whether the namespace can be loaded with stated dependencies
PDF version of manual without hyperrefs or index
whether the package can be unloaded cleanly

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.
File ‘ABCoptim/libs/ABCoptim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘abcrf/libs/abcrf.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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’
File ‘abn/libs/abn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘AbsFilterGSEA/libs/AbsFilterGSEA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘abundant/libs/abundant.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘accelerometry/libs/accelerometry.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘acc/libs/acc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package has no Sweave vignette sources and no VignetteBuilder field.
File ‘ACDm/libs/ACDm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘acepack/libs/acepack.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘acrt/libs/acrt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
cbind:
  function(..., deparse.level)
cbind.acs:
  function(e1, e2)

rbind:
  function(..., deparse.level)
rbind.acs:
  function(e1, e2)

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

Found the following apparent S3 methods exported but not registered:
  cbind.acs rbind.acs
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘ACTCD/libs/ACTCD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘actuar’ ‘hypergeo’ ‘reliaR’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘ActuDistns-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dgumbeld
> ### Title: Gumbel pdf
> ### Aliases: dgumbeld
> ### Keywords: Gumbel distribution
> 
> ### ** Examples
> x=runif(10,min=0,max=1)
> y=dgumbeld(x)
Error in dgumbel(x, mu = mu, sigma = sigma) : 
  unused arguments (mu = mu, sigma = sigma)
Calls: dgumbeld -> ifelse
Execution halted
File ‘adagio/libs/adagio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.amdai.initparam: no visible global function definition for ‘cov’
.amdat.initiparam: no visible global function definition for ‘cov’
amdai: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
File ‘AdaptFitOS/libs/AdaptFitOS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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.
'library' or 'require' calls in package code:
  ‘MASS’ ‘Matrix’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘Rcpp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  asggm.default asggm.formula aslm.default aslm.formula logLik.aslm
  nobs.aslm predict.aslm print.aslm print.summary.aslm summary.aslm
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘AdaptiveSparsity/libs/AdaptiveSparsity.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘adaptivetau/libs/adaptivetau.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘Matrix’ ‘parallel’
  Please remove these calls from your code.
MCMC: no visible global function definition for ‘txtProgressBar’
MCMC: no visible global function definition for ‘setTxtProgressBar’
MCMC: no visible global function definition for ‘rnorm’
MCMC: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rnorm runif setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "rnorm", "runif")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Depends: includes the non-default packages:
  ‘Matrix’ ‘coda’ ‘mvtnorm’ ‘MCMCpack’ ‘spatstat’ ‘parallel’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  ‘MCMCpack’ ‘Matrix’ ‘coda’ ‘mvtnorm’ ‘parallel’ ‘spatstat’
  Please remove these calls from your code.
Package in Depends field not imported from: ‘lattice’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
Found the following apparent S3 methods exported but not registered:
  [.haploGen cbind.SNPbin cbind.genlight rbind.genlight
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘adegenet/libs/adegenet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘adehabitatHR/libs/adehabitatHR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘adehabitatHS/libs/adehabitatHS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘adehabitatLT/libs/adehabitatLT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘adehabitatMA/libs/adehabitatMA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  [.ltraj [<-.ltraj
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘adehabitat/libs/adehabitat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘adephylo/libs/adephylo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘adimpro/libs/adimpro.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package in Depends field not imported from: ‘EbayesThresh’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
artlev: no visible global function definition for ‘quantile’
basisfns: no visible global function definition for ‘plot’
basisfns: no visible global function definition for ‘lines’
basisfns: no visible global function definition for ‘legend’
basisfns: no visible global function definition for ‘dev.cur’
basisfns: no visible global function definition for ‘dev.set’
denoise: no visible global function definition for ‘mad’
denoise: no visible global function definition for ‘ebayesthresh’
denoise2: no visible global function definition for ‘mad’
denoise2: no visible global function definition for ‘ebayesthresh’
denoisehetero: no visible global function definition for ‘ebayesthresh’
denoisehetero2: no visible global function definition for
  ‘ebayesthresh’
denoiseheteromp: no visible global function definition for
  ‘ebayesthresh’
denoiseheteroprop: no visible global function definition for ‘mad’
denoiseheteroprop: no visible global function definition for
  ‘ebayesthresh’
denoiseheteroprop2: no visible global function definition for ‘mad’
denoiseheteroprop2: no visible global function definition for
  ‘ebayesthresh’
dojitter: no visible global function definition for ‘runif’
heterovar: no visible global function definition for ‘mad’
heterovar: no visible global function definition for ‘median’
make.signal2: no visible global function definition for ‘dnorm’
make.signal2: no visible global function definition for ‘rnorm’
make.signal2: no visible global function definition for ‘var’
modjitter: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dev.cur dev.set dnorm ebayesthresh legend lines mad median plot
  quantile rnorm runif var
Consider adding
  importFrom("grDevices", "dev.cur", "dev.set")
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "dnorm", "mad", "median", "quantile", "rnorm",
             "runif", "var")
to your NAMESPACE file.
Rd file 'PointsUpdatemp.Rd':
  \examples lines wider than 100 characters:
     u<-PointsUpdatemp(X,coefflist,p$newinfo[[2]],newnbrs,p$newinfo[[3]],31,order(X),p$results[[4]],lengths)

Rd file 'UndoPointsUpdate.Rd':
  \examples lines wider than 100 characters:
     undo<-UndoPointsUpdate(x,u$coeff,p$newinfo[[2]],p$newinfo[[3]],5,a,99,p2,p$results[[4]],l2,lengths[a])

These lines will be truncated in the PDF manual.
File ‘adlift/libs/adlift.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
ADM3: no visible global function definition for ‘read.table’
ADM3: no visible global function definition for ‘write.table’
dLRs: no visible global function definition for ‘IQR’
dLRs: no visible global function definition for ‘na.omit’
dLRs: no visible global function definition for ‘qnorm’
plotADM3: no visible global function definition for ‘plot’
plotADM3: no visible global function definition for ‘abline’
plotADM3: no visible global function definition for ‘segments’
Undefined global functions or variables:
  IQR abline na.omit plot qnorm read.table segments write.table
Consider adding
  importFrom("graphics", "abline", "plot", "segments")
  importFrom("stats", "IQR", "na.omit", "qnorm")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
File ‘ADM3/libs/ADM3.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘AdMit/libs/AdMit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ADMMnet/libs/ADMMnet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.fads plot.fads.k12fun plot.fads.k12fun plot.fads.kdfun
  plot.fads.kdfun plot.fads.kfun plot.fads.kfun plot.fads.kmfun
  plot.fads.kmfun plot.fads.kp.fun plot.fads.kp.fun plot.fads.kpqfun
  plot.fads.kpqfun plot.fads.krfun plot.fads.krfun plot.fads.ksfun
  plot.fads.ksfun plot.fads.mimetic plot.fads.mimetic plot.mimetic
  plot.spp plot.swin plot.vads plot.vads.dval plot.vads.dval
  plot.vads.k12val plot.vads.k12val plot.vads.kval plot.vads.kval
  print.fads print.fads.k12fun print.fads.k12fun print.fads.kfun
  print.fads.kfun print.fads.kmfun print.fads.kmfun print.fads.kp.fun
  print.fads.kp.fun print.fads.kpqfun print.fads.kpqfun
  print.fads.krfun print.fads.krfun print.fads.ksfun print.fads.ksfun
  print.spp print.summary.dval print.summary.k12val print.summary.kval
  print.summary.spp print.summary.swin print.swin print.vads
  print.vads.dval print.vads.dval print.vads.k12val print.vads.k12val
  print.vads.kval print.vads.kval summary.spp summary.swin summary.vads
  summary.vads.dval summary.vads.dval summary.vads.k12val
  summary.vads.k12val summary.vads.kval summary.vads.kval
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘ads/libs/ads.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
plotsignal: no visible global function definition for ‘plot’
plotsignal: no visible global function definition for ‘abline’
plotsignal: no visible global function definition for ‘polygon’
plotsignal: no visible global function definition for ‘lines’
signal : <anonymous>: no visible global function definition for ‘var’
signal: no visible global function definition for ‘var’
signal : func_filt: no visible global function definition for ‘filter’
signal : func_interp: no visible global function definition for
  ‘approx’
signal: no visible global function definition for ‘approx’
Undefined global functions or variables:
  abline approx filter lines plot polygon var
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "polygon")
  importFrom("stats", "approx", "filter", "var")
to your NAMESPACE file.
aftgee: no visible global function definition for ‘model.extract’
aftgee: no visible global function definition for ‘model.matrix’
aftgee: no visible global function definition for ‘lm’
aftgee: no visible global function definition for ‘vcov’
aftgee.fit: no visible global function definition for ‘lm’
aftgee.fit: no visible global function definition for ‘rexp’
aftgee.fit: no visible global function definition for ‘var’
aftsrr: no visible global function definition for ‘model.extract’
aftsrr: no visible global function definition for ‘model.matrix’
aftsrr.fit: no visible global function definition for ‘lm’
aftsrr.fit: no visible global function definition for ‘rexp’
aftsrr.fit: no visible global function definition for ‘var’
getSmoothSuv: no visible global function definition for ‘pnorm’
print.summary.aftgee: no visible global function definition for
  ‘printCoefmat’
print.summary.aftsrr: no visible global function definition for
  ‘printCoefmat’
solveGehan: no visible global function definition for ‘nlm’
summary.aftgee: no visible global function definition for ‘pnorm’
summary.aftsrr: no visible global function definition for ‘pnorm’
viEmp: no visible global function definition for ‘rexp’
viEmp: no visible global function definition for ‘rnorm’
viEmp: no visible global function definition for ‘var’
zlFun: no visible global function definition for ‘lm’
Undefined global functions or variables:
  lm model.extract model.matrix nlm pnorm printCoefmat rexp rnorm var
  vcov
Consider adding
  importFrom("stats", "lm", "model.extract", "model.matrix", "nlm",
             "pnorm", "printCoefmat", "rexp", "rnorm", "var", "vcov")
to your NAMESPACE file.
File ‘aftgee/libs/aftgee.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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').
Found the following apparent S3 methods exported but not registered:
  plot.report summary.agreement summary.report summary.tir_iir
  summary.unified_agreement
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
IIR: no visible global function definition for ‘qnorm’
TIR: no visible global function definition for ‘qnorm’
agreement: no visible global function definition for ‘var’
agreement: no visible global function definition for ‘pchisq’
agreement: no visible global function definition for ‘dnorm’
agreement: no visible global function definition for ‘qnorm’
html.report: no visible global function definition for ‘plot’
plot.report: no visible global function definition for ‘plot’
plot.report: no visible global function definition for ‘axis’
plot.report: no visible global function definition for ‘points’
unified.agreement: no visible global function definition for ‘lm’
unified.agreement: no visible global function definition for ‘qnorm’
unified.agreement: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  axis dnorm lm pchisq plot pnorm points qnorm var
Consider adding
  importFrom("graphics", "axis", "plot", "points")
  importFrom("stats", "dnorm", "lm", "pchisq", "pnorm", "qnorm", "var")
to your NAMESPACE file.
File ‘AGSDest/libs/AGSDest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ahaz/libs/ahaz.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package unavailable to check Rd xrefs: ‘Starr’
File ‘AhoCorasickTrie/libs/AhoCorasickTrie.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘AHR/libs/AHR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
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.
File ‘airGR/libs/airGR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘akima/libs/akima.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘stats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
File ‘AlgDesign/libs/AlgDesign.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘algstat/libs/algstat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘AlignStat/libs/AlignStat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘alineR/libs/alineR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
gascuel: no visible global function definition for ‘optim’
Undefined global functions or variables:
  optim
Consider adding
  importFrom("stats", "optim")
to your NAMESPACE file.
File ‘ALKr/libs/ALKr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
'library' or 'require' call to ‘pedigree’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Blcl: no visible global function definition for ‘qnorm’
Bucl: no visible global function definition for ‘qnorm’
aRetain : run.one.repl: no visible global function definition for
  ‘split.screen’
aRetain : run.one.repl: no visible global function definition for
  ‘close.screen’
aRetain : run.one.repl: no visible global function definition for
  ‘screen’
aRetain : run.one.repl: no visible global function definition for
  ‘plot’
aRetain : run.one.repl: no visible global function definition for
  ‘flush.console’
aRetain.summary : SE: no visible global function definition for ‘var’
addnew: no visible global function definition for ‘rbinom’
breed: no visible global function definition for ‘rpois’
newinfo: no visible global function definition for ‘rnorm’
newinfo: no visible global function definition for ‘rgamma’
pedigree.summary: no visible global function definition for ‘orderPed’
pedigree.summary: no visible global function definition for
  ‘calcInbreeding’
pedigree.summary: no visible global function definition for ‘var’
Undefined global functions or variables:
  calcInbreeding close.screen flush.console orderPed plot qnorm rbinom
  rgamma rnorm rpois screen split.screen var
Consider adding
  importFrom("graphics", "close.screen", "plot", "screen",
             "split.screen")
  importFrom("stats", "qnorm", "rbinom", "rgamma", "rnorm", "rpois",
             "var")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
File ‘allelic/libs/allelic.so’:
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Object: ‘newallelic.o’
File ‘allelic/libs/allelic.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
It is good practice to register native routines and to disable symbol
search.

