_sub: no visible global function definition for ‘sd’
msea_sub: no visible global function definition for ‘cor.test’
pathway_class: no visible global function definition for ‘untar’
pca_scaled: no visible binding for global variable ‘sd’
pca_scaled: no visible global function definition for ‘cor.test’
pca_scaled: no visible global function definition for ‘p.adjust’
pca_scaled: no visible binding for global variable ‘var’
read_pathway: no visible global function definition for ‘xmlTreeParse’
read_pathway: no visible global function definition for ‘xmlRoot’
read_pathway: no visible global function definition for ‘xmlToList’
read_pathway: no visible global function definition for ‘xmlAttrs’
Undefined global functions or variables:
  append.xmlNode cor.test fisher.test p.adjust read.csv sd untar var
  xmlAttrs xmlNode xmlRoot xmlToList xmlTreeParse
Consider adding
  importFrom("stats", "cor.test", "fisher.test", "p.adjust", "sd", "var")
  importFrom("utils", "read.csv", "untar")
to your NAMESPACE file.
Depends: includes the non-default packages:
  'amap', 'clValid', 'cluster', 'fpc', 'mzR', 'xcms'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  ‘amap’ ‘clValid’ ‘cluster’ ‘fpc’ ‘xcms’
  Please remove these calls from your code.
'library' or 'require' call to ‘tcltk’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘mzR’ ‘xcms’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls to packages already attached by Depends:
  ‘MSeasy’ ‘tcltk’
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘grDevices’ ‘xcms’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  coef.step.dfgps
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
bic.dfgps: no visible global function definition for ‘var’
coef.dfgps: no visible binding for global variable ‘var’
coef.step.dfgps: no visible binding for global variable ‘var’
coefmat.dfgps: no visible binding for global variable ‘var’
cp.dfgps: no visible global function definition for ‘var’
dfgps: no visible global function definition for ‘complete.cases’
msgps: no visible global function definition for ‘complete.cases’
msgps: no visible global function definition for ‘var’
plot.df: no visible global function definition for ‘plot’
plot.df: no visible global function definition for ‘par’
plot.msgps: no visible global function definition for ‘plot’
plot.msgps: no visible global function definition for ‘par’
plot.msgps: no visible global function definition for ‘abline’
predict.msgps: no visible global function definition for
  ‘complete.cases’
Undefined global functions or variables:
  abline complete.cases par plot var
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "complete.cases", "var")
to your NAMESPACE file.
MSIseq.classify: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
BS.var: no visible binding for global variable ‘var’
BS.var: no visible global function definition for ‘cov’
Dist.CIs: no visible global function definition for ‘qnorm’
MSM.CIs: no visible global function definition for ‘qnorm’
plot,msSurv-missing: no visible global function definition for ‘update’
summary,msSurv: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  cov qnorm quantile update var
Consider adding
  importFrom("stats", "cov", "qnorm", "quantile", "update", "var")
to your NAMESPACE file.
'library' or 'require' call to ‘MASS’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Designer.sobol: no visible global function definition for ‘runif’
basicMonteCarlo: no visible global function definition for ‘runif’
lhs003: no visible global function definition for ‘runif’
plmm.mtk : GenereXplmm: no visible binding for global variable ‘poly’
plmm.mtk : calc.plm: no visible global function definition for ‘lm.fit’
plmm.mtk: no visible global function definition for ‘var’
plmm.mtk: no visible global function definition for ‘lm’
plmm.mtk: no visible global function definition for ‘formula’
plmm.mtk: no visible global function definition for ‘update’
plmm.mtk: no visible global function definition for ‘stepAIC’
plot.plmm: no visible global function definition for ‘par’
plot.plmm: no visible global function definition for ‘barplot’
plot.plmm: no visible global function definition for ‘segments’
plot.plmm: no visible global function definition for ‘abline’
plot.plmm: no visible global function definition for ‘title’
plot.plmm: no visible global function definition for ‘legend’
plot.regressionSI: no visible global function definition for ‘par’
plot.regressionSI: no visible global function definition for ‘title’
plot.regressionSI: no visible global function definition for ‘abline’
plot,mtkProcess: no visible global function definition for ‘dev.new’
Undefined global functions or variables:
  abline barplot dev.new formula legend lm lm.fit par poly runif
  segments stepAIC title update var
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "barplot", "legend", "par",
             "segments", "title")
  importFrom("stats", "formula", "lm", "lm.fit", "poly", "runif",
             "update", "var")
to your NAMESPACE file.
'library' or 'require' call to ‘XML’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘NightDay’ ‘RSQLite’ ‘XML’ ‘geosphere’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
drawMap: no visible global function definition for ‘plot’
drawMap: no visible global function definition for ‘box’
drawMap: no visible global function definition for ‘points’
getFlights: no visible binding for global variable ‘htmlTreeParse’
getFlights: no visible binding for global variable ‘xpathSApply’
getFlights: no visible binding for global variable ‘xmlAttrs’
getFlights: no visible binding for global variable ‘free’
movie.routes: no visible global function definition for
  ‘txtProgressBar’
movie.routes: no visible global function definition for ‘jpeg’
movie.routes: no visible global function definition for ‘plot’
movie.routes: no visible global function definition for
  ‘setTxtProgressBar’
movie.routes: no visible global function definition for ‘dev.off’
plot.routes: no visible global function definition for ‘plot’
plot.routes: no visible global function definition for ‘points’
plot.routes: no visible global function definition for ‘mtext’
plot.routes : a: no visible global function definition for ‘points’
plot.routes : a: no visible global function definition for ‘text’
plot.routes : a: no visible global function definition for
  ‘gcIntermediate’
plot.routes : a: no visible global function definition for ‘lines’
routes: no visible global function definition for ‘data’
routes: no visible global function definition for ‘distHaversine’
routes: no visible global function definition for ‘gcIntermediate’
Undefined global functions or variables:
  box data dev.off distHaversine free gcIntermediate htmlTreeParse jpeg
  lines mtext plot points setTxtProgressBar text txtProgressBar
  xmlAttrs xpathSApply
Consider adding
  importFrom("grDevices", "dev.off", "jpeg")
  importFrom("graphics", "box", "lines", "mtext", "plot", "points",
             "text")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Rd file 'flights.Rd':
  \usage lines wider than 90 characters:
     flights(from = NULL, to = NULL, path = system.file("MUCflights.RData", package = "MUCflights"))

These lines will be truncated in the PDF manual.
Packages in Depends field not imported from:
  ‘DiceKriging’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CrossValidationMuFicokm: no visible global function definition for
  ‘covMatrix’
CrossValidationMuFicokmAll: no visible global function definition for
  ‘covMatrix’
MuFicokm: no visible global function definition for ‘km’
compute.beta.hat: no visible global function definition for ‘lm’
computeAuxVariables: no visible global function definition for
  ‘covMatrix’
kmCok: no visible global function definition for ‘new’
kmCok: no visible global function definition for ‘drop.response’
kmCok: no visible global function definition for ‘model.matrix’
kmCok: no visible global function definition for ‘covStruct.create’
kmCok: no visible global function definition for ‘validObject’
kmCok: no visible global function definition for ‘covParametersBounds’
kmCok: no visible binding for global variable ‘kmEstimate’
kmCok : cv: no visible global function definition for ‘leaveOneOut.km’
kmCok: no visible global function definition for ‘plot’
predict.kmCok: no visible global function definition for ‘model.matrix’
predict.kmCok: no visible global function definition for ‘covMat1Mat2’
predict.kmCok: no visible global function definition for ‘qnorm’
predict.kmCok: no visible global function definition for ‘qt’
predict.kmCok: no visible global function definition for ‘covMatrix’
summary.MuFicokm: no visible global function definition for
  ‘covparam2vect’
Undefined global functions or variables:
  covMat1Mat2 covMatrix covParametersBounds covStruct.create
  covparam2vect drop.response km kmEstimate leaveOneOut.km lm
  model.matrix new plot qnorm qt validObject
Consider adding
  importFrom("graphics", "plot")
  importFrom("methods", "new", "validObject")
  importFrom("stats", "lm", "model.matrix", "qnorm", "qt")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Rd file 'CrossValidationMuFicokmAll.Rd':
  \examples lines wider than 100 characters:
                     apply(matrix(1:DNest$n),1,function(x) CrossValidationMuFicokmAll(mymodel,x)$CVerrall)

Rd file 'MuFicokm.Rd':
  \usage lines wider than 90 characters:
                     noise.var = NULL, estim.method = "MLE", penalty = NULL, optim.method = "BFGS", 

Rd file 'predict.MuFicokm.Rd':
  \examples lines wider than 100 characters:
                                                     rev(predictionsSK_UK$mean-2*sqrt(predictionsSK_UK$sig2))),