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
File ‘alphabetr/libs/alphabetr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘alphahull/libs/alphahull.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘alphashape3d/libs/alphashape3d.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package in Depends field not imported from: ‘car’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  ‘car:::bcPower’ ‘car:::bootCase’ ‘car:::deltaMethod’
  ‘car:::infIndexPlot’ ‘car:::invResPlot’ ‘car:::invTranEstimate’
  ‘car:::invTranPlot’ ‘car:::marginalModelPlot’ ‘car:::outlierTest’
  ‘car:::powerTransform’ ‘car:::residualPlot’ ‘car:::residualPlots’
  ‘car:::testTransform’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘car:::residCurvTest’ ‘car:::tukeyNonaddTest’
  See the note in ?`:::` about the use of this operator.
Found the following apparent S3 methods exported but not registered:
  pod.formula sigma.hat
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
alr4Web: no visible global function definition for ‘browseURL’
print.summary.lm: no visible binding for global variable ‘quantile’
print.summary.lm: no visible global function definition for ‘quantile’
print.summary.lm: no visible global function definition for
  ‘printCoefmat’
print.summary.lm: no visible global function definition for ‘naprint’
print.summary.lm: no visible global function definition for ‘pf’
print.summary.lm: no visible global function definition for ‘symnum’
Undefined global functions or variables:
  browseURL naprint pf printCoefmat quantile symnum
Consider adding
  importFrom("stats", "naprint", "pf", "printCoefmat", "quantile",
             "symnum")
  importFrom("utils", "browseURL")
to your NAMESPACE file.
'library' or 'require' call to ‘Biobase’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
File ‘amap/libs/amap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Checking should be performed on sources prepared by ‘R CMD build’.
Found the following apparent S3 methods exported but not registered:
  plot.MCepi plot.epiman plot.optvac print.MCepi print.epiman
  print.optvac print.summary.MCepi print.summary.epiman
  print.summary.optvac summary.MCepi summary.epiman summary.optvac
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘amei/libs/amei.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Amelia/libs/Amelia.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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.
File ‘AMORE/libs/AMORE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘analogue/libs/analogue.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard files/directories found at top level:
  ‘niftidoc’ ‘tst.hdr’ ‘tst.img’
File ‘AnalyzeFMRI/libs/AnalyzeFMRI.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Rd file 'mixgamma.Rd':
  \usage lines wider than 90 characters:
     mixgamma(VAR, dfreedom, var.init, pi.init, nmixt, stop.crit , display = TRUE, niter.max = 50000, criterion = criterion)

These lines will be truncated in the PDF manual.
File ‘anchors/libs/anchors.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
GetTotalValues: no visible global function definition for ‘rgamma’
GetTotalValues: no visible global function definition for ‘runif’
MakeAnglers: no visible global function definition for ‘runif’
MakeAnglers: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  rgamma runif
Consider adding
  importFrom("stats", "rgamma", "runif")
to your NAMESPACE file.
'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.
anominate: no visible global function definition for ‘runif’
anominate: no visible global function definition for ‘na.omit’
anominate.sim: no visible global function definition for ‘runif’
densplot.anominate: no visible global function definition for
  ‘quantile’
plot.anominate: no visible global function definition for ‘na.omit’
plot.anominate: no visible global function definition for ‘dev.new’
plot.anominate: no visible global function definition for ‘plot’
plot.anominate: no visible global function definition for ‘segments’
plot.anominate: no visible global function definition for ‘points’
plot.anominate: no visible global function definition for ‘par’
summary.anominate: no visible global function definition for ‘na.omit’
summary.anominate: no visible global function definition for ‘quantile’
traceplot.anominate: no visible global function definition for
  ‘quantile’
Undefined global functions or variables:
  dev.new na.omit par plot points quantile runif segments
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "par", "plot", "points", "segments")
  importFrom("stats", "na.omit", "quantile", "runif")
to your NAMESPACE file.
File ‘anominate/libs/anominate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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
'library' or 'require' call to ‘boot’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘boot’ ‘lme4’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  AIC.aodml anova.aodml anova.aodql coef.aodml coef.aodql
  deviance.aodml deviance.aodql df.residual.aodml df.residual.aodql
  fitted.aodml fitted.aodql logLik.aodml logLik.aodql predict.aodml
  predict.aodql print.anova.aodml print.aodml print.aodql print.drs
  print.gof print.iccbin print.summary.aodml print.varbin
  print.wald.test residuals.aodml residuals.aodql summary.aodml
  summary.aodql vcov.aodml vcov.aodql
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Running examples in ‘apaTables-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: apa.1way.table
> ### Title: Creates a table of means and standard deviations for a 1-way
> ###   ANOVA design in APA style
> ### Aliases: apa.1way.table
> 
> ### ** Examples
> 
> # Example 1: 1-way from Field et al. (2012) Discovery Statistics Using R
> apa.1way.table(iv=dose,dv=libido,data=viagra,filename="ex1_desc_table.doc")
Error in sprintf("\\tqdec\\tldot\\tx%d", decimalTabPositionTwipsInternal) : 
  invalid format '%d'; use format %f, %e, %g or %a for numeric objects
Calls: apa.1way.table ... one.way.table.console.and.rtf -> <Anonymous> -> getRow -> <Anonymous> -> sprintf
Execution halted
File ‘apcluster/libs/apcluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘tkrplot’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  plot.bagplot plot.faces
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
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’
File ‘appell/libs/appell.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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
File ‘apple/libs/apple.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls in package code:
  ‘ellipse’ ‘lattice’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
bookTheme: no visible global function definition for ‘trellis.par.set’
easyBoundaryFunc: no visible global function definition for ‘runif’
getPackages: no visible global function definition for
  ‘install.packages’
permuteRelief: no visible binding for global variable ‘sd’
quadBoundaryFunc: no visible global function definition for ‘runif’
transparentTheme: no visible global function definition for ‘rgb’
transparentTheme: no visible global function definition for
  ‘trellis.par.set’
upperp: no visible global function definition for ‘ellipse’
upperp: no visible global function definition for ‘panel.xyplot’
upperp: no visible global function definition for ‘trellis.par.get’
Undefined global functions or variables:
  ellipse install.packages panel.xyplot rgb runif sd trellis.par.get
  trellis.par.set
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "runif", "sd")
  importFrom("utils", "install.packages")
to your NAMESPACE file.
Package in Depends field not imported from: ‘emulator’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Afun: no visible global function definition for ‘corr.matrix’
betahat.app.H: no visible global function definition for ‘quad.form’
betahat.app.H: no visible global function definition for
  ‘quad.form.inv’
cdash.fun: no visible global function definition for ‘quad.3form’
cdash.fun: no visible global function definition for ‘quad.form’
generate.toy.observations : delta: no visible global function
  definition for ‘rmvnorm’
generate.toy.observations : delta: no visible global function
  definition for ‘corr.matrix’
object: no visible global function definition for ‘quad.form’
opt.1: no visible global function definition for ‘optim’
opt.gt.1: no visible global function definition for ‘optim’
subsets.fun : select: no visible global function definition for
  ‘rbinom’
Undefined global functions or variables:
  corr.matrix optim quad.3form quad.form quad.form.inv rbinom rmvnorm
Consider adding
  importFrom("stats", "optim", "rbinom")
to your NAMESPACE file.
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.
Found the following apparent S3 methods exported but not registered:
  all.equal.treeshape all.equal.treeshape as.phylo.treeshape
  as.treeshape.phylo as.treeshape.treebalance is.binary.phylo
  plot.treeshape summary.treeshape
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'shift.test.Rd':
  \examples lines wider than 100 characters:
      pv <- sapply(1:135, FUN = function(i) shift.test(tree.birds, i, lambda1 = 1, lambda2 = 100, nrep = 1000, silent = TRUE))

These lines will be truncated in the PDF manual.
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 apparent S3 methods exported but not registered:
  rbind.SoilProfileCollection
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
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.
File ‘aqr/libs/aqr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘arf3DS4/libs/arf3DS4.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘arfima/libs/arfima.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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’
File ‘arrApply/libs/arrApply.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘ars/libs/ars.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ARTP/libs/ARTP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘ash/libs/ash.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages which this enhances but not available for checking:
  ‘REBayes’ ‘Rmosek’
File ‘ashr/libs/ashr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ASMap/libs/ASMap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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.
File ‘ASPBay/libs/ASPBay.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package which this enhances but not available for checking: ‘asreml’
':::' call which should be '::': ‘assertive.base:::print_and_capture’
  See the note in ?`:::` about the use of this operator.
Found the following apparent S3 methods exported but not registered:
  plot.AssetPricing plot.flap
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘assist/libs/assist.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘AssotesteR/libs/AssotesteR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
beamDiskOverlap: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate
Consider adding
  importFrom("stats", "integrate")
to your NAMESPACE file.
fm_unred: no visible global function definition for ‘spline’
galage: no visible global function definition for ‘integrate’
lumdist: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate spline
Consider adding
  importFrom("stats", "integrate", "spline")
to your NAMESPACE file.
VPC.graph : findQuantile: no visible global function definition for
  ‘quantile’
VPC.graph : findQuantileCI : <anonymous>: no visible global function
  definition for ‘quantile’
asVPC.binW: no visible global function definition for ‘median’
asVPC.binW : <anonymous>: no visible global function definition for
  ‘quantile’
asVPC.binW: no visible global function definition for ‘quantile’
asVPC.distanceW: no visible global function definition for ‘median’
asVPC.distanceW : <anonymous>: no visible global function definition
  for ‘quantile’
asVPC.distanceW: no visible global function definition for ‘quantile’
makeCOVbin: no visible global function definition for ‘quantile’
makeCOVbin: no visible global function definition for ‘median’
read_Simdata: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  median quantile read.table
Consider adding
  importFrom("stats", "median", "quantile")
  importFrom("utils", "read.table")
to your NAMESPACE file.
asymp.test.default: no visible global function definition for ‘var’
asymp.test.default: no visible global function definition for ‘pnorm’
asymp.test.default: no visible global function definition for ‘qnorm’
asymp.test.formula: no visible global function definition for ‘terms’
seDMean.default: no visible global function definition for ‘var’
seDMeanG.default: no visible global function definition for ‘var’
seDVar.default: no visible global function definition for ‘var’
seMean.default: no visible global function definition for ‘var’
seRMean.default: no visible global function definition for ‘var’
seRVar.default: no visible global function definition for ‘var’
seVar.default: no visible global function definition for ‘var’
Undefined global functions or variables:
  pnorm qnorm terms var
Consider adding
  importFrom("stats", "pnorm", "qnorm", "terms", "var")
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.
File ‘AtmRay/libs/AtmRay.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
parse_response: 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 ‘attrCUSUM/libs/attrCUSUM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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 apparent S3 methods exported but not registered:
  $.audioInstance $.audioSample $<-.audioSample [.audioSample
  as.audioSample.Sample as.audioSample.default close.audioInstance
  pause.audioInstance play.Sample play.audioInstance play.audioSample
  play.default resume.audioInstance rewind.audioInstance
  wait.audioInstance wait.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘audio/libs/audio.so’:
  Found non-API call to R: ‘R_checkActivity’
File ‘audio/libs/audio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

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.
File ‘autovarCore/libs/autovarCore.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘awsMethods/libs/awsMethods.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘aws/libs/aws.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
best: no visible global function definition for ‘optim’
randomboards: no visible global function definition for ‘runif’
randomprobs: no visible global function definition for ‘runif’
Undefined global functions or variables:
  optim runif
Consider adding
  importFrom("stats", "optim", "runif")
to your NAMESPACE file.
File ‘aylmer/libs/aylmer.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘aylmer.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘aylmer.o’
File ‘aylmer/libs/aylmer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘BaBooN/libs/BaBooN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘BalancedSampling/libs/BalancedSampling.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/BAMBI.Rcheck/00install.out’ for details.
File ‘BAMMtools/libs/BAMMtools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘Barnard/libs/Barnard.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Barycenter/libs/Barycenter.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘base64enc/libs/base64enc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘base64url/libs/base64url.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘BASIX/libs/BASIX.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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
Unexported objects imported by ':::' calls:
  ‘BatchJobs:::addIntModulo’ ‘BatchJobs:::buffer’
  ‘BatchJobs:::checkDir’ ‘BatchJobs:::checkId’ ‘BatchJobs:::checkIds’
  ‘BatchJobs:::checkPart’ ‘BatchJobs:::createShardedDirs’
  ‘BatchJobs:::dbConnectToJobsDB’ ‘BatchJobs:::dbCreateJobStatusTable’
  ‘BatchJobs:::dbDoQuery’ ‘BatchJobs:::dbFindDone’
  ‘BatchJobs:::dbFindRunning’ ‘BatchJobs:::dbRemoveJobs’
  ‘BatchJobs:::dbSelectWithIds’ ‘BatchJobs:::getJobDirs’
  ‘BatchJobs:::getJobInfoInternal’ ‘BatchJobs:::getKillJob’
  ‘BatchJobs:::getListJobs’ ‘BatchJobs:::getRandomSeed’
  ‘BatchJobs:::getResult’ ‘BatchJobs:::isRegistryDir’
  ‘BatchJobs:::makeRegistryInternal’ ‘BatchJobs:::saveRegistry’
  ‘BatchJobs:::seeder’ ‘BatchJobs:::syncRegistry’
  See the note in ?`:::` about the use of this operator.
addExperiments.ExperimentRegistry: no visible global function
  definition for ‘is’
applyJobFunction.ExperimentRegistry: no visible global function
  definition for ‘setNames’
calcDynamic: no visible global function definition for ‘setNames’
checkExperimentRegistry: no visible global function definition for
  ‘head’
dbSummarizeExperiments: no visible global function definition for
  ‘setNames’
designIterator: no visible global function definition for ‘setNames’
getIndex : exprToIndex: no visible global function definition for
  ‘capture.output’
getProblemFilePaths: no visible global function definition for
  ‘setNames’
updateRegistry.ExperimentRegistry: no visible global function
  definition for ‘packageVersion’
Undefined global functions or variables:
  capture.output head is packageVersion setNames
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "setNames")
  importFrom("utils", "capture.output", "head", "packageVersion")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' call to ‘parallel’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' call which should be '::': ‘parallel:::detectCores’
  See the note in ?`:::` about the use of this operator.
asyncRunCommands: no visible global function definition for ‘runif’
mergeCsv: no visible global function definition for ‘read.csv’
mergeCsv: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  read.csv runif write.csv
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
File ‘batman/libs/batman.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘BayClone2/libs/BayClone2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘bayesAB/libs/bayesAB.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘BayesBD/libs/BayesBD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
bridge.nmix.R: no visible global function definition for ‘rnorm’
draw.alpha: no visible global function definition for ‘runif’
draw.alpha: no visible global function definition for ‘dbeta’
draw.alpha.2: no visible global function definition for ‘runif’
draw.beta.2: no visible global function definition for ‘runif’
draw.sig2: no visible global function definition for ‘rgamma’
draw.tau: no visible global function definition for ‘rgamma’
draw.u: no visible global function definition for ‘runif’
draw.w: no visible global function definition for ‘runif’
draw.w: no visible global function definition for ‘rgamma’
draw.w.marg: no visible global function definition for ‘runif’
draw.w.marg: no visible global function definition for ‘rgamma’
trace.beta: no visible global function definition for ‘plot’
trace.beta: no visible global function definition for ‘lines’
trace.beta: no visible global function definition for ‘legend’
trace.beta.mcmc: no visible global function definition for ‘sd’
trace.beta.mcmc: no visible binding for global variable ‘sd’
trace.beta.mcmc: no visible global function definition for ‘plot’
trace.beta.mcmc: no visible global function definition for ‘title’
trace.beta.mcmc: no visible global function definition for ‘hsv’
trace.beta.mcmc: no visible global function definition for ‘lines’
trace.beta.mcmc: no visible global function definition for ‘points’
Undefined global functions or variables:
  dbeta hsv legend lines plot points rgamma rnorm runif sd title
Consider adding
  importFrom("grDevices", "hsv")
  importFrom("graphics", "legend", "lines", "plot", "points", "title")
  importFrom("stats", "dbeta", "rgamma", "rnorm", "runif", "sd")
to your NAMESPACE file.
File ‘BayesBridge/libs/BayesBridge.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘BayesComm/libs/BayesComm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘bayescount/libs/bayescount.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
BugReports field is not a suitable URL but contains an email address
  which will be used as from R 3.4.0
File ‘bayesDccGarch/libs/bayesDccGarch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘BayesFactor/libs/BayesFactor.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘bayesGARCH/libs/bayesGARCH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘BayesH/libs/BayesH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘bayesianETAS/libs/bayesianETAS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘BayesLogit/libs/BayesLogit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘bayesloglin/libs/bayesloglin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Depends: includes the non-default packages:
  ‘gplots’ ‘xtable’ ‘mnormt’ ‘MASS’ ‘bayesm’ ‘boa’ ‘e1071’ ‘gtools’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  ‘MASS’ ‘bayesm’ ‘boa’ ‘e1071’ ‘gplots’ ‘gtools’ ‘mnormt’ ‘xtable’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'MNLAuxMix.Rd':
  \examples lines wider than 100 characters:
                      X = cbind( intercept=1, alrateBezNew, unskilled, skilled, angStart ) ),                         

These lines will be truncated in the PDF manual.
File ‘bayesm/libs/bayesm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘bayesPop/libs/bayesPop.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘bayesQR/libs/bayesQR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  print.summary.BayesSAE
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
BayesFH: no visible global function definition for ‘rnorm’
BayesFH: no visible global function definition for ‘rgamma’
BayesSAE: no visible global function definition for ‘runif’
BayesSAE: no visible global function definition for ‘as.formula’
BayesSAE: no visible global function definition for ‘terms’
BayesSAE: no visible global function definition for ‘delete.response’
BayesSAE: no visible global function definition for ‘model.response’
BayesSAE: no visible global function definition for ‘model.matrix’
BayesSAE: no visible global function definition for ‘coef’
BayesSAE: no visible global function definition for ‘lm’
BayesSFH: no visible global function definition for ‘rnorm’
BayesSFH: no visible global function definition for ‘runif’
BayesSFH: no visible global function definition for ‘rgamma’
BayesSYC: no visible global function definition for ‘rnorm’
BayesSYC: no visible global function definition for ‘runif’
BayesSYC: no visible global function definition for ‘rgamma’
BayesUFH: no visible global function definition for ‘rnorm’
BayesUFH: no visible global function definition for ‘rgamma’
BayesUYC: no visible global function definition for ‘rnorm’
BayesUYC: no visible global function definition for ‘rgamma’
BayesYC: no visible global function definition for ‘rnorm’
BayesYC: no visible global function definition for ‘rgamma’
model.compare: no visible global function definition for ‘dnorm’
print.summary.BayesSAE: no visible global function definition for
  ‘printCoefmat’
replication: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  as.formula coef delete.response dnorm lm model.matrix model.response
  printCoefmat rgamma rnorm runif terms
Consider adding
  importFrom("stats", "as.formula", "coef", "delete.response", "dnorm",
             "lm", "model.matrix", "model.response", "printCoefmat",
             "rgamma", "rnorm", "runif", "terms")
to your NAMESPACE file.
Found the following Makefile(s) without a final LF:
  src/Makevars
Some ‘make’ programs ignore lines not ending in LF.
File ‘BayesSAE/libs/BayesSAE.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘HBsae.o’
File ‘BayesSAE/libs/BayesSAE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘BayesSingleSub/libs/BayesSingleSub.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Depends: includes the non-default packages:
  ‘lme4’ ‘MASS’ ‘VGAM’ ‘mvtnorm’ ‘matrixcalc’ ‘coda’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  ‘MASS’ ‘VGAM’ ‘coda’ ‘lme4’ ‘matrixcalc’ ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'Bayesthresh.Rd':
  \examples lines wider than 100 characters:
                                                                                                                                             ... [TRUNCATED]

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

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

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

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

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

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

These lines will be truncated in the PDF manual.
File ‘Bayesthresh/libs/Bayesthresh.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘BayesTree/libs/BayesTree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘BayesVarSel/libs/BayesVarSel.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following file(s) containing GNU extensions:
  src/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
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’
File ‘BayHap/libs/BayHap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
It is good practice to register native routines and to disable symbol
search.

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.
File ‘bayou/libs/bayou.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘fields’ ‘poibin’ ‘rjags’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
BMR.plot: no visible global function definition for ‘heat.colors’
BMR.plot: no visible global function definition for ‘image.plot’
BMR.plot: no visible global function definition for ‘title’
BMR.plot: no visible global function definition for ‘mtext’
BMR.plot: no visible global function definition for ‘par’
baysic.data: no visible global function definition for ‘layout’
baysic.data: no visible global function definition for ‘barplot’
baysic.data: no visible global function definition for ‘rainbow’
baysic.fit: no visible global function definition for ‘jags.model’
baysic.fit: no visible global function definition for ‘update’
baysic.fit: no visible global function definition for ‘coda.samples’
baysic.test: no visible global function definition for ‘ppois’
baysic.test : <anonymous>: no visible global function definition for
  ‘ppoibin’
baysic.test: no visible global function definition for ‘pbinom’
fuzzy.FDR.approx: no visible global function definition for ‘p.adjust’
fuzzy.FDR.approx: no visible global function definition for ‘runif’
Undefined global functions or variables:
  barplot coda.samples heat.colors image.plot jags.model layout mtext
  p.adjust par pbinom ppoibin ppois rainbow runif title update
Consider adding
  importFrom("grDevices", "heat.colors", "rainbow")
  importFrom("graphics", "barplot", "layout", "mtext", "par", "title")
  importFrom("stats", "p.adjust", "pbinom", "ppois", "runif", "update")
to your NAMESPACE file.
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.
File ‘BCBCSF/libs/BCBCSF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable 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.
File ‘Bchron/libs/Bchron.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Bclim/libs/Bclim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘bclust/libs/bclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘bcpa/libs/bcpa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘bcp/libs/bcp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
check.summary: no visible global function definition for ‘sd’
risk.summary: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  sd write.csv
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
File ‘bcROCsurface/libs/bcROCsurface.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘bcrypt/libs/bcrypt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘bcv/libs/bcv.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Running examples in ‘bdrift-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BDA.loader
> ### Title: Beta Drift Anaylsis Data Loader
> ### Aliases: BDA.loader
> 
> ### ** Examples
> 
> testframe <- BDA.loader(symbol = "XOM")
‘getSymbols’ currently uses auto.assign=TRUE by default, but will
use auto.assign=FALSE in 0.5-0. You will still be able to use
‘loadSymbols’ to automatically load data. getOption("getSymbols.env")
and getOption("getSymbols.auto.assign") will still be checked for
alternate defaults.

This message is shown once per session and may be disabled by setting 
options("getSymbols.warning4.0"=FALSE). See ?getSymbols for details.
Warning in if (as.character(sc[[1]]) != calling.fun) return() :
  the condition has length > 1 and only the first element will be used

WARNING: There have been significant changes to Yahoo Finance data.
Please see the Warning section of ‘?getSymbols.yahoo’ for details.