These lines will be truncated in the PDF manual.
Found the following apparent S3 methods exported but not registered:
  print.pehaz summary.muhaz
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
kphaz.plot: no visible global function definition for ‘stepfun’
muhaz: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx stepfun
Consider adding
  importFrom("stats", "approx", "stepfun")
to your NAMESPACE file.
multeq.diff: no visible global function definition for ‘cov’
multeq.diff: no visible global function definition for ‘pt’
multeq.diff: no visible global function definition for ‘qt’
multeq.rat: no visible global function definition for ‘cov’
multeq.rat: no visible global function definition for ‘pt’
multeq.rat: no visible global function definition for ‘qt’
Undefined global functions or variables:
  cov pt qt
Consider adding
  importFrom("stats", "cov", "pt", "qt")
to your NAMESPACE file.
plotOptionValues: no visible global function definition for ‘plot’
plotOptionValues: no visible global function definition for ‘persp’
Undefined global functions or variables:
  persp plot
Consider adding
  importFrom("graphics", "persp", "plot")
to your NAMESPACE file.
synthetic_multiband: no visible global function definition for ‘runif’
synthetic_multiband: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
calculate_direction: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
betas_plot: no visible global function definition for ‘cov2cor’
betas_plot: no visible global function definition for
  ‘colorRampPalette’
betas_plot: no visible global function definition for ‘pdf’
betas_plot: no visible global function definition for ‘dev.off’
mhplot: no visible global function definition for ‘read.table’
mhplot: no visible global function definition for ‘pdf’
mhplot: no visible global function definition for ‘plot’
mhplot: no visible global function definition for ‘points’
mhplot: no visible global function definition for ‘abline’
mhplot: no visible global function definition for ‘axis’
mhplot: no visible global function definition for ‘dev.off’
multi_meta: no visible global function definition for ‘write.table’
multi_meta: no visible global function definition for ‘read.table’
multi_meta: no visible global function definition for ‘pchisq’
qqplotter: no visible global function definition for ‘read.table’
qqplotter: no visible global function definition for ‘qchisq’
qqplotter: no visible global function definition for ‘ppoints’
qqplotter: no visible global function definition for ‘median’
qqplotter: no visible global function definition for ‘pchisq’
qqplotter: no visible global function definition for ‘pdf’
qqplotter: no visible global function definition for ‘plot’
qqplotter: no visible global function definition for ‘abline’
qqplotter: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  abline axis colorRampPalette cov2cor dev.off median pchisq pdf plot
  points ppoints qchisq read.table write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf")
  importFrom("graphics", "abline", "axis", "plot", "points")
  importFrom("stats", "cov2cor", "median", "pchisq", "ppoints", "qchisq")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
multinb.fit: no visible global function definition for ‘nlminb’
multinbmod: no visible global function definition for ‘is.empty.model’
multinbmod: no visible global function definition for ‘model.matrix’
multinbmod: no visible binding for global variable ‘contrasts’
multinbmod: no visible global function definition for ‘model.response’
multinbmod: no visible global function definition for ‘model.offset’
Undefined global functions or variables:
  contrasts is.empty.model model.matrix model.offset model.response
  nlminb
Consider adding
  importFrom("stats", "contrasts", "is.empty.model", "model.matrix",
             "model.offset", "model.response", "nlminb")
to your NAMESPACE file.
.moments: no visible global function definition for ‘ppois’
.truncpoi: no visible global function definition for ‘ppois’
Undefined global functions or variables:
  ppois
Consider adding
  importFrom("stats", "ppois")
to your NAMESPACE file.
Package in Depends field not imported from: ‘rgenoud’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.onAttach: no visible global function definition for
  ‘packageDescription’
genoudRob: no visible global function definition for ‘genoud’
get.XYdata: no visible global function definition for ‘terms’
get.xdata: no visible global function definition for ‘terms’
get.xdata: no visible global function definition for ‘model.matrix’
get.xy: no visible global function definition for ‘terms’
get.xynames: no visible global function definition for ‘terms’
get.ydata: no visible global function definition for ‘terms’
get.ydata: no visible global function definition for ‘model.response’
get.ydata: no visible global function definition for ‘model.frame’
mt.dev: no visible global function definition for ‘pt’
mt.dev.grad: no visible global function definition for ‘pt’
mt.dev.grad: no visible global function definition for ‘dt’
mt.mle: no visible global function definition for ‘optim’
multinomRob: no visible global function definition for ‘var’
plot.multinomRob: no visible global function definition for ‘par’
plot.multinomRob: no visible global function definition for ‘plot’
plot.multinomRob: no visible global function definition for ‘title’
rdirich: no visible global function definition for ‘rgamma’
residual.generator: no visible global function definition for ‘median’
rmultinomial: no visible global function definition for ‘runif’
rmultinomial: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  dt genoud median model.frame model.matrix model.response optim
  packageDescription par plot pt rbinom rgamma runif terms title var
Consider adding
  importFrom("graphics", "par", "plot", "title")
  importFrom("stats", "dt", "median", "model.frame", "model.matrix",
             "model.response", "optim", "pt", "rbinom", "rgamma",
             "runif", "terms", "var")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
multiPIM : expand.factors: no visible global function definition for
  ‘formula’
multiPIM : expand.factors: no visible global function definition for
  ‘model.matrix’
multiPIM : <anonymous>: no visible global function definition for ‘glm’
multiPIM : <anonymous>: no visible binding for global variable
  ‘binomial’
multiPIM : <anonymous>: no visible global function definition for
  ‘qlogis’
multiPIM : <anonymous>: no visible global function definition for
  ‘as.formula’
multiPIM : <anonymous>: no visible global function definition for ‘lm’
multiPIM: no visible global function definition for ‘glm’
multiPIM: no visible global function definition for ‘qlogis’
multiPIM: no visible binding for global variable ‘binomial’
multiPIM: no visible global function definition for ‘plogis’
multiPIM: no visible global function definition for ‘sd’
multiPIM: no visible global function definition for ‘lm’
summary.multiPIM: no visible binding for global variable ‘sd’
summary.multiPIM: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as.formula binomial formula glm lm model.matrix plogis pnorm qlogis
  sd
Consider adding
  importFrom("stats", "as.formula", "binomial", "formula", "glm", "lm",
             "model.matrix", "plogis", "pnorm", "qlogis", "sd")
to your NAMESPACE file.
CCM_boot : <anonymous>: no visible global function definition for ‘sd’
SSR_check_signal: no visible global function definition for ‘cor’
SSR_check_signal: no visible global function definition for ‘cor.test’
SSR_check_signal: no visible global function definition for ‘lm’
SSR_pred_boot: no visible global function definition for ‘cor’
make_ccm_data: no visible global function definition for ‘rnorm’
make_ccm_data: no visible global function definition for ‘runif’
make_ccm_data: no visible global function definition for ‘rlnorm’
Undefined global functions or variables:
  cor cor.test lm rlnorm rnorm runif sd
Consider adding
  importFrom("stats", "cor", "cor.test", "lm", "rlnorm", "rnorm",
             "runif", "sd")
to your NAMESPACE file.
PrbMlt.default: no visible binding for global variable ‘na.omit’
PrbMlt.default: no visible global function definition for ‘anova’
Undefined global functions or variables:
  anova na.omit
Consider adding
  importFrom("stats", "anova", "na.omit")
to your NAMESPACE file.
File ‘multxpert/R/zzz.R’:
  .onLoad calls:
    cat("multxpert: Implementation of commonly used p-value based and parametric\n",     "multiple testing procedures and parallel gatekeeping procedures.\n",     "For more information visit http://multxpert.com/wiki/MultXpert_package\n",     sep = "")

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

paradjp: no visible global function definition for ‘pt’
parci: no visible global function definition for ‘qt’
pdunnett: no visible global function definition for ‘GenzBretz’
pvalci: no visible global function definition for ‘qnorm’
qdunnett: no visible global function definition for ‘GenzBretz’
Undefined global functions or variables:
  GenzBretz pt qnorm qt
Consider adding
  importFrom("stats", "pt", "qnorm", "qt")
to your NAMESPACE file.
Depends: includes the non-default packages:
  'car', 'pdist', 'pls', 'gplots', 'mvtnorm', 'robustbase', 'gtools',
  'bitops', 'caTools', 'pcaPP', 'rrcov'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  ‘car’ ‘gplots’ ‘pdist’ ‘pls’ ‘rrcov’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘bitops’ ‘caTools’ ‘car’ ‘gplots’ ‘gtools’ ‘mvtnorm’ ‘pcaPP’ ‘pdist’
  ‘pls’ ‘robustbase’ ‘rrcov’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'Plot.pca.score.Rd':
  \examples lines wider than 100 characters:
             ylab = ylab, xlim = lim, ylim = lim, pch = 19, sub = paste("Cumulative Proportion of Variance Explained = ", 