This message is shown once per session and may be disabled by setting
options("getSymbols.yahoo.warning"=FALSE).
Error in new.session(curl::new_handle()) : 
  Could not establish session after 5 attempts.
Calls: BDA.loader ... do.call -> getSymbols.yahoo -> .getHandle -> new.session
Execution halted
bdsmatrix.ibd: no visible global function definition for ‘median’
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
File ‘bdsmatrix/libs/bdsmatrix.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
beep: no visible global function definition for ‘download.file’
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
'library' or 'require' call to ‘multcomp’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
File ‘BenfordTests/libs/BenfordTests.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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').
File ‘Bessel/libs/Bessel.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
'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.
File ‘betategarch/libs/betategarch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘bfa/libs/bfa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘bfork/libs/bfork.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  binommh.default binommh.formula expmh.default expmh.formula
  poissmh.default poissmh.formula
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
binommh.default : log_lik: no visible global function definition for
  ‘dbinom’
binommh.default: no visible global function definition for ‘dbinom’
binommh.default: no visible global function definition for ‘runif’
binommh.formula: no visible global function definition for
  ‘model.frame’
binommh.formula: no visible global function definition for
  ‘model.matrix’
binommh.formula: no visible global function definition for
  ‘model.response’
expmh.default : log_lik: no visible global function definition for
  ‘dexp’
expmh.default: no visible global function definition for ‘dexp’
expmh.default: no visible global function definition for ‘runif’
expmh.formula: no visible global function definition for ‘model.frame’
expmh.formula: no visible global function definition for ‘model.matrix’
expmh.formula: no visible global function definition for
  ‘model.response’
poissmh.default : log_lik: no visible global function definition for
  ‘dpois’
poissmh.default: no visible global function definition for ‘dpois’
poissmh.default: no visible global function definition for ‘runif’
poissmh.formula: no visible global function definition for
  ‘model.frame’
poissmh.formula: no visible global function definition for
  ‘model.matrix’
poissmh.formula: no visible global function definition for
  ‘model.response’
Undefined global functions or variables:
  dbinom dexp dpois model.frame model.matrix model.response runif
Consider adding
  importFrom("stats", "dbinom", "dexp", "dpois", "model.frame",
             "model.matrix", "model.response", "runif")
to your NAMESPACE file.
File ‘BGLR/libs/BGLR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘BiasedUrn/libs/BiasedUrn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
arrange.single.author: no visible global function definition for
  ‘person’
write.bib: no visible global function definition for
  ‘installed.packages’
write.bib : <anonymous>: no visible global function definition for
  ‘citation’
write.bib: no visible global function definition for ‘toBibtex’
Undefined global functions or variables:
  citation installed.packages person toBibtex
Consider adding
  importFrom("utils", "citation", "installed.packages", "person",
             "toBibtex")
to your NAMESPACE file.
File ‘bibtex/libs/bibtex.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘biclust/libs/biclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  print.BiDimRegression print.summary.BiDimRegression
  summary.BiDimRegression
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
BiDimRegression: no visible global function definition for ‘lm’
BiDimRegression: no visible global function definition for ‘pf’
print.BiDimRegression: no visible global function definition for
  ‘printCoefmat’
print.summary.BiDimRegression: no visible global function definition
  for ‘printCoefmat’
Undefined global functions or variables:
  lm pf printCoefmat
Consider adding
  importFrom("stats", "lm", "pf", "printCoefmat")
to your NAMESPACE file.
'library' or 'require' call to ‘mvtnorm’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘bifactorial/libs/bifactorial.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘misc.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Objects: ‘krit.o’, ‘pv.o’
File ‘bifactorial/libs/bifactorial.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘bigalgebra/libs/bigalgebra.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘biganalytics/libs/biganalytics.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Packages in Depends field not imported from:
  ‘Matrix’ ‘glmnet’ ‘lattice’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
lasso.stars: no visible global function definition for ‘glmnet’
plot.stars: no visible global function definition for ‘par’
plot.stars: no visible global function definition for ‘plot’
plot.stars: no visible global function definition for ‘lines’
Undefined global functions or variables:
  glmnet lines par plot
Consider adding
  importFrom("graphics", "lines", "par", "plot")
to your NAMESPACE file.
File ‘bigGP/libs/bigGP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘biglars/libs/biglars.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ 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’.
File ‘biglm/libs/biglm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘bigmemory/libs/bigmemory.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘BigQuic/libs/BigQuic.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘bigReg/libs/bigReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
bigRR: no visible global function definition for ‘gaussian’
bigRR.default: no visible global function definition for ‘gaussian’
bigRR.formula: no visible global function definition for ‘gaussian’
bigRR.formula: no visible global function definition for ‘as.formula’
bigRR.formula: no visible global function definition for ‘model.frame’
bigRR.formula: no visible global function definition for ‘model.matrix’
bigRR.formula: no visible global function definition for
  ‘model.response’
bigRR_update: no visible global function definition for ‘gaussian’
hugeRR: no visible global function definition for ‘gaussian’
hugeRR_update: no visible global function definition for ‘gaussian’
plot.bigRR: no visible global function definition for ‘par’
plot.bigRR: no visible global function definition for ‘plot’
plot.bigRR: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  as.formula gaussian model.frame model.matrix model.response par plot
  rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.formula", "gaussian", "model.frame",
             "model.matrix", "model.response")
to your NAMESPACE file.
File ‘bigsplines/libs/bigsplines.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘bigtabulate/libs/bigtabulate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘bigtcr/libs/bigtcr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘bild/libs/bild.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘Binarize/libs/Binarize.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘bindrcpp/libs/bindrcpp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  binMto.default binMto.formula
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Mtoquant: no visible global function definition for ‘qnorm’
NHS: no visible global function definition for ‘qnorm’
NHS : WilsonScore: no visible global function definition for ‘qnorm’
binMto.formula: no visible global function definition for ‘model.frame’
plot.binMto: no visible global function definition for ‘plot.new’
plot.binMto: no visible global function definition for ‘par’
plot.binMto: no visible global function definition for ‘strwidth’
plot.binMto: no visible global function definition for ‘axis’
plot.binMto: no visible global function definition for ‘box’
plot.binMto: no visible global function definition for ‘segments’
plot.binMto: no visible global function definition for ‘points’
plot.binMto: no visible global function definition for ‘abline’
simPowerI: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  abline axis box model.frame par plot.new points qnorm rbinom segments
  strwidth
Consider adding
  importFrom("graphics", "abline", "axis", "box", "par", "plot.new",
             "points", "segments", "strwidth")
  importFrom("stats", "model.frame", "qnorm", "rbinom")
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.
File ‘binom/libs/binom.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable 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.
File ‘bio3d/libs/bio3d.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
'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.
extractPDB : atom.select : sel.txt2nums: no visible global function
  definition for ‘na.omit’
extractPDB : read.pdb: no visible global function definition for
  ‘na.omit’
mat.read: no visible global function definition for ‘read.table’
mat.write: no visible global function definition for ‘write.table’
scpcp: no visible global function definition for ‘pgamma’
sim : sim.func: no visible global function definition for ‘write.table’
simc: no visible global function definition for ‘write.table’
simc : simc.func: no visible global function definition for
  ‘write.table’
sims: no visible global function definition for ‘write.table’
sims : sims.func: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  na.omit pgamma read.table write.table
Consider adding
  importFrom("stats", "na.omit", "pgamma")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
File ‘BioPhysConnectoR/libs/BioPhysConnectoR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘bioPN/libs/bioPN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Found the following apparent S3 methods exported but not registered:
  plot.BIPOD
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.BIPOD: no visible global function definition for ‘par’
plot.BIPOD: no visible global function definition for ‘matplot’
plot.BIPOD: no visible global function definition for ‘abline’
plot.BIPOD: no visible global function definition for ‘plot’
plot.BIPOD: no visible global function definition for ‘density’
plot.BIPOD: no visible global function definition for ‘curve’
plot.BIPOD: no visible global function definition for ‘dlnorm’
plot.BIPOD: no visible global function definition for ‘dnorm’
plot.BIPOD: no visible global function definition for ‘acf’
plot.BIPOD: no visible global function definition for ‘pairs’
plot.BIPOD : standfun: no visible global function definition for ‘sd’
plot.BIPOD: no visible global function definition for ‘sd’
plot.BIPOD: no visible global function definition for ‘points’
plot.BIPOD: no visible global function definition for ‘tail’
plot.BIPOD: no visible global function definition for ‘matlines’
plot.BIPOD: no visible binding for global variable ‘quantile’
plot.BIPOD: no visible global function definition for ‘lines’
Undefined global functions or variables:
  abline acf curve density dlnorm dnorm lines matlines matplot pairs
  par plot points quantile sd tail
Consider adding
  importFrom("graphics", "abline", "curve", "lines", "matlines",
             "matplot", "pairs", "par", "plot", "points")
  importFrom("stats", "acf", "density", "dlnorm", "dnorm", "quantile",
             "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
File ‘BIPOD/libs/BIPOD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
aveslope: no visible global function definition for ‘pbeta’
bisoreg : <anonymous>: no visible global function definition for
  ‘pbeta’
bisoreg: no visible global function definition for ‘rgamma’
bisoreg: no visible global function definition for ‘rbeta’
bisoreg: no visible global function definition for ‘rnorm’
bisoreg: no visible global function definition for ‘rbinom’
bisoreg: no visible global function definition for ‘dnorm’
bisoreg: no visible global function definition for ‘var’
fitted.biso : <anonymous>: no visible global function definition for
  ‘median’
get.W : <anonymous>: no visible global function definition for ‘pbeta’
loess.wrapper : theta.fit: no visible global function definition for
  ‘loess’
loess.wrapper : theta.predict: no visible global function definition
  for ‘predict’
loess.wrapper: no visible global function definition for ‘loess’
nd2004 : initfun: no visible global function definition for ‘rnorm’
nd2004 : initfun: no visible global function definition for ‘rgamma’
plot.biso: no visible global function definition for ‘plot’
plot.biso : <anonymous>: no visible global function definition for
  ‘quantile’
plot.biso: no visible global function definition for ‘polygon’
plot.biso: no visible global function definition for ‘gray’
plot.biso: no visible global function definition for ‘points’
plot.biso : <anonymous>: no visible global function definition for
  ‘median’
plot.biso: no visible global function definition for ‘lines’
summary.biso: no visible binding for global variable ‘fivenum’
Undefined global functions or variables:
  dnorm fivenum gray lines loess median pbeta plot points polygon
  predict quantile rbeta rbinom rgamma rnorm var
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "lines", "plot", "points", "polygon")
  importFrom("stats", "dnorm", "fivenum", "loess", "median", "pbeta",
             "predict", "quantile", "rbeta", "rbinom", "rgamma", "rnorm",
             "var")
to your NAMESPACE file.
File ‘bisoreg/libs/bisoreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘bitops/libs/bitops.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  rev.rlepack unique.rlepack xor.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘bit/libs/bit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘BiTrinA/libs/BiTrinA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘bitrugs/libs/bitrugs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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
File ‘biwavelet/libs/biwavelet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘BKPC/libs/BKPC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘blackbox/libs/blackbox.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File
  LICENCE
is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  ‘misc’
blighty: no visible global function definition for ‘par’
blighty: no visible global function definition for ‘polygon’
blighty: no visible global function definition for ‘points’
blighty: no visible global function definition for ‘box’
blighty: no visible global function definition for ‘axis’
blighty: no visible global function definition for ‘abline’
map.scale: no visible global function definition for ‘locator’
map.scale: no visible global function definition for ‘segments’
map.scale: no visible global function definition for ‘text’
north.pointer: no visible global function definition for ‘locator’
north.pointer: no visible global function definition for ‘text’
north.pointer: no visible global function definition for ‘arrows’
north.pointer: no visible global function definition for ‘segments’
sqlimits: no visible global function definition for ‘frame’
sqlimits: no visible global function definition for ‘par’
Undefined global functions or variables:
  abline arrows axis box frame locator par points polygon segments text
Consider adding
  importFrom("graphics", "abline", "arrows", "axis", "box", "frame",
             "locator", "par", "points", "polygon", "segments", "text")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘blighty/R/blighty.r’:
  assign("blighty.mapinfo", blighty.mapinfo, envir = .GlobalEnv)

Found the following calls to data() loading into the global environment:
File ‘blighty/R/blighty.r’:
  data(list = place)
  data(list = objectnames)
  data(list = tmp.objectnames[ctr])
See section ‘Good practice’ in ‘?data’.
Rd file 'blighty.Rd':
  \usage lines wider than 90 characters:
     blighty(place="set.British.Isles", set=TRUE, grid=FALSE, xlimits, ylimits, xpadding=0, ypadding=0, parcol, parbor, parwdh, sarcol, sarb ... [TRUNCATED]
  \examples lines wider than 100 characters:
     blighty(parang=45, parden=30, parbor="transparent", parcol="black", sarbor="transparent", tlncol="transparent")

These lines will be truncated in the PDF manual.
Package suggested but not available for checking: ‘bigrf’
Missing or unexported object: ‘xgboost::predict’
File ‘blkergm/libs/blkergm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Found the following significant warnings:
  Warning: GNU Extension: Different type kinds at (1)
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/blockmodeling.Rcheck/00install.out’ for details.
'library' or 'require' calls in package code:
  ‘Matrix’ ‘sna’
  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.mat.nm
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'plot.mat':
  ‘plot.mat’ ‘plot.mat.nm’