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

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

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

These lines will be truncated in the PDF manual.
plotFID: no visible global function definition for ‘plot’
plotFID: no visible global function definition for ‘points’
Undefined global functions or variables:
  plot points
Consider adding
  importFrom("graphics", "plot", "points")
to your NAMESPACE file.
prentice.test: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
mvb.simu: no visible global function definition for ‘runif’
plot.lps: no visible global function definition for ‘matplot’
unifit: no visible global function definition for ‘model.frame’
unifit: no visible global function definition for ‘model.matrix’
unifit: no visible global function definition for ‘model.response’
unilps: no visible global function definition for ‘model.frame’
unilps: no visible global function definition for ‘model.matrix’
unilps: no visible global function definition for ‘model.response’
Undefined global functions or variables:
  matplot model.frame model.matrix model.response runif
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "runif")
to your NAMESPACE file.
':::' calls which should be '::':
  ‘base:::call’ ‘base:::importIntoEnv’ ‘base:::lockEnvironment’
  ‘base:::match.call’ ‘base:::print.default’ ‘base:::print.function’
  ‘tools:::Rd2txt’ ‘utils:::?’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘tools:::.Rd_get_metadata’ ‘tools:::.get_package_metadata’
  ‘tools:::.install_package_Rd_indices’
  ‘tools:::.install_package_Rd_objects’
  ‘tools:::.install_package_description’
  ‘tools:::.install_package_namespace_info’ ‘tools:::.read_description’
  ‘tools:::.writePkgIndices’ ‘tools:::.writeVignetteHtmlIndex’
  ‘tools:::RdTags’ ‘tools:::fetchRdDB’ ‘tools:::makeLazyLoadDB’
  ‘tools:::prepare_Rd’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘Save’ ‘body.print.function’ ‘cd’ ‘rbind.data.frame’
  ‘search.task.trees’ ‘untetherBalloon’
Found the following apparent S3 methods exported but not registered:
  plot.cdtree plot.foodweb
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
conceptIndicesSkm: no visible global function definition for
  ‘txtProgressBar’
conceptIndicesSkm: no visible global function definition for
  ‘setTxtProgressBar’
conceptVectorsSkm: no visible global function definition for
  ‘txtProgressBar’
conceptVectorsSkm: no visible global function definition for
  ‘setTxtProgressBar’
mvcmb: no visible global function definition for ‘runif’
mvcmb: no visible global function definition for ‘str’
mvcsph: no visible global function definition for ‘pdf’
mvcsph: no visible global function definition for ‘heatmap’
mvcsph: no visible global function definition for ‘dev.off’
mvcsph: no visible global function definition for ‘hclust’
mvcsph: no visible global function definition for ‘dist’
mvcsph: no visible global function definition for ‘str’
Undefined global functions or variables:
  dev.off dist hclust heatmap pdf runif setTxtProgressBar str
  txtProgressBar
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("stats", "dist", "hclust", "heatmap", "runif")
  importFrom("utils", "setTxtProgressBar", "str", "txtProgressBar")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  contour.mvcwt image.mvcwt plot.mvcwt
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
contour.mvcwt: no visible global function definition for ‘par’
get.min.scale: no visible global function definition for ‘median’
image.mvcwt: no visible global function definition for ‘par’
plot.mvcwt: no visible global function definition for ‘par’
print.mvcwt: no visible global function definition for ‘str’
Undefined global functions or variables:
  median par str
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "median")
  importFrom("utils", "str")
to your NAMESPACE file.
mvnpermute: no visible global function definition for ‘lm’
mvnpermute: no visible global function definition for ‘coef’
mvnpermute: no visible global function definition for ‘resid’
Undefined global functions or variables:
  coef lm resid
Consider adding
  importFrom("stats", "coef", "lm", "resid")
to your NAMESPACE file.
mvorpb: no visible global function definition for ‘pnorm’
mvorpb: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm pnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm")
to your NAMESPACE file.
rtn: no visible global function definition for ‘runif’
rtn: no visible global function definition for ‘qnorm’
rtn: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm runif
Consider adding
  importFrom("stats", "pnorm", "qnorm", "runif")
to your NAMESPACE file.
prepare_Rd: mvsf.Rd:16-17: Dropping empty section \details
mvtmeta_fe: no visible global function definition for ‘combinations’
Undefined global functions or variables:
  combinations
'library' or 'require' call to ‘RColorBrewer’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘RColorBrewer’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plot.matchedwake: no visible global function definition for
  ‘filled.contour’
plot.matchedwake: no visible binding for global variable ‘gray.colors’
plot.matchedwake: no visible global function definition for ‘axis’
plot.matchedwake: no visible global function definition for ‘rect’
slideWakeMatch: no visible binding for global variable ‘lm’
slideWakeMatch: no visible global function definition for ‘as.formula’
slideWakeMatch: no visible global function definition for ‘summary.glm’
Undefined global functions or variables:
  as.formula axis filled.contour gray.colors lm rect summary.glm
Consider adding
  importFrom("grDevices", "gray.colors")
  importFrom("graphics", "axis", "filled.contour", "rect")
  importFrom("stats", "as.formula", "lm", "summary.glm")
to your NAMESPACE file.
mxkssd: no visible global function definition for ‘txtProgressBar’
mxkssd: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
abcpred_nmer: no visible global function definition for ‘write.table’
algpred: no visible global function definition for ‘read.table’
algpred: no visible global function definition for ‘write.table’
allermatch: no visible global function definition for ‘read.table’
allermatch: no visible global function definition for ‘write.table’
bcepred_nmer: no visible global function definition for ‘write.table’
bimas_nmer: no visible global function definition for ‘write.table’
filter.firstlayer: no visible global function definition for
  ‘read.table’
filter.firstlayer: no visible global function definition for
  ‘write.table’
iedb_arb_mhci_nmer: no visible global function definition for
  ‘write.table’
iedb_arb_mhcii_nmer: no visible global function definition for
  ‘write.table’
iedb_consensus_mhci_nmer: no visible global function definition for
  ‘write.table’
iedb_consensus_mhcii_nmer: no visible global function definition for
  ‘write.table’
netmhcNN_nmer: no visible global function definition for ‘write.table’
netmhcWT_nmer: no visible global function definition for ‘write.table’
propred_nmer: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
update_episode: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
Rd file 'myepisodes_feed_url.Rd':
  \examples lines wider than 100 characters:
     ## Not run: myepisodes_feed_url("foouser", "321654321654321", feed = "mylist", onlyunacquired = TRUE, showignored = FALSE)

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

These lines will be truncated in the PDF manual.
abs_dif: no visible global function definition for ‘as.formula’
env_dif: no visible global function definition for ‘lm’
env_dif: no visible global function definition for ‘as.formula’
env_dif_logistic: no visible global function definition for
  ‘as.formula’
fam_env: no visible global function definition for ‘as.formula’
log_dif: no visible global function definition for ‘as.formula’
Undefined global functions or variables:
  as.formula lm
Consider adding
  importFrom("stats", "as.formula", "lm")
to your NAMESPACE file.
Found the following significant warnings:
  Functions.cpp:785:39: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  Functions.cpp:785:66: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  Functions.cpp:792:39: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  Functions.cpp:792:66: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/NAM.Rcheck/00install.out’ for details.
NAPPA: no visible binding for global variable ‘sd’
NAPPA: no visible global function definition for ‘sd’
calibrate.sigmoid.curve : <anonymous> : <anonymous>: no visible global
  function definition for ‘coef’
calibrate.sigmoid.curve : <anonymous> : <anonymous>: no visible global
  function definition for ‘lm’
calibrate.sigmoid.curve: no visible global function definition for
  ‘nls’
calibrate.sigmoid.curve: no visible binding for global variable
  ‘weights’
calibrate.sigmoid.curve: no visible global function definition for
  ‘coef’
calibrate.sigmoid.curve: no visible global function definition for
  ‘plot’
calibrate.sigmoid.curve: no visible global function definition for
  ‘rgb’
calibrate.sigmoid.curve: no visible global function definition for
  ‘box’
calibrate.sigmoid.curve: no visible global function definition for
  ‘axis’
calibrate.sigmoid.curve: no visible global function definition for
  ‘abline’
calibrate.sigmoid.curve: no visible global function definition for
  ‘lines’
calibrate.sigmoid.curve: no visible global function definition for
  ‘predict’
calibrate.sigmoid.curve: no visible global function definition for
  ‘smooth.spline’
calibrate.sigmoid.curve : <anonymous>: no visible global function
  definition for ‘nls’
calibrate.sigmoid.curve : <anonymous>: no visible binding for global
  variable ‘weights’
calibrate.sigmoid.curve: no visible binding for global variable ‘coef’
calibrate.sigmoid.curve: no visible global function definition for ‘pf’
calibrate.sigmoid.curve: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  abline axis box coef legend lines lm nls pf plot predict rgb sd
  smooth.spline weights
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "abline", "axis", "box", "legend", "lines",
             "plot")
  importFrom("stats", "coef", "lm", "nls", "pf", "predict", "sd",
             "smooth.spline", "weights")
to your NAMESPACE file.
NB.estimator: no visible global function definition for ‘optimize’
NB.estimator: no visible global function definition for ‘uniroot’
NB.example.dataset: no visible global function definition for
  ‘write.table’
NB.plot.likelihood: no visible global function definition for ‘plot’
Undefined global functions or variables:
  optimize plot uniroot write.table
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "optimize", "uniroot")
  importFrom("utils", "write.table")
to your NAMESPACE file.
ncbit : FUN: no visible global function definition for ‘read.table’
ncbit : FUN: no visible global function definition for ‘head’
Undefined global functions or variables:
  head read.table
Consider adding
  importFrom("utils", "head", "read.table")
to your NAMESPACE file.
get.split.filename.cmip5: no visible global function definition for
  ‘tail’
nc.conform.data : <anonymous>: no visible global function definition
  for ‘na.omit’
nc.get.subset.recursive: no visible global function definition for
  ‘head’
nc.get.subset.recursive: no visible global function definition for
  ‘tail’
nc.put.subset.recursive: no visible global function definition for
  ‘head’
nc.put.subset.recursive: no visible global function definition for
  ‘tail’
Undefined global functions or variables:
  head na.omit tail
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
infoNcdfVars: no visible global function definition for ‘na.omit’
modifyNcdfDefAtts: no visible global function definition for ‘na.omit’
plotDatacube: no visible global function definition for ‘runif’
plotDatacube: no visible global function definition for
  ‘colorRampPalette’
plotDatacube: no visible global function definition for ‘dev.cur’
plotDatacube: no visible global function definition for ‘dev.new’
plotDatacube: no visible global function definition for ‘layout’
plotDatacube: no visible global function definition for ‘par’
plotDatacube: no visible global function definition for ‘points’
plotDatacube: no visible global function definition for ‘text’
plotDatacube: no visible global function definition for ‘plot.new’
plotDatacube: no visible global function definition for ‘mtext’
plotDatacube: no visible global function definition for ‘rgb’
plotDatacube: no visible global function definition for ‘legend’
transNcdfRotate: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  colorRampPalette dev.cur dev.new layout legend mtext na.omit par
  plot.new points rgb runif text
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.cur", "dev.new",
             "rgb")
  importFrom("graphics", "layout", "legend", "mtext", "par", "plot.new",
             "points", "text")
  importFrom("stats", "na.omit", "runif")
to your NAMESPACE file.
d0: no visible global function definition for ‘qnorm’
dncgamma: no visible global function definition for ‘dpois’
indncgamma: no visible global function definition for ‘pgamma’
indncgamma: no visible global function definition for ‘dpois’
inxncgamma: no visible global function definition for ‘qnorm’
inxncgamma: no visible global function definition for ‘pgamma’
inxncgamma: no visible global function definition for ‘dpois’
pncgamma: no visible global function definition for ‘pgamma’
pncgamma: no visible global function definition for ‘dpois’
Undefined global functions or variables:
  dpois pgamma qnorm
Consider adding
  importFrom("stats", "dpois", "pgamma", "qnorm")
to your NAMESPACE file.
data.reduction: no visible global function definition for ‘prcomp’
data.reduction: no visible global function definition for ‘hclust’
data.reduction: no visible global function definition for ‘as.dist’
data.reduction: no visible global function definition for ‘cor’
data.reduction: no visible global function definition for ‘dist’
heatmap1: no visible global function definition for ‘sd’
lineplot: no visible global function definition for ‘sd’
normalize: no visible global function definition for ‘sd’
profileplot3d : ColorFunction: no visible global function definition
  for ‘rgb’
profileplot3d : ColorFunction: no visible global function definition
  for ‘colorRamp’
profileplot3d: no visible global function definition for ‘sd’
profileplot3d: no visible global function definition for ‘gray’
Undefined global functions or variables:
  as.dist colorRamp cor dist gray hclust prcomp rgb sd
Consider adding
  importFrom("grDevices", "colorRamp", "gray", "rgb")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "prcomp", "sd")
to your NAMESPACE file.
File ‘NeatMap/libs/NeatMap.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘nMDS_R.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘nMDS_R.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
population: no visible global function definition for ‘weighted.mean’
population: no visible global function definition for ‘rpois’
population: no visible global function definition for ‘lm’
population: no visible global function definition for ‘coefficients’
population: no visible global function definition for ‘sd’
population: no visible global function definition for ‘par’
population: no visible global function definition for ‘plot’
population: no visible global function definition for ‘lines’
Undefined global functions or variables:
  coefficients lines lm par plot rpois sd weighted.mean
Consider adding
  importFrom("graphics", "lines", "par", "plot")
  importFrom("stats", "coefficients", "lm", "rpois", "sd",
             "weighted.mean")
to your NAMESPACE file.
The following files look like leftovers/mistakes:
  ‘Rplots.pdf’, ‘Rplots.ps’
Please remove them from your package.
nestedRanksTest.default: no visible global function definition for
  ‘setNames’
nestedRanksTest.default: no visible global function definition for
  ‘quantile’
nestedRanksTest.formula: no visible global function definition for
  ‘terms’
plot.htest_boot: no visible global function definition for ‘hist’
plot.htest_boot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline hist quantile setNames terms
Consider adding
  importFrom("graphics", "abline", "hist")
  importFrom("stats", "quantile", "setNames", "terms")
to your NAMESPACE file.
clustConfigurations: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
netVal: no visible global function definition for ‘cutree’
netVal: no visible global function definition for ‘hclust’
netVal: no visible global function definition for ‘as.dist’
Undefined global functions or variables:
  as.dist cutree hclust
Consider adding
  importFrom("stats", "as.dist", "cutree", "hclust")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘buildcmds’
EnvInd: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: ‘fastshp’
simulate.sisnetwork: no visible global function definition for ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
balloon: no visible global function definition for ‘convolve’
physnoise: no visible global function definition for ‘sd’
physnoise: no visible global function definition for ‘rnorm’
rrice: no visible global function definition for ‘rnorm’
simTSrestingstate: no visible global function definition for ‘runif’
simTSrestingstate: no visible global function definition for ‘fft’
spatialnoise: no visible global function definition for ‘rnorm’
spatialnoise: no visible global function definition for ‘qgamma’
spatialnoise: no visible global function definition for ‘pnorm’
specifydesign: no visible global function definition for ‘convolve’
systemnoise: no visible global function definition for ‘rnorm’
tasknoise: no visible global function definition for ‘rnorm’
tasknoise: no visible global function definition for ‘sd’
temporalnoise: no visible global function definition for ‘arima.sim’
Undefined global functions or variables:
  arima.sim convolve fft pnorm qgamma rnorm runif sd
Consider adding
  importFrom("stats", "arima.sim", "convolve", "fft", "pnorm", "qgamma",
             "rnorm", "runif", "sd")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘MASS’ ‘boot’ ‘lattice’ ‘psych’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
nfca : nFCAmain: no visible global function definition for ‘hist’
nfca : nFCAmain: no visible global function definition for
  ‘flush.console’
nfca : nFCAmain: no visible global function definition for ‘qnorm’
nfca : nFCAmain: no visible global function definition for ‘read.csv’
nfca : nFCAmain: no visible global function definition for ‘cor’
nfca : nFCAmain: no visible global function definition for ‘as.dist’
nfca : nFCAmain: no visible global function definition for ‘cophenetic’
nfca : nFCAmain: no visible global function definition for ‘hclust’
nfca : thresholdTEST: no visible global function definition for
  ‘read.csv’
nfca : gScript: no visible global function definition for ‘read.csv’
nfca : gScript0: no visible global function definition for ‘read.csv’
nfca : gMatrix: no visible global function definition for ‘read.csv’
nfca: no visible global function definition for ‘cor’
Undefined global functions or variables:
  as.dist cophenetic cor flush.console hclust hist qnorm read.csv
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "as.dist", "cophenetic", "cor", "hclust", "qnorm")
  importFrom("utils", "flush.console", "read.csv")
to your NAMESPACE file.
Package suggested but not available for checking: ‘NFPdata’
compare.CDF: no visible global function definition for ‘quantile’
download.single.game: no visible global function definition for
  ‘download.file’
fit.shot.probs.simple: no visible global function definition for
  ‘predict’
integrate.old.pieces: no visible global function definition for
  ‘na.omit’
prob.score.simple.objects: no visible global function definition for
  ‘binomial’
prob.score.simple.objects: no visible binding for global variable
  ‘logit’
prob.score.simple.objects: no visible global function definition for
  ‘predict’
process.pl.new: no visible global function definition for ‘na.omit’
read.gif: no visible global function definition for ‘download.file’
read.gif: no visible global function definition for ‘rgb’
solver.with.nlm: no visible global function definition for ‘nlm’
team.table : thisplot: no visible global function definition for ‘par’
team.table : thisplot: no visible global function definition for ‘plot’
team.table : thisplot: no visible global function definition for ‘text’
team.table : thisplot: no visible global function definition for
  ‘abline’
Undefined global functions or variables:
  abline binomial download.file logit na.omit nlm par plot predict
  quantile rgb text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "abline", "par", "plot", "text")
  importFrom("stats", "binomial", "na.omit", "nlm", "predict",
             "quantile")
  importFrom("utils", "download.file")
to your NAMESPACE file.
nlmeODE: no visible global function definition for ‘deriv’
Undefined global functions or variables:
  deriv
Consider adding
  importFrom("stats", "deriv")
to your NAMESPACE file.
Pwr.lme: no visible global function definition for ‘anova’
Pwr.lme: no visible global function definition for ‘qf’
Pwr.lme: no visible global function definition for ‘pf’
logLik1.lme: no visible global function definition for ‘coef’
logLik1.lme: no visible global function definition for ‘model.matrix’
logLik1.lme: no visible global function definition for ‘predict’
logLik1.lme: no visible global function definition for ‘formula’
runScript: no visible binding for global variable ‘example’
sigmaTolme: no visible global function definition for ‘vcov’
simulateY.lme: no visible global function definition for ‘runif’
simulateY.lme: no visible global function definition for ‘fitted’
simulateY.lme: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  anova coef example fitted formula model.matrix pf predict qf rnorm
  runif vcov
Consider adding
  importFrom("stats", "anova", "coef", "fitted", "formula",
             "model.matrix", "pf", "predict", "qf", "rnorm", "runif",
             "vcov")
  importFrom("utils", "example")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  all.profiles.nlreg fitted.values.nlreg
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Package in Depends field not imported from: ‘proto’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘stats:::nlsModel’ ‘stats:::nlsModel.plinear’
  See the note in ?`:::` about the use of this operator.
nls2: no visible global function definition for ‘nls.control’
nls2: no visible global function definition for ‘as.formula’
nls2: no visible global function definition for ‘coef’
nls2: no visible global function definition for ‘runif’
nls2 : <anonymous>: no visible global function definition for
  ‘deviance’
Undefined global functions or variables:
  as.formula coef deviance nls.control runif
Consider adding
  importFrom("stats", "as.formula", "coef", "deviance", "nls.control",
             "runif")
to your NAMESPACE file.
Rd file 'smsn.nl.Rd':
  \usage lines wider than 90 characters:
             nu = NULL, nlf = NULL, rho.func = 1, reg.type = "Homoscedastic", criteria = FALSE, 