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.
File ‘blockmodeling/libs/blockmodeling.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘blockmodels/libs/blockmodels.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 ‘blockseg/libs/blockseg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘blockTools/libs/blockTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Blossom/libs/Blossom.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
BLR: no visible global function definition for ‘weighted.mean’
BLR: no visible global function definition for ‘var’
BLR: no visible global function definition for ‘model.matrix’
BLR: no visible global function definition for ‘rnorm’
BLR: no visible global function definition for ‘rchisq’
BLR: no visible global function definition for ‘rgamma’
BLR: no visible global function definition for ‘dnorm’
dLambda: no visible global function definition for ‘dgamma’
dScaledInvChisq: no visible global function definition for ‘dchisq’
metropLambda: no visible global function definition for ‘rgamma’
metropLambda: no visible global function definition for ‘dexp’
metropLambda: no visible global function definition for ‘dbeta’
metropLambda: no visible global function definition for ‘dgamma’
metropLambda: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dbeta dchisq dexp dgamma dnorm model.matrix rchisq rgamma rnorm runif
  var weighted.mean
Consider adding
  importFrom("stats", "dbeta", "dchisq", "dexp", "dgamma", "dnorm",
             "model.matrix", "rchisq", "rgamma", "rnorm", "runif", "var",
             "weighted.mean")
to your NAMESPACE file.
File ‘BLR/libs/BLR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
pandoc: unable to decommit memory: Invalid argument
pandoc: Could not fetch https://www.datascienceriot.com/wp-content/uploads/2017/01/bus_fl_map.png
TlsExceptionHostPort (HandshakeFailed (Error_Protocol ("certificate rejected: [NameMismatch \"www.datascienceriot.com\"]",True,CertificateUnknown))) "www.datascienceriot.com" 443
Error: processing vignette ‘Mapping_BLS_Data.Rmd’ failed with diagnostics:
pandoc document conversion failed with error 67
Execution halted
File
  inst/LICENCE
will install at top-level and is not mentioned in the DESCRIPTION file.
Package in Depends field not imported from: ‘drc’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bmd: no visible global function definition for ‘qnorm’
bmd: no visible global function definition for ‘predict’
bmd: no visible global function definition for ‘LL.2’
bmd: no visible global function definition for ‘LN.2’
bmd: no visible global function definition for ‘W1.2’
bmd: no visible global function definition for ‘W2.2’
bmd: no visible global function definition for ‘LL.5’
bmd: no visible global function definition for ‘LN.4’
bmd: no visible global function definition for ‘W1.4’
bmd: no visible global function definition for ‘W2.4’
bmd: no visible global function definition for ‘FPL.4’
bmd: no visible global function definition for ‘maED’
bmd: no visible global function definition for ‘ED’
Undefined global functions or variables:
  ED FPL.4 LL.2 LL.5 LN.2 LN.4 W1.2 W1.4 W2.2 W2.4 maED predict qnorm
Consider adding
  importFrom("stats", "predict", "qnorm")
to your NAMESPACE file.
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.
File ‘Bmix/libs/Bmix.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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.
File ‘bmlm/libs/bmlm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
GibbsIteration: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  rbinom
Consider adding
  importFrom("stats", "rbinom")
to your NAMESPACE file.
File ‘BMN/libs/BMN.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
    Objects: ‘JunctionTree.o’, ‘pseudoLikelihood.o’
File ‘BMN/libs/BMN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘BMRV/libs/BMRV.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
make_topology: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
File ‘bnlearn/libs/bnlearn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Rd file 'bnpmr.Rd':
  \usage lines wider than 90 characters:
     bnpmr(y, x, prior = NULL, start = NULL, niter = 10000, pMoves = NULL, thin = 1, burnIn = 0, prop = NULL, seed = 1, size = 50)

These lines will be truncated in the PDF manual.
File ‘bnpmr/libs/bnpmr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘bnstruct/libs/bnstruct.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Found the following apparent S3 methods exported but not registered:
  coef.boolean logLik.boolean model.matrix.boolean nobs.boolean
  plot.boolprob plot.boolprof predict.boolean print.boolboot
  print.boolean print.boolprob print.boolprof print.boolsum
  summary.boolboot summary.boolean
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
print.boolprob: no visible global function definition for ‘plot’
print.boolprof: no visible global function definition for ‘plot’
start_msg: no visible global function definition for
  ‘packageDescription’
Undefined global functions or variables:
  packageDescription plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
File ‘BoolNet/libs/BoolNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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.
Rd file 'mdcc.Rd':
  \examples lines wider than 100 characters:
     dc.mov2 <- mdcc(rt.spruce, list(rt.temp, rt.prec), vnames = c("temp", "prec"), method = "corr", win.size = 20,

These lines will be truncated in the PDF manual.
File ‘bootruin/libs/bootruin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘bootstrap/libs/bootstrap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Found the following apparent S3 methods exported but not registered:
  boxplotdou.data.frame boxplotdou.default boxplotdou.factor
  boxplotdou.formula boxplotdou.list
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
boxplotdou.formula: no visible global function definition for
  ‘model.frame’
bxpdou: no visible global function definition for ‘rainbow’
bxpdou.abox: no visible global function definition for ‘rect’
bxpdou.abox: no visible global function definition for ‘segments’
bxpdou.abox: no visible global function definition for ‘points’
bxpdou.boxplot.stat: no visible global function definition for
  ‘boxplot’
bxpdou.sheer.color: no visible global function definition for
  ‘adjustcolor’
bxpdou.stats: no visible global function definition for ‘formula’
do.call.with.par: no visible global function definition for
  ‘modifyList’
only.graphic.pars: no visible global function definition for ‘par’
Undefined global functions or variables:
  adjustcolor boxplot formula model.frame modifyList par points rainbow
  rect segments
Consider adding
  importFrom("grDevices", "adjustcolor", "rainbow")
  importFrom("graphics", "boxplot", "par", "points", "rect", "segments")
  importFrom("stats", "formula", "model.frame")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  bpca.default bpca.prcomp plot.bpca.2d plot.bpca.3d plot.qbpca
  print.latex.bpca summary.bpca summary.latex.bpca
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
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.
File ‘BPEC/libs/BPEC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘bpkde/libs/bpkde.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘bqtl/libs/bqtl.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
scene4d: no visible global function definition for ‘rainbow’
write4D.file : <anonymous>: no visible global function definition for
  ‘col2rgb’
writeWebGL_split : split_triangles: no visible global function
  definition for ‘rgb’
Undefined global functions or variables:
  col2rgb rainbow rgb
Consider adding
  importFrom("grDevices", "col2rgb", "rainbow", "rgb")
to your NAMESPACE file.
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’
File ‘brainwaver/libs/brainwaver.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Branching/libs/Branching.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

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.
'library' or 'require' call to ‘RColorBrewer’ 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: ‘profileModel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘brglm/libs/brglm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  bride.default print.bride summary.bride
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘brnn/libs/brnn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  print.brob print.glub
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot,ANY-brob: no visible global function definition for ‘plot.default’
plot,ANY-glub: no visible global function definition for ‘plot.default’
plot,brob-ANY: no visible global function definition for ‘plot.default’
plot,brob-missing: no visible global function definition for
  ‘plot.default’
plot,glub-ANY: no visible global function definition for ‘plot.default’
plot,glub-missing: no visible global function definition for
  ‘plot.default’
Undefined global functions or variables:
  plot.default
Consider adding
  importFrom("graphics", "plot.default")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  CInp.CCDiff CInp.CCRatio CInp.bugs CInp.default SCSnp.CCDiff
  SCSnp.CCRatio SCSnp.bugs SCSnp.default UnlogCI.glht
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
BOOTSimpsonD : BSimpson: no visible global function definition for
  ‘estSimpsonf’
BOOTSimpsonR : BSimpson: no visible global function definition for
  ‘estSimpsonf’
CIGLM: no visible global function definition for ‘confint’
CIGLM: no visible global function definition for ‘univariate_calpha’
CIGLM: no visible global function definition for ‘adjusted_calpha’
CInp.default : <anonymous>: no visible global function definition for
  ‘quantile’
CInp.default: no visible binding for global variable ‘median’
R2Bugsdat1w: no visible global function definition for ‘model.frame’
R2Bugsdat1w: no visible global function definition for ‘model.matrix’
R2Bugsdat1w.data.frame: no visible global function definition for
  ‘as.formula’
R2Bugsdat1w.data.frame: no visible global function definition for
  ‘model.frame’
R2Bugsdat1w.data.frame: no visible global function definition for
  ‘model.matrix’
SCSnp.default: no visible binding for global variable ‘median’
modelparm.gamlss: no visible binding for global variable ‘coef’
modelparm.gamlss: no visible binding for global variable ‘vcov’
modelparm.geeglm: no visible binding for global variable ‘coef’
modelparm.geeglm: no visible binding for global variable ‘vcov’
simplesimint: no visible global function definition for ‘cov2cor’
summary.simplesimint: no visible global function definition for
  ‘cov2cor’
Undefined global functions or variables:
  adjusted_calpha as.formula coef confint cov2cor estSimpsonf median
  model.frame model.matrix quantile univariate_calpha vcov
Consider adding
  importFrom("stats", "as.formula", "coef", "confint", "cov2cor",
             "median", "model.frame", "model.matrix", "quantile", "vcov")
to your NAMESPACE file.
'library' or 'require' call to ‘e1071’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘e1071’ ‘lattice’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'Housing.Rd':
  \examples lines wider than 100 characters:
     stripchart(x=list(X1984,X1993),method="stack",pch=1,cex=1.2,col=c("orange","pink"),group.names=c("1984","1993"))

These lines will be truncated in the PDF manual.
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.
Found the following apparent S3 methods exported but not registered:
  bshazard.default lines.bshazard plot.bshazard print.bshazard
  summary.bshazard
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
bs.design: no visible global function definition for ‘spline.des’
bshazard.default: no visible global function definition for
  ‘model.frame’
bshazard.default: no visible global function definition for
  ‘model.matrix’
bshazard.default: no visible global function definition for
  ‘model.response’
bshazard_fit: no visible global function definition for ‘aggregate’
bspois: no visible global function definition for ‘dpois’
bspois: no visible global function definition for ‘var’
bspois: no visible global function definition for ‘qnorm’
lines.bshazard: no visible global function definition for ‘lines’
plot.bshazard: no visible global function definition for ‘plot’
plot.bshazard: no visible global function definition for ‘lines’
print.bshazard: no visible global function definition for ‘aggregate’
Undefined global functions or variables:
  aggregate dpois lines model.frame model.matrix model.response plot
  qnorm spline.des var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "aggregate", "dpois", "model.frame",
             "model.matrix", "model.response", "qnorm", "var")
to your NAMESPACE file.
LenthPlot: no visible global function definition for ‘grey’
plot.BsProb : spikes: no visible global function definition for ‘grey’
Undefined global functions or variables:
  grey
Consider adding
  importFrom("grDevices", "grey")
to your NAMESPACE file.
File ‘BsMD/libs/BsMD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
'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.
File ‘BSquare/libs/BSquare.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘BSSasymp/libs/BSSasymp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘BTR/libs/BTR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘BTYDplus/libs/BTYDplus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘BuyseTest/libs/BuyseTest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘bvarsv/libs/bvarsv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘bvls/libs/bvls.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘bvpSolve/libs/bvpSolve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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.
File ‘bytescircle/libs/bytescircle.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
C5.0.formula: no visible binding for global variable ‘na.pass’
C5.0.formula: no visible global function definition for ‘model.extract’
C5.0.formula: no visible global function definition for ‘.getXlevels’
as.party.C5.0: no visible global function definition for ‘model.frame’
as.party.C5.0: no visible global function definition for ‘as.formula’
as.party.C5.0: no visible global function definition for ‘terms’
as.party.C5.0 : C5.0_fitted: no visible global function definition for
  ‘model.weights’
model.frame.C5.0: no visible binding for global variable ‘na.omit’
plot.C5.0: no visible global function definition for ‘plot’
predict.C5.0: no visible binding for global variable ‘na.pass’
predict.C5.0: no visible global function definition for
  ‘delete.response’
predict.C5.0: no visible global function definition for ‘model.frame’
Undefined global functions or variables:
  .getXlevels as.formula delete.response model.extract model.frame
  model.weights na.omit na.pass plot terms
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", ".getXlevels", "as.formula", "delete.response",
             "model.extract", "model.frame", "model.weights", "na.omit",
             "na.pass", "terms")
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.
bcMer: no visible global function definition for ‘family’
biasCorrectionBernoulli: no visible global function definition for
  ‘qlogis’
biasCorrectionBernoulli : <anonymous>: no visible global function
  definition for ‘qlogis’
biasCorrectionGaussian: no visible global function definition for
  ‘model.matrix’
cAIC: no visible global function definition for ‘family’
conditionalBootstrap: no visible global function definition for
  ‘simulate’
conditionalBootstrap : <anonymous>: no visible global function
  definition for ‘predict’
conditionalBootstrap: no visible global function definition for ‘sigma’
deleteZeroComponents: no visible global function definition for ‘lm’
deleteZeroComponents: no visible global function definition for
  ‘formula’
deleteZeroComponents: no visible global function definition for
  ‘model.frame’
deleteZeroComponents: no visible global function definition for ‘terms’
deleteZeroComponents: no visible global function definition for
  ‘reformulate’
getcondLL: no visible global function definition for ‘family’
getcondLL: no visible global function definition for ‘dbinom’
getcondLL: no visible global function definition for ‘dpois’
getcondLL: no visible global function definition for ‘dnorm’
getcondLL: no visible global function definition for ‘sigma’
Undefined global functions or variables:
  dbinom dnorm dpois family formula lm model.frame model.matrix predict
  qlogis reformulate sigma simulate terms
Consider adding
  importFrom("stats", "dbinom", "dnorm", "dpois", "family", "formula",
             "lm", "model.frame", "model.matrix", "predict", "qlogis",
             "reformulate", "sigma", "simulate", "terms")
to your NAMESPACE file.
File ‘cairoDevice/libs/cairoDevice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Cairo/libs/Cairo.so’:
  Found non-API calls to R: ‘R_InputHandlers’, ‘addInputHandler’
File ‘Cairo/libs/Cairo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
makemar : predictions: no visible global function definition for
  ‘rbinom’
mice.impute.rfcat : <anonymous>: no visible global function definition
  for ‘predict’
mice.impute.rfcont: no visible global function definition for ‘predict’
mice.impute.rfcont: no visible global function definition for ‘rnorm’
simdata: no visible global function definition for ‘rbinom’
simdata: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  predict rbinom rnorm
Consider adding
  importFrom("stats", "predict", "rbinom", "rnorm")
to your NAMESPACE file.
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.
File ‘CAMAN/libs/CAMAN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.slim
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘camel/libs/camel.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘SFGen.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘SFGen.o’
File ‘camel/libs/camel.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘CampaR1/libs/CampaR1.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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').
Found the following apparent S3 methods exported but not registered:
  [.comparative.data anova.caic anova.caiclist anova.pgls
  anova.pglslist as.comparative.data.growTree coef.caic coef.pgls
  fitted.pgls logLik.caic logLik.pgls na.omit.comparative.data
  nobs.pgls plot.caic plot.fusco plot.pgls plot.pgls.profile
  plot.phylo.d predict.caic predict.pgls print.caic
  print.caic.diagnostics print.comparative.data print.fusco print.pgls
  print.phylo.d print.phylo.d.subset print.summary.pgls
  reorder.comparative.data residuals.caic residuals.pgls
  subset.comparative.data summary.caic summary.fusco summary.pgls
  summary.phylo.d summary.phylo.d.subset
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
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.
File ‘CARrampsOcl/libs/CARrampsOcl.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘catdap/libs/catdap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘catIrt/libs/catIrt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘catnet/libs/catnet.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  predict.LogitBoost
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
colAUC: no visible global function definition for ‘plot’
colAUC: no visible global function definition for ‘title’
colAUC: no visible global function definition for ‘abline’
colAUC: no visible global function definition for ‘legend’
colAUC: no visible global function definition for ‘lines’
read.ENVI: no visible global function definition for ‘read.table’
read.gif: no visible global function definition for ‘download.file’
read.gif: no visible global function definition for ‘rgb’
runmad: no visible global function definition for ‘runmed’
runmad: no visible binding for global variable ‘mad’
runquantile: no visible binding for global variable ‘quantile’
runsd: no visible binding for global variable ‘sd’
sample.split: no visible global function definition for ‘runif’
write.gif: no visible global function definition for ‘gray’
write.gif: no visible global function definition for ‘colorRampPalette’
write.gif: no visible global function definition for ‘col2rgb’
Undefined global functions or variables:
  abline col2rgb colorRampPalette download.file gray legend lines mad
  plot quantile read.table rgb runif runmed sd title
Consider adding
  importFrom("grDevices", "col2rgb", "colorRampPalette", "gray", "rgb")
  importFrom("graphics", "abline", "legend", "lines", "plot", "title")
  importFrom("stats", "mad", "quantile", "runif", "runmed", "sd")
  importFrom("utils", "download.file", "read.table")
to your NAMESPACE file.
File ‘caTools/libs/caTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘cat/libs/cat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  ‘HISTORY’
'library' or 'require' call to ‘gam’ which was already attached by Depends.
  Please remove these calls from your code.
File ‘CausalGAM/R/zzz.R’:
  .onAttach calls:
    cat("##\n## CausalGAM Package\n")
    cat("## Copyright (C) 2009", " Adam Glynn and Kevin Quinn\n",     sep = "")
    require(gam, 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'.