These lines will be truncated in the PDF manual.
nnmf_als: no visible global function definition for ‘rnorm’
nnmf_mm: no visible global function definition for ‘rnorm’
nnmf_prob: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
gimli.11224hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
makeRules: no visible global function definition for ‘sd’
makeRules: no visible global function definition for ‘rnorm’
nodeHarvest: no visible global function definition for ‘capture.output’
nodeHarvest: no visible global function definition for ‘lm’
nodeHarvest: no visible global function definition for ‘coef’
plot.nodeHarvest: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  capture.output coef lm rgb rnorm sd
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "coef", "lm", "rnorm", "sd")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Depends: includes the non-default packages:
  'lpSolve', 'gdata', 'Hmisc', 'rms', 'geometry', 'psych', 'pwt'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  ‘Hmisc’ ‘gdata’ ‘geometry’ ‘lpSolve’ ‘psych’ ‘rms’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Hmisc’ ‘gdata’ ‘geometry’ ‘lpSolve’ ‘psych’ ‘pwt’ ‘rms’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
additive: no visible global function definition for ‘lp’
ar.dual.dea: no visible global function definition for ‘lp’
cost.dea: no visible global function definition for ‘lp’
ddf: no visible global function definition for ‘lp’
dea: no visible global function definition for ‘lp’
direc.dea: no visible global function definition for ‘lp’
dual.dea: no visible global function definition for ‘lp’
effdea.b.f: no visible global function definition for ‘convhulln’
effdea.b.f: no visible global function definition for ‘lp’
faremalm2: no visible binding for global variable ‘Lag’
faremalm2: no visible global function definition for ‘na.omit’
int.dea: no visible global function definition for ‘lp’
lp2: no visible global function definition for ‘lp’
revenue.dea: no visible global function definition for ‘lp’
sbm.tone: no visible global function definition for ‘lp’
sbm.vrs: no visible global function definition for ‘lp’
Undefined global functions or variables:
  Lag convhulln lp na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
'library' or 'require' call to ‘colorspace’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
Packages in Depends field not imported from:
  ‘histogram’ ‘optimx’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dnormgam: no visible global function definition for ‘qgamma’
dnormgam: no visible global function definition for ‘fft’
dnormgam: no visible global function definition for ‘dgamma’
dnormgam: no visible global function definition for ‘approx’
normgam.fit : mkdfftNormalGammaOptim : <anonymous>: no visible global
  function definition for ‘dnorm’
normgam.fit : estimation_param_normexp_RMA : max.density: no visible
  global function definition for ‘density’
normgam.fit: no visible global function definition for ‘sd’
normgam.fit: no visible global function definition for ‘median’
normgam.fit: no visible global function definition for ‘IQR’
normgam.fit: no visible global function definition for ‘optimx’
normgam.fit: no visible global function definition for ‘coef’
normgam.signal: no visible global function definition for ‘approx’
normgam.signal: no visible global function definition for ‘hist’
Undefined global functions or variables:
  IQR approx coef density dgamma dnorm fft hist median optimx qgamma sd
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "IQR", "approx", "coef", "density", "dgamma",
             "dnorm", "fft", "median", "qgamma", "sd")
to your NAMESPACE file.
ajb.norm.test: no visible global function definition for ‘rnorm’
frosini.norm.test: no visible global function definition for ‘var’
frosini.norm.test: no visible global function definition for ‘pnorm’
frosini.norm.test: no visible global function definition for ‘rnorm’
geary.norm.test: no visible global function definition for ‘rnorm’
hegazy1.norm.test: no visible global function definition for ‘var’
hegazy1.norm.test: no visible global function definition for ‘qnorm’
hegazy1.norm.test: no visible global function definition for ‘rnorm’
hegazy2.norm.test: no visible global function definition for ‘var’
hegazy2.norm.test: no visible global function definition for ‘qnorm’
hegazy2.norm.test: no visible global function definition for ‘rnorm’
jb.norm.test: no visible global function definition for ‘rnorm’
kurtosis.norm.test: no visible global function definition for ‘rnorm’
skewness.norm.test: no visible global function definition for ‘rnorm’
spiegelhalter.norm.test: no visible global function definition for
  ‘rnorm’
wb.norm.test: no visible global function definition for ‘qnorm’
wb.norm.test: no visible global function definition for ‘var’
wb.norm.test: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  pnorm qnorm rnorm var
Consider adding
  importFrom("stats", "pnorm", "qnorm", "rnorm", "var")
to your NAMESPACE file.
normality.test1: no visible global function definition for ‘cov.wt’
normality.test1: no visible global function definition for ‘cor’
normality.test1: no visible global function definition for ‘pnorm’
normality.test1: no visible global function definition for ‘pchisq’
normality.test2: no visible global function definition for ‘cov.wt’
normality.test2: no visible global function definition for ‘cor’
normality.test2: no visible global function definition for ‘acf’
normality.test2: no visible global function definition for ‘pnorm’
normality.test2: no visible global function definition for ‘pchisq’
whitenoise.test: no visible global function definition for ‘acf’
whitenoise.test: no visible global function definition for ‘spec.pgram’
whitenoise.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  acf cor cov.wt pchisq pnorm spec.pgram
Consider adding
  importFrom("stats", "acf", "cor", "cov.wt", "pchisq", "pnorm",
             "spec.pgram")
to your NAMESPACE file.
CIPW: no visible global function definition for ‘data’
CIPW: no visible binding for global variable ‘AtomWeight’
CIPW: no visible binding for global variable ‘MinWeight’
CIPW: no visible binding for global variable ‘OxiWeight’
CIPW.trace: no visible global function definition for ‘data’
CIPW.trace: no visible binding for global variable ‘AtomWeight’
CIPW.trace: no visible binding for global variable ‘MinWeight’
CIPW.trace: no visible binding for global variable ‘OxiWeight’
Undefined global functions or variables:
  AtomWeight MinWeight OxiWeight data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
BoundingRA: no visible global function definition for ‘rnorm’
check_y_estimator: no visible global function definition for ‘rnorm’
genNORTARA: no visible global function definition for ‘rnorm’
genNORTARA: no visible global function definition for ‘pnorm’
valid_input_cormat: no visible global function definition for ‘rnorm’
valid_input_cormat: no visible global function definition for ‘pnorm’
valid_input_cormat: no visible global function definition for ‘cor’
y_control_estimator: no visible global function definition for ‘pnorm’
y_control_estimator: no visible global function definition for ‘cor’
y_control_estimator : <anonymous>: no visible global function
  definition for ‘cor’
y_control_estimator: no visible global function definition for ‘cov’
y_control_estimator: no visible global function definition for ‘var’
y_crude_estimator: no visible global function definition for ‘pnorm’
y_crude_estimator: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor cov pnorm rnorm var
Consider adding
  importFrom("stats", "cor", "cov", "pnorm", "rnorm", "var")
to your NAMESPACE file.
Rd file 'notifyR-package.Rd':
  \examples lines wider than 100 characters:
     send_push(userkey,message="finished.",title="World Simulation",url="http://www.myRresults.com/",url_title="View Results online.",priori ... [TRUNCATED]

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

These lines will be truncated in the PDF manual.
.newReportId : <anonymous>: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  utilities.c:175:32: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/npcp.Rcheck/00install.out’ for details.
Packages in Depends field not imported from:
  ‘smcure’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
NPHMC: no visible global function definition for ‘integrate’
NPHMC: no visible global function definition for ‘qnorm’
NPHMC: no visible global function definition for ‘pnorm’
NPHMC: no visible global function definition for ‘plot’
NPHMC: no visible global function definition for ‘lines’
NPHMC: no visible global function definition for ‘smcure’
NPHMC: no visible global function definition for ‘coxph’
Undefined global functions or variables:
  coxph integrate lines plot pnorm qnorm smcure
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "integrate", "pnorm", "qnorm")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘tmp.R’
nppbib: no visible global function definition for ‘read.table’
nppbib: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq read.table
Consider adding
  importFrom("stats", "pchisq")
  importFrom("utils", "read.table")
to your NAMESPACE file.
File ‘NPsimex/R/onload.R’:
  .onLoad calls:
    packageStartupMessage("NPsimex 0.2-1 loaded")

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

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

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

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

These lines will be truncated in the PDF manual.
Found the following apparent S3 methods exported but not registered:
  print.fkk.test print.hogg.test print.rank.test
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
nps.test: no visible global function definition for ‘qnorm’
nps.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
'library' or 'require' call to ‘parallel’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
npst: no visible global function definition for ‘mclapply’
Undefined global functions or variables:
  mclapply
Depends: includes the non-default packages:
  'R.methodsS3', 'MASS', 'matrixStats', 'R.oo', 'R.utils',
  'aroma.core', 'aroma.affymetrix', 'DNAcopy'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Non-standard file/directory found at top level:
  ‘incl’
Packages in Depends field not imported from:
  ‘DNAcopy’ ‘MASS’ ‘R.methodsS3’ ‘R.oo’ ‘aroma.affymetrix’ ‘aroma.core’
  ‘matrixStats’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  NSAByTotalAndFracB.matrix allocateOutputDataSets.NSANormalization
  allocateOutputDataSets.SNPsNormalization
  allocateOutputDataSets.SampleNormalization
  as.character.NSANormalization as.character.SNPsNormalization
  as.character.SampleNormalization findArraysTodo.NSANormalization
  findArraysTodo.SampleNormalization findUnitsTodo.SNPsNormalization
  fitNSA.matrix fitNSAcnPs.matrix getDataSets.NSANormalization
  getDataSets.SNPsNormalization getDataSets.SampleNormalization
  getName.NSANormalization getName.SNPsNormalization
  getName.SampleNormalization getOutputDataSets.NSANormalization
  getOutputDataSets.SNPsNormalization
  getOutputDataSets.SampleNormalization getPath.NSANormalization
  getPath.SNPsNormalization getPath.SampleNormalization
  getRootPath.NSANormalization getRootPath.SNPsNormalization
  getRootPath.SampleNormalization process.NSANormalization
  process.SNPsNormalization process.SampleNormalization
  sampleNByTotalAndFracB.numeric snpsNByTotalAndFracB.matrix
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'NSANormalization.Rd':
  \examples lines wider than 100 characters:
     by <- 50e3; # 50kb bins; you may want to try with other amounts of smoothing xOut <- seq(from=xRange[1], to=xRange[2], by=by);
     plot(getSignals(cnCNPS), getSignals(cnSNPS), xlim=Clim, ylim=Clim); abline(a=0, b=1, col="red", lwd=2);

These lines will be truncated in the PDF manual.
Running ‘testthat.R’ [10m/10m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(nseval)
  > 
  > test_check("nseval")
  Killed
Package in Depends field not imported from: ‘mco’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
boundedPolyMutation: no visible global function definition for ‘runif’
boundedSBXover: no visible global function definition for ‘runif’
nsga2R : <anonymous>: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
.mcmc.bar: no visible global function definition for ‘rnorm’
.mcmc.bar: no visible global function definition for ‘runif’
.mcmc.comb: no visible global function definition for ‘rnorm’
.mcmc.comb: no visible global function definition for ‘runif’
.mcmc.rd: no visible global function definition for ‘rnorm’
.mcmc.rd: no visible global function definition for ‘runif’
.mcmc.trans: no visible global function definition for ‘rnorm’
.mcmc.trans: no visible global function definition for ‘runif’
.simulate.bar: no visible global function definition for ‘rlnorm’
.simulate.bar: no visible global function definition for ‘rbeta’
.simulate.bar: no visible global function definition for ‘rbinom’
.simulate.comb: no visible global function definition for ‘rlnorm’
.simulate.comb: no visible global function definition for ‘rbeta’
.simulate.comb: no visible global function definition for ‘rbinom’
.simulate.rd: no visible global function definition for ‘rlnorm’
.simulate.rd: no visible global function definition for ‘rbinom’
.simulate.trans: no visible global function definition for ‘rlnorm’
.simulate.trans: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  rbeta rbinom rlnorm rnorm runif
Consider adding
  importFrom("stats", "rbeta", "rbinom", "rlnorm", "rnorm", "runif")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Deprecated license: CC BY-NC-SA 3.0
Malformed Description field: should contain one or more complete sentences.
Deprecated license: CC BY-NC-ND 3.0 US
Packages in Depends field not imported from:
  ‘nutshell.audioscrobbler’ ‘nutshell.bbdb’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘nws/R/zzz.R’:
  .onLoad calls:
    require(methods)

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

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

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

These lines will be truncated in the PDF manual.
Malformed Title field: should not end in a period.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘objectSignals’
A package should be listed in only one of these fields.
Color: no visible global function definition for ‘new’
NegativeInteger: no visible global function definition for ‘new’
NonnegativeInteger: no visible global function definition for ‘new’
NonpositiveInteger: no visible global function definition for ‘new’
PositiveInteger: no visible global function definition for ‘new’
setMultipleEnum: no visible global function definition for ‘setClass’
setMultipleEnum: no visible global function definition for ‘prototype’
setNumericWithRange: no visible global function definition for
  ‘setClass’
setNumericWithRange: no visible global function definition for
  ‘prototype’
setPropertySet: no visible binding for global variable ‘extends’
setPropertySet: no visible global function definition for ‘setRefClass’
setSingleEnum: no visible global function definition for ‘setClass’
setSingleEnum: no visible global function definition for ‘prototype’
as.list,PropertySet: no visible global function definition for ‘as’
initialize,SingleEnum: no visible global function definition for
  ‘callNextMethod’
initialize,SingleEnum: no visible global function definition for ‘head’
Undefined global functions or variables:
  as callNextMethod extends head new prototype setClass setRefClass
Consider adding
  importFrom("methods", "as", "callNextMethod", "extends", "new",
             "prototype", "setClass", "setRefClass")
  importFrom("utils", "head")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Rd file 'Enum-class.Rd':
  \examples lines wider than 100 characters:
     PointSizeSingleEnum.gen <- setGlyphEnum("PointSize", levels = c("1", "2", "5", "10"), contains = "GlyphEnum")

These lines will be truncated in the PDF manual.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
Signal.gen: no visible global function definition for ‘new’
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
obliclus: no visible global function definition for ‘rnorm’
obliclus: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  kmeans rnorm
Consider adding
  importFrom("stats", "kmeans", "rnorm")
to your NAMESPACE file.
File ‘obliclus/libs/obliclus.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘random_cluster_C.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘random_cluster_C.o’

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

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

These lines will be truncated in the PDF manual.
Packages in Depends field not imported from:
  ‘DBI’ ‘RJDBC’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  as.vector.multifactor
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
multifactor: no visible global function definition for ‘na.omit’
ruuid: no visible global function definition for ‘runif’
Undefined global functions or variables:
  na.omit runif
Consider adding
  importFrom("stats", "na.omit", "runif")
to your NAMESPACE file.
Found the following hidden files and directories:
  .Rapp.history
  data/.Rapp.history
  data/.Rhistory
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘RCurl’ ‘maps’
A package should be listed in only one of these fields.
mapvar: no visible global function definition for ‘data’
mapvar: no visible binding for global variable ‘state.fips’
mapvar: no visible global function definition for ‘rgb’
mapvar: no visible global function definition for ‘rect’
mapvar: no visible global function definition for ‘text’
rowScrape: no visible global function definition for ‘tail’
rowScrape: no visible global function definition for ‘head’
scrapeTable: no visible binding for global variable ‘tail’
Undefined global functions or variables:
  data head rect rgb state.fips tail text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "rect", "text")
  importFrom("utils", "data", "head", "tail")
to your NAMESPACE file.

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

These lines will be truncated in the PDF manual.
generate.data: no visible global function definition for ‘rbinom’
least.common.ancestor: no visible global function definition for
  ‘na.omit’
oncotree.fit : estimate.error.rates: no visible global function
  definition for ‘optim’
plot.boottree: no visible global function definition for ‘par’
plot.boottree: no visible global function definition for
  ‘dev.interactive’
plot.boottree: no visible global function definition for ‘mtext’
plot.oncotree: no visible global function definition for ‘par’
plot.oncotree: no visible global function definition for ‘xinch’
plot.oncotree: no visible global function definition for ‘yinch’
plot.oncotree: no visible global function definition for ‘lines’
plot.oncotree: no visible global function definition for ‘rect’
plot.oncotree: no visible global function definition for ‘strwidth’
plot.oncotree: no visible global function definition for ‘strheight’
plot.oncotree: no visible global function definition for ‘text’
Undefined global functions or variables:
  dev.interactive lines mtext na.omit optim par rbinom rect strheight
  strwidth text xinch yinch
Consider adding
  importFrom("grDevices", "dev.interactive")
  importFrom("graphics", "lines", "mtext", "par", "rect", "strheight",
             "strwidth", "text", "xinch", "yinch")
  importFrom("stats", "na.omit", "optim", "rbinom")
to your NAMESPACE file.
ci.prop: no visible global function definition for ‘qf’
ci.prop: no visible global function definition for ‘qnorm’
ePCP: no visible global function definition for ‘qnorm’
sevennum: no visible global function definition for ‘na.omit’
sevennum: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  na.omit qf qnorm quantile
Consider adding
  importFrom("stats", "na.omit", "qf", "qnorm", "quantile")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  [.clFloat [<-.clFloat as.character.clFloat as.double.clFloat
  as.integer.clFloat length.clFloat length<-.clFloat oclInfo.clDeviceID
  oclInfo.clPlatformID oclInfo.list print.clFloat
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
gimli.13962hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Package suggested but not available for checking: ‘openNLPmodels.en’
Df2SpLinesDf: no visible global function definition for ‘slot’
PlotTraj: no visible global function definition for ‘par’
PlotTraj: no visible global function definition for ‘grid’
PlotTraj: no visible global function definition for ‘box’
PlotTrajFreq: no visible global function definition for ‘par’
PlotTrajFreq: no visible global function definition for ‘grid’
PlotTrajFreq: no visible global function definition for
  ‘colorRampPalette’
PlotTrajFreq: no visible global function definition for ‘legend’
PlotTrajFreq: no visible binding for global variable ‘title’
PlotTrajFreq: no visible global function definition for ‘dev.off’
ReadFiles: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  box colorRampPalette dev.off grid legend par read.table slot title
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off")
  importFrom("graphics", "box", "grid", "legend", "par", "title")
  importFrom("methods", "slot")
  importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
prepare_Rd: distance.Rd:21-22: Dropping empty section \details
prepare_Rd: distance.Rd:32-33: Dropping empty section \note
prepare_Rd: filter.Rd:26-27: Dropping empty section \details
prepare_Rd: filter.Rd:28-29: Dropping empty section \value
prepare_Rd: filter.Rd:36-37: Dropping empty section \note
prepare_Rd: findP.Rd:21-22: Dropping empty section \details
prepare_Rd: findP.Rd:34-35: Dropping empty section \note
prepare_Rd: ops-package.Rd:30-31: Dropping empty section \seealso
nlsolve: no visible global function definition for ‘optim’
nlsolve: no visible global function definition for ‘runif’
optAUC: no visible global function definition for ‘var’
Undefined global functions or variables:
  optim runif var
Consider adding
  importFrom("stats", "optim", "runif", "var")
to your NAMESPACE file.
Rd file 'optAUC-package.Rd':
  \examples lines wider than 100 characters:
     Y1Y2<-mvrnorm(n, c(y1.mean,y2.mean), matrix(c(y1.sd^2,rho*y1.sd*y2.sd, rho*y1.sd*y2.sd, y2.sd^2),2,2))
     # two markers in the model, the AUC from GCV is smaller than just first marker in the model, because the second marker is noise
     # the AUC from ACV (apearent estimate by substituting the estimated beta into the model) is larger than previous model, because overfit ... [TRUNCATED]

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

These lines will be truncated in the PDF manual.
avg2Lower: no visible global function definition for ‘optimize’
classificationError.data.frame: no visible binding for global variable
  ‘na.omit’
classificationError.data.frame: no visible global function definition
  for ‘terms’
classificationError.data.frame: no visible binding for global variable
  ‘predict’
classpredict.lda: no visible global function definition for ‘predict’
simData: no visible global function definition for ‘rnorm’
simData: no visible global function definition for ‘runif’
simData: no visible global function definition for ‘var’
tnormAvg: no visible global function definition for ‘dnorm’
tnormAvg: no visible global function definition for ‘pnorm’
yapprox: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx dnorm na.omit optimize pnorm predict rnorm runif terms var
Consider adding
  importFrom("stats", "approx", "dnorm", "na.omit", "optimize", "pnorm",
             "predict", "rnorm", "runif", "terms", "var")
to your NAMESPACE file.
calculate.empirical.AUC: no visible global function definition for
  ‘qnorm’
ci.AgrestiCoull: no visible global function definition for ‘qnorm’
ci.GartNam: no visible global function definition for ‘qnorm’
ci.NotTransformed: no visible global function definition for ‘qnorm’
ci.RubinSchenker: no visible global function definition for ‘qnorm’
ci.RubinSchenker: no visible global function definition for ‘plogis’
ci.RubinSchenker: no visible global function definition for ‘qlogis’
ci.exact: no visible global function definition for ‘qf’
ci.quadratic: no visible global function definition for ‘qnorm’
ci.transformed: no visible global function definition for ‘qnorm’
ci.wald: no visible global function definition for ‘qnorm’
function.MinPvalue: no visible global function definition for
  ‘chisq.test’
function.MinPvalue : PADJMS: no visible global function definition for
  ‘qnorm’
function.MinPvalue : PADJMS: no visible global function definition for
  ‘dnorm’
optimal.cutpoints.default: no visible global function definition for
  ‘na.omit’
optimal.cutpoints.formula: no visible global function definition for
  ‘terms’
plot.optimal.cutpoints: no visible global function definition for ‘par’
plot.optimal.cutpoints: no visible global function definition for
  ‘plot’
plot.optimal.cutpoints: no visible global function definition for
  ‘abline’
plot.optimal.cutpoints: no visible global function definition for
  ‘lines’
plot.optimal.cutpoints: no visible global function definition for
  ‘points’
Undefined global functions or variables:
  abline chisq.test dnorm lines na.omit par plogis plot points qf
  qlogis qnorm terms
Consider adding
  importFrom("graphics", "abline", "lines", "par", "plot", "points")
  importFrom("stats", "chisq.test", "dnorm", "na.omit", "plogis", "qf",
             "qlogis", "qnorm", "terms")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘gurobi’
print.optimbase: no visible global function definition for ‘str’
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
Rd file 'TestStage.Rd':
  \examples lines wider than 100 characters:
     object1 <- OptimDes(B.init,m.init,alpha,beta,param,x,target="EDA",sf="futility",num.arm=1,num.stage=2)
     mda <- ifelse(l>1,B.init[l-1]+(B.init[l]-B.init[l-1])*(n-sum(m.init[1:(l-1)]))/m.init[l],B.init[l]*(n/m.init[l]))