balance.IPW: no visible global function definition for ‘predict’
balance.IPW: no visible binding for global variable ‘sd’
estimate.ATE: no visible global function definition for ‘predict’
estimate.ATE: no visible global function definition for
  ‘model.response’
estimate.ATE: no visible global function definition for ‘model.frame’
estimate.ATE: no visible global function definition for ‘residuals’
estimate.ATE: no visible global function definition for ‘as.formula’
estimate.ATE: no visible global function definition for ‘gaussian’
estimate.ATE: no visible global function definition for ‘par’
estimate.ATE: no visible global function definition for ‘plot’
estimate.ATE: no visible global function definition for ‘lines’
estimate.ATE: no visible global function definition for ‘sd’
print.CausalGAM: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as.formula gaussian lines model.frame model.response par plot pnorm
  predict residuals sd
Consider adding
  importFrom("graphics", "lines", "par", "plot")
  importFrom("stats", "as.formula", "gaussian", "model.frame",
             "model.response", "pnorm", "predict", "residuals", "sd")
to your NAMESPACE file.
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.
File ‘cbird/libs/cbird.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ccaPP/libs/ccaPP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘cccp/libs/cccp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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.
File ‘ccgarch/libs/ccgarch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘CCMnet/libs/CCMnet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.CCM predict.CCM
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
cor.by.class: no visible global function definition for ‘cor’
create.CCM: no visible global function definition for ‘cor’
create.CCM: no visible binding for global variable ‘cor’
plot.CCM: no visible global function definition for ‘boxplot’
Undefined global functions or variables:
  boxplot cor
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "cor")
to your NAMESPACE file.
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.
File ‘cda/libs/cda.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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.
File ‘cdcsis/libs/cdcsis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘CDF.PSIdekick/libs/CDF.PSIdekick.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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
File ‘CDLasso/libs/CDLasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘cdlTools/libs/cdlTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘CDVine/libs/CDVine.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘cec2005benchmark/libs/cec2005benchmark.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘cec2013/libs/cec2013.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘CEC/libs/CEC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘CEGO/libs/CEGO.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.getcos: no visible global function definition for ‘data’
cosdist : temp: no visible global function definition for ‘integrate’
cosdistAngDist : temp: no visible global function definition for
  ‘integrate’
cosdistAngSize : temp: no visible global function definition for
  ‘integrate’
cosdistCoDist : temp: no visible global function definition for
  ‘integrate’
cosdistCoDistTran : temp: no visible global function definition for
  ‘integrate’
cosdistCoVol : temp: no visible global function definition for
  ‘integrate’
cosdistDistMod : temp: no visible global function definition for
  ‘integrate’
cosdistLumDist : temp: no visible global function definition for
  ‘integrate’
cosdistRelError : temp: no visible global function definition for
  ‘integrate’
cosdistTravelTime : temp: no visible global function definition for
  ‘integrate’
cosdistUniAgeAtz : temp: no visible global function definition for
  ‘integrate’
cosdistUniAgeNow : temp: no visible global function definition for
  ‘integrate’
cosgrow : temp: no visible global function definition for ‘integrate’
cosgrowFactor : temp: no visible global function definition for
  ‘integrate’
cosmapfunc: no visible global function definition for ‘approxfun’
Undefined global functions or variables:
  approxfun data integrate
Consider adding
  importFrom("stats", "approxfun", "integrate")
  importFrom("utils", "data")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  .buildNeighborhood.CellularAutomaton .generateRule.CellularAutomaton
  .initializeGrid.CellularAutomaton .run.CellularAutomaton
  .validateOptions.CellularAutomaton getLattice.CellularAutomaton
  getNumberOfColors.CellularAutomaton getRadius.CellularAutomaton
  getRuleNumber.CellularAutomaton getSteps.CellularAutomaton
  getTotalistic.CellularAutomaton plot.CellularAutomaton
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.CellularAutomaton: no visible global function definition for
  ‘image’
Undefined global functions or variables:
  image
Consider adding
  importFrom("graphics", "image")
to your NAMESPACE file.
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.
File ‘cems/libs/cems.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
cenNID: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
File ‘censNID/libs/censNID.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘cents/libs/cents.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘igraph’ ‘snow’
  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.cepa plot.cepa.all plot.pathway.catalogue print.cepa
  print.cepa.all print.pathway.catalogue
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'cepa.Rd':
  \usage lines wider than 90 characters:
     cepa(dif = NULL, bk = NULL, mat = NULL, label = NULL, pc, pathway = NULL, id = NULL, cen = "equal.weight",
         cen.name = if(is.function(cen)) deparse(substitute(cen)) else if(mode(cen) == "name") deparse(cen) else cen,

Rd file 'cepa.all.Rd':
  \examples lines wider than 100 characters:
     label = read.cls("http://mcube.nju.edu.cn/jwang/lab/soft/cepa/P53.cls", treatment="MUT", control="WT")

Rd file 'cepa.all.parallel.Rd':
  \usage lines wider than 90 characters:
     cepa.all.parallel(dif = NULL, bk = NULL, mat = NULL, label = NULL, pc, cen = default.centralities,
  \examples lines wider than 100 characters:
     label = read.cls("http://mcube.nju.edu.cn/jwang/lab/soft/cepa/P53.cls", treatment="MUT", control="WT")

Rd file 'cepa.ora.Rd':
  \usage lines wider than 90 characters:
              cen.name = if(is.function(cen)) deparse(substitute(cen)) else if(mode(cen) == "name") deparse(cen) else cen,

Rd file 'cepa.univariate.Rd':
  \usage lines wider than 90 characters:
         cen.name = if(is.function(cen)) deparse(substitute(cen)) else if(mode(cen) == "name") deparse(cen) else cen,

Rd file 'cepa.univariate.all.Rd':
  \examples lines wider than 100 characters:
     label = read.cls("http://mcube.nju.edu.cn/jwang/lab/soft/cepa/P53.cls", treatment="MUT", control="WT")

Rd file 'plotGraph.Rd':
  \usage lines wider than 90 characters:
         graph.node.max.size = 20, graph.node.min.size = 3, graph.layout.method = NULL, ...)                 

Rd file 'read.cls.Rd':
  \examples lines wider than 100 characters:
     label = read.cls("http://mcube.nju.edu.cn/jwang/lab/soft/cepa/P53.cls", treatment="MUT", control="WT")

Rd file 'report.Rd':
  \usage lines wider than 90 characters:
            template.file = paste(system.file(package = "CePa"), "/extdata/cepa.template", sep=""),

These lines will be truncated in the PDF manual.
select_lambda: no visible global function definition for ‘median’
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
File ‘CFC/libs/CFC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘cgAUC/libs/cgAUC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following hidden files and directories:
  .project
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Non-standard file/directory found at top level:
  ‘try1.r’
Found the following apparent S3 methods exported but not registered:
  plot.cggd predict.cggd
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
get.switch.time: warning in uniroot(f = switch.func, int =
  c(last_boundary, boundary), lower = last_boundary, upper = boundary,
  maxiter = 1000, tol = tol, e): partial argument match of ‘int’ to
  ‘interval’
plot.cggd: warning in axis(4, at = b[nrow(b), ], label = paste(cnums),
  cex = 0.8, adj = 0): partial argument match of ‘label’ to ‘labels’
plot.cggd: no visible global function definition for ‘gen.beta’
plotCVcggd: no visible binding for global variable ‘cv’
plotCVcggd: no visible binding for global variable ‘cv.error’
predict.cggd: no visible binding for global variable ‘max.tk’
predict.cggd: no visible global function definition for ‘gen.beta’
Undefined global functions or variables:
  cv cv.error gen.beta max.tk

Found the following calls to attach():
File ‘cggd/R/cggd.r’:
  attach(cv.lars.object)
See section ‘Good practice’ in ‘?attach’.
Rd file 'cggd-internal.Rd':
  \usage lines wider than 90 characters:
     get.switch.time(switch.func,e, boundary=0,terminate_value=1e15,tol = .Machine$double.eps^0.5, fctr=1e8, TRACE=FALSE)
     cggd.mgd.one.step(x, y, a.set, beta_init,    t1 = 1, alpha1 = 0, alpha2 = 0, w = 1, tau = 1, tautil = -1, eps = -1, TRACE=FALSE, fctr=1 ... [TRUNCATED]
     cggd.trr.one.step(x, y, a.set, beta_init, t1 = 1, t0 = 1, tau = 1, tautil = -1, eps = -1, fctr=1e8)

Rd file 'plot.cggd.Rd':
  \usage lines wider than 90 characters:
     plot.cggd(x, steps=5, breaks = TRUE, first_k=1,last_k=Inf, xvar=c("step","t"),omit.zeros = TRUE, eps = 1e-10, ...)