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

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

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

These lines will be truncated in the PDF manual.
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of ‘nr’ to ‘nrow’
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of ‘nc’ to ‘ncol’
bgmm: no visible global function definition for ‘ecdf’
bgmm : SplineGMM: no visible global function definition for
  ‘constrOptim’
blr: no visible global function definition for ‘ecdf’
blr: no visible global function definition for ‘constrOptim’
blr: no visible global function definition for ‘lm’
parentcdf : combinations: no visible global function definition for
  ‘combn’
parentcdf : solver: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  combn constrOptim ecdf lm uniroot
Consider adding
  importFrom("stats", "constrOptim", "ecdf", "lm", "uniroot")
  importFrom("utils", "combn")
to your NAMESPACE file.
'library' or 'require' call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘grid’ ‘lattice’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  predict.orderedLasso predict.orderedLasso.path predict.timeLagLasso
  predict.timeLagLasso.path
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
error.bars: no visible global function definition for ‘segments’
lambda.interp: no visible global function definition for ‘approx’
orderedLasso: no visible binding for global variable ‘sd’
orderedLasso.cv: no visible binding for global variable ‘var’
plot.orderedLasso.cv: no visible global function definition for ‘par’
plot.orderedLasso.cv: no visible global function definition for ‘plot’
plot.orderedLasso.cv: no visible global function definition for ‘axis’
plot.orderedLasso.cv: no visible global function definition for ‘mtext’
plot.orderedLasso.cv: no visible global function definition for
  ‘points’
plot.orderedLasso.cv: no visible global function definition for
  ‘abline’
plot.timeLagLasso.cv: no visible global function definition for ‘par’
plot.timeLagLasso.cv: no visible global function definition for ‘plot’
plot.timeLagLasso.cv: no visible global function definition for ‘axis’
plot.timeLagLasso.cv: no visible global function definition for ‘mtext’
plot.timeLagLasso.cv: no visible global function definition for
  ‘points’
plot.timeLagLasso.cv: no visible global function definition for
  ‘abline’
timeLagLasso: no visible binding for global variable ‘sd’
timeLagLasso.cv: no visible binding for global variable ‘sd’
timeLagLasso.cv: no visible binding for global variable ‘var’
timeLagLasso.path: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  abline approx axis mtext par plot points sd segments var
Consider adding
  importFrom("graphics", "abline", "axis", "mtext", "par", "plot",
             "points", "segments")
  importFrom("stats", "approx", "sd", "var")
to your NAMESPACE file.
genRidge: no visible global function definition for ‘plogis’
ordGene: no visible global function definition for ‘anova’
ordGene: no visible global function definition for ‘lm’
ordSelect: no visible binding for global variable ‘sd’
ordSmooth: no visible binding for global variable ‘sd’
plot.ordPen: no visible global function definition for ‘grey’
plot.ordPen: no visible global function definition for ‘devAskNewPage’
plot.ordPen: no visible global function definition for ‘plot’
plot.ordPen: no visible global function definition for ‘lines’
predict.ordPen: no visible global function definition for ‘plogis’
Undefined global functions or variables:
  anova devAskNewPage grey lines lm plogis plot sd
Consider adding
  importFrom("grDevices", "devAskNewPage", "grey")
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "anova", "lm", "plogis", "sd")
to your NAMESPACE file.
ORICC1: no visible binding for global variable ‘sd’
ORICC1: no visible global function definition for ‘write.table’
ORICC1: no visible global function definition for ‘postscript’
ORICC1: no visible global function definition for ‘jpeg’
ORICC1: no visible global function definition for ‘plot’
ORICC1: no visible global function definition for ‘points’
ORICC1: no visible global function definition for ‘dev.off’
ORICC1: no visible global function definition for ‘par’
ORICC2: no visible binding for global variable ‘sd’
ORICC2: no visible global function definition for ‘write.table’
ORICC2: no visible global function definition for ‘postscript’
ORICC2: no visible global function definition for ‘jpeg’
ORICC2: no visible global function definition for ‘plot’
ORICC2: no visible global function definition for ‘points’
ORICC2: no visible global function definition for ‘dev.off’
ORICC2: no visible global function definition for ‘par’
Undefined global functions or variables:
  dev.off jpeg par plot points postscript sd write.table
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "postscript")
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
boat3d: no visible global function definition for ‘rgl.cur’
boat3d: no visible global function definition for ‘open3d’
boat3d: no visible global function definition for ‘clear3d’
boat3d: no visible global function definition for ‘bg3d’
boat3d: no visible global function definition for ‘rgl.set’
boat3d: no visible global function definition for ‘triangles3d’
boat3d: no visible global function definition for ‘quads3d’
boat3d: no visible global function definition for ‘decorate3d’
boat3d: no visible global function definition for ‘scatterplot3d’
orientlm: no visible global function definition for ‘model.matrix’
orientlm: no visible global function definition for ‘lm’
Undefined global functions or variables:
  bg3d clear3d decorate3d lm model.matrix open3d quads3d rgl.cur
  rgl.set scatterplot3d triangles3d
Consider adding
  importFrom("stats", "lm", "model.matrix")
to your NAMESPACE file.
File ‘OriGen/libs/OriGen.so’:
  Found ‘_gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘_gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘_gfortran_st_read’, possibly from ‘read’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘_gfortran_st_rewind’, possibly from ‘rewind’ (Fortran)
    Object: ‘OriGen.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
mdr.c: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
dicomTable: no visible global function definition for ‘txtProgressBar’
dicomTable: no visible global function definition for
  ‘setTxtProgressBar’
readDICOM: no visible global function definition for ‘txtProgressBar’
readDICOM: no visible global function definition for
  ‘setTxtProgressBar’
writeHeader: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar write.table
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar",
             "write.table")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘genefilter’ ‘gtools’ ‘nlme’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
est.lme : <anonymous>: warning in rank(iru, ties = "min"): partial
  argument match of ‘ties’ to ‘ties.method’
est.lme : <anonymous>: no visible global function definition for ‘lme’
est.lme : <anonymous>: no visible global function definition for
  ‘VarCorr’
guo: no visible global function definition for ‘p.adjust’
guo: no visible global function definition for ‘na.omit’
pttest : ptest: no visible global function definition for ‘na.omit’
srt : <anonymous>: no visible global function definition for
  ‘rowttests’
Undefined global functions or variables:
  VarCorr lme na.omit p.adjust rowttests
Consider adding
  importFrom("stats", "na.omit", "p.adjust")
to your NAMESPACE file.
plot.SplineBasis: no visible global function definition for ‘matplot’
plot,SplineBasis-matrix: no visible global function definition for
  ‘matplot’
plot,SplineBasis-missing: no visible global function definition for
  ‘matplot’
Undefined global functions or variables:
  matplot
Consider adding
  importFrom("graphics", "matplot")
to your NAMESPACE file.
'library' or 'require' call to ‘polynom’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘polynom’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
chebyshev.c.polynomials: no visible global function definition for
  ‘polynomial’
chebyshev.s.polynomials: no visible global function definition for
  ‘polynomial’
chebyshev.t.polynomials: no visible global function definition for
  ‘polynomial’
chebyshev.u.polynomials: no visible global function definition for
  ‘polynomial’
gegenbauer.polynomials: no visible global function definition for
  ‘polynomial’
ghermite.h.polynomials: no visible global function definition for
  ‘polynomial’
glaguerre.polynomials: no visible global function definition for
  ‘polynomial’
hermite.h.polynomials: no visible global function definition for
  ‘polynomial’
hermite.he.polynomials: no visible global function definition for
  ‘polynomial’
jacobi.g.polynomials: no visible global function definition for
  ‘polynomial’
jacobi.p.polynomials: no visible global function definition for
  ‘polynomial’
legendre.polynomials: no visible global function definition for
  ‘polynomial’
monic.polynomials: no visible global function definition for
  ‘polynomial’
orthogonal.polynomials: no visible global function definition for
  ‘polynomial’
orthonormal.polynomials: no visible global function definition for
  ‘polynomial’
polynomial.derivatives: no visible global function definition for
  ‘deriv’
polynomial.integrals: no visible global function definition for
  ‘integral’
polynomial.values: no visible global function definition for ‘predict’
schebyshev.t.polynomials: no visible global function definition for
  ‘polynomial’
schebyshev.u.polynomials: no visible global function definition for
  ‘polynomial’
slegendre.polynomials: no visible global function definition for
  ‘polynomial’
Undefined global functions or variables:
  deriv integral polynomial predict
Consider adding
  importFrom("stats", "deriv", "predict")
to your NAMESPACE file.
Found the following significant warnings:
  ccaRevolution.c:31:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:44:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:97:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:98:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:110:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:111:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/osc.Rcheck/00install.out’ for details.
'library' or 'require' calls in package code:
  ‘igraph’ ‘sp’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
as_igraph : <anonymous>: no visible global function definition for
  ‘distHaversine’
as_igraph: no visible global function definition for ‘graph.edgelist’
as_igraph: no visible global function definition for ‘E’
as_igraph: no visible global function definition for ‘E<-’
as_sp_lines: no visible global function definition for ‘Lines’
as_sp_points: no visible global function definition for
  ‘SpatialPointsDataFrame’
as_sp_polygons: no visible global function definition for ‘Polygons’
as_sp_polygons: no visible global function definition for
  ‘SpatialPolygons’
as_sp_polygons: no visible global function definition for
  ‘SpatialPolygonsDataFrame’
make_SLDF: no visible global function definition for ‘SpatialLines’
make_SLDF: no visible global function definition for
  ‘SpatialLinesDataFrame’
osm_crs: no visible global function definition for ‘CRS’
plot.osmar: no visible global function definition for ‘gray’
plot_nodes: no visible global function definition for ‘points’
plot_nodes: no visible global function definition for ‘plot’
plot_ways: no visible global function definition for ‘plot’
plot_ways: no visible global function definition for ‘lines’
ways_nodes2Line: no visible global function definition for ‘Line’
ways_nodes2Polygon: no visible global function definition for ‘Polygon’
Undefined global functions or variables:
  CRS E E<- Line Lines Polygon Polygons SpatialLines
  SpatialLinesDataFrame SpatialPointsDataFrame SpatialPolygons
  SpatialPolygonsDataFrame distHaversine graph.edgelist gray lines plot
  points
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
odm: no visible binding for global variable ‘sd’
odm : <anonymous>: no visible global function definition for ‘sd’
odm : <anonymous>: no visible global function definition for ‘quantile’
odm: no visible global function definition for ‘prcomp’
quant.const: no visible global function definition for ‘quantile’
quant.const.D: no visible global function definition for ‘reshape’
quant.const.D: no visible global function definition for ‘quantile’
quant.linear.D: no visible global function definition for ‘reshape’
quant.nonlin : FrankModel: no visible global function definition for
  ‘qt’
quant.nonlin : FrankModel: no visible global function definition for
  ‘pt’
quant.nonlin: no visible global function definition for ‘predict’
quant.nonlin.D: no visible global function definition for ‘reshape’
quant.nonlin.D: no visible global function definition for ‘predict’
quant.nonpar.D: no visible global function definition for ‘reshape’
rgrubbs.test: no visible global function definition for ‘sd’
plot,OutlierDM-missing: no visible binding for global variable ‘pch’
summary,OutlierDM: no visible global function definition for ‘head’
Undefined global functions or variables:
  head pch prcomp predict pt qt quantile reshape sd
Consider adding
  importFrom("stats", "prcomp", "predict", "pt", "qt", "quantile",
             "reshape", "sd")
  importFrom("utils", "head")
to your NAMESPACE file.
Electre3_AlphaBetaThresholds: no visible global function definition for
  ‘plot’
Electre3_SimpleThresholds: no visible global function definition for
  ‘plot’
Electre_1: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'genealogicalSorting', 'phybase'
gimli.31314hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
ms.exec: no visible global function definition for ‘tail’
p2c2m.readstarb: no visible global function definition for ‘head’
p2c2m.readstarb: no visible binding for global variable ‘head’
rmOutlrs: no visible global function definition for ‘boxplot.stats’
rmext: no visible global function definition for ‘tail’
rowMedians: no visible binding for global variable ‘median’
stats.acrGenes: no visible binding for global variable ‘sd’
stats.perGene: no visible binding for global variable ‘sd’
statshelpers.cv: no visible binding for global variable ‘sd’
statshelpers.qntls: no visible binding for global variable ‘quantile’
Undefined global functions or variables:
  boxplot.stats head median quantile sd tail
Consider adding
  importFrom("grDevices", "boxplot.stats")
  importFrom("stats", "median", "quantile", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
loadCSVtoP2distance: no visible global function definition for
  ‘read.table’
p2distance : calcularDistancia: no visible binding for global variable
  ‘sd’
p2distance : ordenarVariables: no visible global function definition
  for ‘cor’
p2distance : calculoFactoresPonderacion: no visible global function
  definition for ‘lm’
p2distance: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor lm read.table sd
Consider adding
  importFrom("stats", "cor", "lm", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'library' or 'require' call to ‘survival’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
p3state: no visible global function definition for ‘survfit’
p3state: no visible global function definition for ‘terms’
p3state: no visible global function definition for ‘as.formula’
p3state: no visible global function definition for ‘coxph’
p3state: no visible binding for global variable ‘na.exclude’
plot.p3state: no visible global function definition for ‘matplot’
plot.p3state: no visible global function definition for ‘devAskNewPage’
plot.p3state: no visible global function definition for ‘persp’
plot.p3state: no visible global function definition for ‘colours’
plot.p3state: no visible global function definition for
  ‘filled.contour’
Undefined global functions or variables:
  as.formula colours coxph devAskNewPage filled.contour matplot
  na.exclude persp survfit terms
Consider adding
  importFrom("grDevices", "colours", "devAskNewPage")
  importFrom("graphics", "filled.contour", "matplot", "persp")
  importFrom("stats", "as.formula", "na.exclude", "terms")
to your NAMESPACE file.
pacbpred : thetaFunc: no visible global function definition for ‘lsfit’
pacbpred : thetaFunc: no visible global function definition for ‘rnorm’
pacbpred: no visible global function definition for ‘var’
pacbpred: no visible global function definition for ‘runif’
pacbpred: no visible global function definition for ‘rnorm’
pacbpred: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  lsfit rbinom rnorm runif var
Consider adding
  importFrom("stats", "lsfit", "rbinom", "rnorm", "runif", "var")
to your NAMESPACE file.
Non-standard files/directories found at top level:
  ‘DESCRIPTION_EX’ ‘divers’ ‘main.R’ ‘testsDev’
[,ClassW: warning in switch(EXP = i, u1 = {: partial argument match of
  ‘EXP’ to ‘EXPR’
[,ClassW: warning in return(x@u1): partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in }, u2 = {: partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in return(x@u2): partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in }, w1 = {: partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in return(x@w1): partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in }): partial argument match of ‘EXP’ to ‘EXPR’
[<-,ClassW: warning in switch(EXP = i, u1 = {: partial argument match
  of ‘EXP’ to ‘EXPR’
[<-,ClassW: warning in x@u1 <- value: partial argument match of ‘EXP’
  to ‘EXPR’
[<-,ClassW: warning in }, u2 = {: partial argument match of ‘EXP’ to
  ‘EXPR’
[<-,ClassW: warning in x@u2 <- value: partial argument match of ‘EXP’
  to ‘EXPR’
[<-,ClassW: warning in }, w1 = {: partial argument match of ‘EXP’ to
  ‘EXPR’
[<-,ClassW: warning in x@w1 <- value: partial argument match of ‘EXP’
  to ‘EXPR’
[<-,ClassW: warning in }): partial argument match of ‘EXP’ to ‘EXPR’
paf: no visible global function definition for ‘as.formula’
paf: no visible global function definition for ‘model.response’
paf: no visible global function definition for ‘model.frame’
paf: no visible global function definition for ‘model.matrix’
plot.paf: no visible global function definition for ‘plot’
plot.paf: no visible global function definition for ‘lines’
Undefined global functions or variables:
  as.formula lines model.frame model.matrix model.response plot
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response")
to your NAMESPACE file.
CalGIF: no visible binding for global variable ‘PAGIData’
CalGIF2: no visible binding for global variable ‘PAGIData’
PAGI.Main: no visible binding for global variable ‘PAGIData’
PAGI.Main: no visible global function definition for ‘p.adjust’
PAGI.Main: no visible global function definition for ‘pt’
getclass.labels: no visible binding for global variable ‘ExampleData’
getdataset: no visible binding for global variable ‘ExampleData’
Undefined global functions or variables:
  ExampleData PAGIData p.adjust pt
Consider adding
  importFrom("stats", "p.adjust", "pt")
to your NAMESPACE file.
Rd file 'CalGIF.Rd':
  \examples lines wider than 100 characters:
     ###calculate the global influence factor (GIF) by using the random walk with restart (RWR) algorithm###
     #Each element is the GIF score and whose name correspond to gene symbol in the gene expression data. 
     #Each element is the GIF score and whose name correspond to gene symbol in the gene expression data. 

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

These lines will be truncated in the PDF manual.
paired.Loc: no visible global function definition for ‘qt’
paired.Loc: no visible global function definition for ‘median’
paired.Loc: no visible global function definition for ‘qsignrank’
paired.Loc: no visible global function definition for ‘qnorm’
paired.Scale: no visible global function definition for ‘var’
paired.Scale: no visible global function definition for ‘cor’
paired.Scale: no visible global function definition for ‘qt’
paired.Scale: no visible global function definition for ‘median’
paired.Scale: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  cor median qnorm qsignrank qt var
Consider adding
  importFrom("stats", "cor", "median", "qnorm", "qsignrank", "qt", "var")
to your NAMESPACE file.
Rd file 'pairheatmap.Rd':
  \examples lines wider than 100 characters:
              groupBorder.selectList=list(xgroup.start=c(8), xgroup.end=c(11), ygroup.start=c(22), ygroup.end=c(25)),
              groupBorder.selectList=list(xgroup.start=c(8), xgroup.end=c(11), ygroup.start=c(22), ygroup.end=c(25)),
              groupBorder.selectList=list(xgroup.start=c(8), xgroup.end=c(11), ygroup.start=c(22), ygroup.end=c(25)),

These lines will be truncated in the PDF manual.
pairsD3: no visible global function definition for ‘gray.colors’
Undefined global functions or variables:
  gray.colors
Consider adding
  importFrom("grDevices", "gray.colors")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘lattice’ ‘vegan’
  Please remove these calls from your code.
Rd file 'syas.Rd':
  \examples lines wider than 100 characters:
     bcrossv.sa(modernq[,1],perq2,a.d,delta=25,method="canberra",quant=0.05,trials=c(5, 0.05),detrend=FALSE)

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

These lines will be truncated in the PDF manual.
EAMM: no visible global function definition for ‘anova’
EAMM: no visible global function definition for ‘rand’
PAMM: no visible global function definition for ‘rand’
PAMM: no visible global function definition for ‘anova’
SSF: no visible global function definition for ‘rand’
SSF: no visible global function definition for ‘anova’
Undefined global functions or variables:
  anova rand
Consider adding
  importFrom("stats", "anova")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  print.pamrcved print.pamrtrained
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
GOpredict: no visible global function definition for ‘fisher.test’
KEGGpredict: no visible global function definition for ‘fisher.test’
ProteinCluster: no visible global function definition for ‘ecdf’
ProteinCluster: no visible global function definition for ‘as.hclust’
ProteinCluster: no visible global function definition for
  ‘as.dendrogram’
ProteinCluster : addE: no visible global function definition for
  ‘is.leaf’
ProteinCluster: no visible global function definition for ‘plot’
SignificantSubcluster: no visible global function definition for
  ‘order.dendrogram’
SignificantSubcluster: no visible global function definition for
  ‘fisher.test’
SignificantSubcluster: no visible global function definition for ‘plot’
Undefined global functions or variables:
  as.dendrogram as.hclust ecdf fisher.test is.leaf order.dendrogram
  plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "as.dendrogram", "as.hclust", "ecdf",
             "fisher.test", "is.leaf", "order.dendrogram")
to your NAMESPACE file.
Paneldata.formula: no visible global function definition for
  ‘model.frame’
Paneldata.formula: no visible global function definition for
  ‘model.matrix’
Paneldata.formula: no visible global function definition for
  ‘model.response’
summary.Paneldata: no visible global function definition for ‘coef’
summary.Paneldata: no visible global function definition for ‘pt’
Undefined global functions or variables:
  coef model.frame model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.frame", "model.matrix",
             "model.response", "pt")
to your NAMESPACE file.