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Malformed Title field: should not end in a period.
Malformed Description field: should contain one or more complete sentences.
Found the following apparent S3 methods exported but not registered:
  plot.cghFLasso print.summary.cghFLasso summary.cghFLasso
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
CGH.fused.lasso.one.fast: no visible global function definition for
  ‘lowess’
L2L1ExpandFit: no visible global function definition for
  ‘L2L1PathExtract’
consensusFDR: no visible global function definition for ‘pbinom’
my.mad: no visible global function definition for ‘median’
output.cghFLasso: no visible global function definition for
  ‘write.table’
plot.CGH.FL.All: no visible global function definition for ‘plot’
plot.CGH.FL.All: no visible global function definition for ‘segments’
plot.CGH.FL.All: no visible global function definition for ‘text’
plot.CGH.FL.Consensus: no visible global function definition for
  ‘rainbow’
plot.CGH.FL.Consensus: no visible global function definition for ‘plot’
plot.CGH.FL.Consensus: no visible global function definition for
  ‘segments’
plot.CGH.FL.Consensus: no visible global function definition for ‘gray’
plot.CGH.FL.Consensus: no visible global function definition for ‘text’
plot.CGH.FL.Single: no visible global function definition for ‘plot’
plot.CGH.FL.Single: no visible global function definition for ‘gray’
plot.CGH.FL.Single: no visible global function definition for
  ‘segments’
plot.CGH.FL.Single: no visible global function definition for ‘text’
plot.cghFLasso: no visible global function definition for ‘plot’
plot.cghFLasso: no visible global function definition for ‘gray’
plot.cghFLasso: no visible global function definition for ‘abline’
plot.cghFLasso: no visible global function definition for ‘points’
segment.score: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  L2L1PathExtract abline gray lowess median pbinom plot pnorm points
  rainbow segments text write.table
Consider adding
  importFrom("grDevices", "gray", "rainbow")
  importFrom("graphics", "abline", "plot", "points", "segments", "text")
  importFrom("stats", "lowess", "median", "pbinom", "pnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Rd file 'cghFLasso.Rd':
  \usage lines wider than 90 characters:
     cghFLasso(CGH.Array, chromosome=NULL, nucleotide.position=NULL, FL.norm=NULL, FDR=NULL, filter=NULL, missing.PlugIn=TRUE, smooth.size=5 ... [TRUNCATED]
  \examples lines wider than 100 characters:
     Disease.FL<-cghFLasso(CGH$DiseaseArray, chromosome=CGH$chromosome, nucleotide.position=CGH$nucposition, FL.norm=Normal.FL, FDR=0.01)

Rd file 'cghFLasso.ref.Rd':
  \examples lines wider than 100 characters:
     Disease.FL<-cghFLasso(CGH$DiseaseArray, chromosome=CGH$chromosome, nucleotide.position=CGH$nucposition, FL.norm=Normal.FL, FDR=0.01)

Rd file 'output.cghFLasso.Rd':
  \examples lines wider than 100 characters:
     Disease.FL<-cghFLasso(CGH$DiseaseArray, chromosome=CGH$chromosome, nucleotide.position=CGH$nucposition, FL.norm=Normal.FL, FDR=0.01)

Rd file 'plot.cghFLasso.Rd':
  \examples lines wider than 100 characters:
     Disease.FL<-cghFLasso(CGH$DiseaseArray, chromosome=CGH$chromosome, nucleotide.position=CGH$nucposition, FL.norm=Normal.FL, FDR=0.01)

Rd file 'summary.cghFLasso.Rd':
  \examples lines wider than 100 characters:
     Disease.FL<-cghFLasso(CGH$DiseaseArray, chromosome=CGH$chromosome, nucleotide.position=CGH$nucposition, FL.norm=Normal.FL, FDR=0.01)

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

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

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.
File ‘cghFLasso/libs/cghFLasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘cgh/libs/cgh.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘cghseg/libs/cghseg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  CGP.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
CGPEst: no visible global function definition for ‘dist’
CGPEst : PSI: no visible global function definition for ‘dist’
CGPEst : Stand_PSI: no visible global function definition for ‘dist’
CGPEst : Fop: no visible global function definition for ‘optim’
CGPEst: no visible global function definition for ‘optim’
plotCGP: no visible global function definition for ‘plot’
Undefined global functions or variables:
  dist optim plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dist", "optim")
to your NAMESPACE file.
!: no visible global function definition for ‘dev.new’
lssize : s4gonebyte : fb4: no visible global function definition for
  ‘setNames’
lssize : s4gonebyte : fb4: no visible global function definition for
  ‘slotNames’
lssize : s4gonebyte : fb4: no visible binding for global variable
  ‘slot’
lssize : s4gonebyte : fb4: no visible global function definition for
  ‘object.size’
lssize : s4gone : fs4: no visible global function definition for
  ‘setNames’
lssize : s4gone : fs4: no visible global function definition for
  ‘slotNames’
lssize : s4gone : fs4: no visible binding for global variable ‘slot’
mystat: no visible global function definition for ‘median’
mystat: no visible global function definition for ‘sd’
seqle: no visible global function definition for ‘head’
thekurt: no visible global function definition for ‘var’
theskew: no visible global function definition for ‘sd’
Undefined global functions or variables:
  dev.new head median object.size sd setNames slot slotNames var
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("methods", "slot", "slotNames")
  importFrom("stats", "median", "sd", "setNames", "var")
  importFrom("utils", "head", "object.size")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘changepoint.np/libs/changepoint.np.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘changepoint/libs/changepoint.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ChannelAttribution/libs/ChannelAttribution.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Chaos01/libs/Chaos01.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘ChargeTransport/libs/ChargeTransport.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable 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.
'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.
File ‘cheb/libs/cheb.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘checkmate/libs/checkmate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  $<-.Community $<-.CommunityCollection [.CommunityCollection
  [<-.Community [<-.CommunityCollection [[<-.Community
  [[<-.CommunityCollection
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘cheddar/libs/cheddar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘gurobi’
DAGmethod: no visible global function definition for ‘flush.console’
curveFisher: no visible global function definition for ‘qchisq’
curveFisher: no visible global function definition for ‘lines’
curveFisher: no visible global function definition for ‘legend’
curveMeinshausen: no visible global function definition for ‘lines’
curveMeinshausen: no visible global function definition for ‘legend’
curveSimes: no visible global function definition for ‘lines’
curveSimes: no visible global function definition for ‘legend’
curveSimes_old: no visible global function definition for ‘lines’
curveSimes_old: no visible global function definition for ‘legend’
pick: no visible global function definition for ‘barplot’
pick: no visible global function definition for ‘text’
pickFisher : <anonymous>: no visible global function definition for
  ‘qchisq’
regionmethod: no visible global function definition for ‘flush.console’
regionplot: no visible global function definition for ‘plot’
regionplot: no visible global function definition for ‘axis’
regionplot: no visible global function definition for ‘polygon’
regionplot: no visible global function definition for ‘par’
regionplot: no visible global function definition for ‘legend’
regionplot2 : drawsegment: no visible global function definition for
  ‘segments’
regionplot2: no visible global function definition for ‘plot’
regionplot2: no visible global function definition for ‘axis’
regionplot2: no visible global function definition for ‘par’
regionplot2: no visible global function definition for ‘legend’
structuredHolm: no visible global function definition for
  ‘flush.console’
Undefined global functions or variables:
  axis barplot flush.console legend lines par plot polygon qchisq
  segments text
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines", "par",
             "plot", "polygon", "segments", "text")
  importFrom("stats", "qchisq")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
File ‘ChIPtest/libs/ChIPtest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
cp.scree: no visible global function definition for ‘plot’
dcm.design: no visible global function definition for ‘flush.console’
dcm.design: no visible global function definition for ‘model.matrix’
dcm.design.cand: no visible global function definition for
  ‘flush.console’
dcm.design.cand: no visible global function definition for
  ‘model.matrix’
dcm.design.sort: no visible global function definition for ‘runif’
get.file: no visible global function definition for ‘read.table’
pw.eval: no visible global function definition for ‘sd’
tradeoff.des: no visible global function definition for ‘flush.console’
tradeoff.des: no visible global function definition for ‘sd’
write.tab: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  flush.console model.matrix plot read.table runif sd write.table
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "model.matrix", "runif", "sd")
  importFrom("utils", "flush.console", "read.table", "write.table")
to your NAMESPACE file.
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.
File ‘chopthin/libs/chopthin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘CHsharp/libs/CHsharp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘CIDnetworks/libs/CIDnetworks.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘CIFsmry/libs/CIFsmry.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
CircE.Plot: no visible global function definition for ‘dev.new’
CircE.Plot: no visible global function definition for ‘par’
CircE.Plot: no visible global function definition for ‘plot’
CircE.Plot: no visible global function definition for ‘axis’
CircE.Plot: no visible global function definition for ‘title’
CircE.Plot: no visible global function definition for ‘text’
CircE.Plot: no visible global function definition for ‘points’
CircE.Plot: no visible global function definition for ‘abline’
CircE.Plot: no visible global function definition for ‘segments’
Undefined global functions or variables:
  abline axis dev.new par plot points segments text title
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axis", "par", "plot", "points",
             "segments", "text", "title")
to your NAMESPACE file.
Non-standard files/directories found at top level:
  ‘COPYRIGHT’ ‘COPYRIGHT.original’ ‘CREDITS’
Copyright information should be in file inst/COPYRIGHTS
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘boot’
  Please remove these calls from your code.
Found the following apparent S3 methods exported but not registered:
  plot.edf
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
median:
  function(x, na.rm, ...)
median.circular:
  function(x, na.rm)

median:
  function(x, na.rm, ...)
median.circular:
  function(x, na.rm)

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

Found the following apparent S3 methods exported but not registered:
  as.data.frame.circular lines.edf modal.region.circular
  modal.region.default plot.edf plot.function.circular
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Call with DUP:
   .C("R_distance", x = as.double(x), nr = N, nc = ncol(x), d = double(N * 
       (N - 1)/2), diag = as.integer(FALSE), method = as.integer(method), 
       DUP = FALSE, NAOK = TRUE, PACKAGE = "circular")
DUP is no longer supported and will be ignored.
File ‘circular/libs/circular.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘cit/libs/cit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
areas_list_to_states_list_old: no visible global function definition
  for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
File ‘cladoRcpp/libs/cladoRcpp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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.
File ‘classify/libs/classify.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.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.
File ‘cleanEHR/libs/cleanEHR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘clere/libs/clere.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ClickClust/libs/ClickClust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
climdexInput.csv : get.and.check.data: no visible global function
  definition for ‘read.csv’
get.prec.var.quantiles: no visible global function definition for
  ‘quantile’
growing.season.length : <anonymous>: no visible global function
  definition for ‘head’
Undefined global functions or variables:
  head quantile read.csv
Consider adding
  importFrom("stats", "quantile")
  importFrom("utils", "head", "read.csv")
to your NAMESPACE file.
File ‘climdex.pcic/libs/climdex.pcic.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘clogitboost/libs/clogitboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.clogitL1 plot.cv.clogitL1 print.clogitL1 summary.clogitL1
  summary.cv.clogitL1
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
cv.clogitL1 : <anonymous>: no visible global function definition for
  ‘var’
plot.clogitL1: no visible global function definition for ‘matplot’
plot.clogitL1: no visible global function definition for ‘legend’
plot.clogitL1: no visible global function definition for ‘text’
plot.cv.clogitL1: no visible global function definition for ‘matplot’
plot.cv.clogitL1: no visible global function definition for ‘matlines’
plot.cv.clogitL1: no visible global function definition for ‘points’
plot.cv.clogitL1: no visible global function definition for ‘axis’
plot.cv.clogitL1: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline axis legend matlines matplot points text var
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "matlines",
             "matplot", "points", "text")
  importFrom("stats", "var")
to your NAMESPACE file.
File ‘clogitL1/libs/clogitL1.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘clues/libs/clues.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘clusrank/libs/clusrank.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘clusterCrit/libs/clusterCrit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘ggplot2’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
File ‘clustering.sc.dp/libs/clustering.sc.dp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
fixed.effect: no visible global function definition for ‘glm’
fixed.effect: no visible global function definition for ‘qnorm’
fixed.effect.cluster.level: no visible global function definition for
  ‘aggregate’
fixed.effect.cluster.level: no visible global function definition for
  ‘formula’
fixed.effect.cluster.level: no visible global function definition for
  ‘glm’
fixed.effect.cluster.level: no visible global function definition for
  ‘qnorm’
hayes.power.poisson: no visible global function definition for ‘qnorm’
hayes.power.poisson: no visible global function definition for ‘pnorm’
power.sim.binomial: no visible global function definition for ‘rnorm’
power.sim.binomial: no visible global function definition for ‘rbinom’
power.sim.normal: no visible global function definition for ‘rnorm’
power.sim.poisson: no visible global function definition for ‘rnorm’
power.sim.poisson: no visible global function definition for ‘rnbinom’
power.sim.poisson: no visible global function definition for ‘rpois’
random.effect: no visible global function definition for ‘qt’
random.effect: no visible global function definition for ‘coef’
weighted.crossover.cluster.level: no visible global function definition
  for ‘aggregate’
weighted.crossover.cluster.level: no visible global function definition
  for ‘reshape’
weighted.crossover.cluster.level: no visible global function definition
  for ‘lm’
Undefined global functions or variables:
  aggregate coef formula glm lm pnorm qnorm qt rbinom reshape rnbinom
  rnorm rpois
Consider adding
  importFrom("stats", "aggregate", "coef", "formula", "glm", "lm",
             "pnorm", "qnorm", "qt", "rbinom", "reshape", "rnbinom",
             "rnorm", "rpois")
to your NAMESPACE file.
IGP.clusterRepro: no visible global function definition for ‘cor’
permuteCol: no visible global function definition for ‘runif’
Undefined global functions or variables:
  cor runif
Consider adding
  importFrom("stats", "cor", "runif")
to your NAMESPACE file.
File ‘ClusterR/libs/ClusterR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ClusterStability/libs/ClusterStability.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable 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.
File ‘clusteval/libs/clusteval.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
hclustgeo.uniq: no visible global function definition for ‘dist’
plot.hclustgeo: no visible global function definition for ‘pdf’
plot.hclustgeo: no visible global function definition for ‘par’
plot.hclustgeo: no visible global function definition for ‘plot’
plot.hclustgeo: no visible global function definition for ‘axis’
plot.hclustgeo: no visible global function definition for ‘points’
plot.hclustgeo: no visible global function definition for ‘legend’
plot.hclustgeo: no visible global function definition for ‘dev.off’
plot.hclustgeo.uniq: no visible global function definition for ‘pdf’
plot.hclustgeo.uniq: no visible global function definition for ‘par’
plot.hclustgeo.uniq: no visible global function definition for ‘plot’
plot.hclustgeo.uniq: no visible global function definition for
  ‘recordPlot’
plot.hclustgeo.uniq: no visible global function definition for
  ‘dev.off’
plot.hclustgeo.uniq: no visible global function definition for ‘cutree’
summary.hclustgeo.uniq: no visible global function definition for
  ‘cutree’
Undefined global functions or variables:
  axis cutree dev.off dist legend par pdf plot points recordPlot
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "recordPlot")
  importFrom("graphics", "axis", "legend", "par", "plot", "points")
  importFrom("stats", "cutree", "dist")
to your NAMESPACE file.
File ‘ClustMMDD/libs/ClustMMDD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  print.clustvar
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
cutreevar: no visible global function definition for ‘cutree’
kmeansvar : eta2: no visible global function definition for ‘var’
plot.clustab: no visible global function definition for ‘plot’
plot.clustab: no visible global function definition for ‘axis’
plot.hclustvar: no visible global function definition for ‘par’
plot.hclustvar: no visible global function definition for
  ‘dev.interactive’
plot.hclustvar: no visible global function definition for ‘plot’
plot.hclustvar: no visible global function definition for ‘points’
plot.hclustvar: no visible global function definition for ‘axis’
rand: no visible global function definition for ‘combn’
recodquant: no visible binding for global variable ‘sd’
stability: no visible global function definition for ‘plot’
stability: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis combn cutree dev.interactive par plot points sd var
Consider adding
  importFrom("grDevices", "dev.interactive")
  importFrom("graphics", "axis", "par", "plot", "points")
  importFrom("stats", "cutree", "sd", "var")
  importFrom("utils", "combn")
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.
File ‘ClustVarLV/libs/ClustVarLV.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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.
File ‘clv/libs/clv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable 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.
File ‘CMF/libs/CMF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
MarginalModelFit: no visible global function definition for ‘ftable’
RecordsToFrequencies: no visible global function definition for
  ‘ftable’
getbasicstatistics: no visible global function definition for ‘pchisq’
getmodelstats: no visible global function definition for ‘ftable’
getsamplestats: no visible global function definition for ‘ftable’
gsk: no visible global function definition for ‘pchisq’
spec.allmokkenhj: no visible binding for global variable ‘var’
spec.cronbachalpha: no visible binding for global variable ‘var’
spec.mokkenh: no visible binding for global variable ‘var’
Undefined global functions or variables:
  ftable pchisq var
Consider adding
  importFrom("stats", "ftable", "pchisq", "var")
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.
File ‘cmprskQR/libs/cmprskQR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘cmprsk/libs/cmprsk.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘CNVassoc/libs/CNVassoc.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘coala/libs/coala.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘COBRA/libs/COBRA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
CoClust: no visible binding for global variable ‘median’
CoClust: no visible global function definition for ‘cor’
fit.margin : ecdfc: no visible global function definition for
  ‘approxfun’
fit.margin3: no visible global function definition for ‘optim’
fit.margin3: no visible global function definition for ‘sd’
fit.margin3: no visible global function definition for ‘pnorm’
stima_cop: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  approxfun cor median optim pnorm sd
Consider adding
  importFrom("stats", "approxfun", "cor", "median", "optim", "pnorm",
             "sd")
to your NAMESPACE file.
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.
File ‘codadiags/libs/codadiags.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘codep/libs/codep.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘coenoflex/libs/coenoflex.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘coin/libs/coin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘collUtils/libs/collUtils.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘colorspace/libs/colorspace.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Hopkins.index: no visible global function definition for ‘runif’
MBM.em: no visible global function definition for ‘runif’
PAM.cluster: no visible global function definition for ‘dist’
calculate.layout: no visible global function definition for ‘optim’
min.distance: no visible global function definition for ‘dist’
plot.conceptmap: no visible global function definition for ‘par’
plot.conceptmap: no visible global function definition for ‘plot’
plot.conceptmaps: no visible global function definition for ‘plot’
Undefined global functions or variables:
  dist optim par plot runif
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "dist", "optim", "runif")
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.
Found the following apparent S3 methods exported but not registered:
  plot.CommunityClimateInput plot.CommunityClimateStatistics
  summary.CommunityClimateInput summary.CommunityClimateStatistics
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘cometExactTest/libs/cometExactTest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
showGuideForJavaGUIs: no visible global function definition for
  ‘browseURL’
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
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.
Error in re-building vignettes:
  ...
Loading required package: cluster
Loading required package: clValid
Loading required package: fpc
Loading required package: kohonen
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
The "ward" method has been renamed to "ward.D"; note new "ward.D2"

Error: processing vignette ‘COMMUNAL.Rnw’ failed with diagnostics:
 chunk 1 
Error in !toroidal : invalid argument type
Execution halted
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.
File ‘compareC/libs/compareC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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’
glm.comp: no visible global function definition for ‘model.frame’
glm.comp: no visible global function definition for ‘model.response’
glm.comp: no visible global function definition for ‘model.matrix’
glm.comp: no visible global function definition for ‘model.offset’
glm.comp: no visible global function definition for ‘glm.fit’
glm.comp: no visible global function definition for ‘poisson’
glm.comp: no visible global function definition for ‘optim’
predict.Comp: no visible global function definition for
  ‘delete.response’
predict.Comp: no visible global function definition for ‘model.frame’
predict.Comp: no visible global function definition for ‘model.matrix’
print.Comp: no visible global function definition for ‘AIC’
print.summary.Comp: no visible global function definition for
  ‘printCoefmat’
summary.Comp: no visible global function definition for ‘pt’
summary.Comp: no visible global function definition for ‘AIC’
Undefined global functions or variables:
  AIC delete.response glm.fit model.frame model.matrix model.offset
  model.response optim poisson printCoefmat pt
Consider adding
  importFrom("stats", "AIC", "delete.response", "glm.fit", "model.frame",
             "model.matrix", "model.offset", "model.response", "optim",
             "poisson", "printCoefmat", "pt")
to your NAMESPACE file.
File ‘CompGLM/libs/CompGLM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Found the following apparent S3 methods exported but not registered:
  *.acomp *.rcomp *.rmult *.rplus +.acomp +.rcomp +.rmult +.rplus
  -.acomp -.rcomp -.rmult -.rplus /.acomp /.rcomp /.rmult /.rplus
  MahalanobisDist.aplus MahalanobisDist.rcomp MahalanobisDist.rplus
  R2.default R2.lm acompGOF.test.formula acompGOF.test.list
  balanceBase.aplus balanceBase.rplus barplot.ccomp bit<-.character
  bit<-.numeric cdt.ccomp cdtInv.ccomp groupparts.ccomp idt.ccomp
  idtInv.ccomp mean.ccomp missingProjector.rmult names.ccomp
  names<-.acomp names<-.aplus names<-.ccomp names<-.rcomp names<-.rmult
  names<-.rplus plot.ccomp plot.logratioVariogram split.ccomp
  totals.ccomp var.lm var.mlm
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘compositions/libs/compositions.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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.
File ‘CompRandFld/libs/CompRandFld.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘ConConPiWiFun/libs/ConConPiWiFun.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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
File ‘concreg/libs/concreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘conditions/libs/conditions.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘condmixt/libs/condmixt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  cond.glm family.cond family.summary.cond plot.cond print.cond
  print.summary.cond summary.cond
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
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.
File ‘condSURV/libs/condSURV.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘coneproj/libs/coneproj.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
conf: no visible global function definition for ‘read.csv’
conf: no visible global function definition for ‘write.csv’
mya.conf_input : <anonymous>: no visible global function definition for
  ‘sd’
mya.conf_input : <anonymous>: no visible global function definition for
  ‘qt’
mya.conf_input : <anonymous>: no visible global function definition for
  ‘pt’
plot.mya: no visible global function definition for ‘dt’
plot.mya: no visible global function definition for ‘rgb’
write_html.conf_input: no visible global function definition for
  ‘browseURL’
Undefined global functions or variables:
  browseURL dt pt qt read.csv rgb sd write.csv
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "dt", "pt", "qt", "sd")
  importFrom("utils", "browseURL", "read.csv", "write.csv")
to your NAMESPACE file.
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.
Conjoint: no visible global function definition for ‘dev.new’
Conjoint: no visible global function definition for ‘barplot’
caFactorialDesign: no visible global function definition for ‘cor’
caModel: no visible global function definition for ‘as.formula’
caModel: no visible global function definition for ‘lm’
caModel: no visible global function definition for ‘summary.lm’
caSegmentation: no visible global function definition for ‘kmeans’
caUtilities: no visible global function definition for ‘as.formula’
caUtilities: no visible global function definition for ‘lm’
caUtilities: no visible global function definition for ‘summary.lm’
partutilities: no visible global function definition for ‘as.formula’
partutilities: no visible global function definition for ‘lm’
partutils: no visible global function definition for ‘as.formula’
partutils: no visible global function definition for ‘lm’
profsimcode: no visible global function definition for ‘as.formula’
profsimcode: no visible global function definition for ‘lm’
profsimcode: no visible global function definition for ‘model.matrix’
totalutilities: no visible global function definition for ‘as.formula’
totalutilities: no visible global function definition for ‘lm’
totalutilities: no visible global function definition for
  ‘model.matrix’
utlsplot: no visible global function definition for ‘dev.new’
utlsplot: no visible global function definition for ‘barplot’
Undefined global functions or variables:
  as.formula barplot cor dev.new kmeans lm model.matrix summary.lm
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "barplot")
  importFrom("stats", "as.formula", "cor", "kmeans", "lm",
             "model.matrix", "summary.lm")
to your NAMESPACE file.
File ‘constrainedKriging/libs/constrainedKriging.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ContaminatedMixt/libs/ContaminatedMixt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘contfrac/libs/contfrac.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘contoureR/libs/contoureR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
control_median_test: no visible global function definition for
  ‘quantile’
control_median_test : Qp: no visible global function definition for
  ‘quantile’
control_median_test : Qp: no visible global function definition for
  ‘stepfun’
control_median_test: no visible global function definition for ‘sd’
control_median_test: no visible global function definition for ‘pnorm’
control_median_test: no visible global function definition for ‘plot’
control_median_test: no visible global function definition for ‘lines’
control_median_test: no visible global function definition for ‘legend’
Undefined global functions or variables:
  legend lines plot pnorm quantile sd stepfun
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "pnorm", "quantile", "sd", "stepfun")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘COPYRIGHTS’
Copyright information should be in file inst/COPYRIGHTS
File ‘ConvCalendar/libs/ConvCalendar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
convnum: no visible global function definition for ‘points’
convnum: no visible global function definition for ‘arrows’
convnumsig: no visible global function definition for ‘hist’
maxdist: no visible global function definition for ‘dist’
plotellipse: no visible global function definition for ‘lines’
Undefined global functions or variables:
  arrows dist hist lines points
Consider adding
  importFrom("graphics", "arrows", "hist", "lines", "points")
  importFrom("stats", "dist")
to your NAMESPACE file.
File ‘coop/libs/coop.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘coRanking/libs/coRanking.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
h.inv: no visible global function definition for ‘pnorm’
h.inv: no visible global function definition for ‘qnorm’
hfunc: no visible global function definition for ‘pnorm’
hfunc: no visible global function definition for ‘qnorm’
modified.cvine.alg: no visible global function definition for ‘qpois’
modified.cvine.alg: no visible global function definition for ‘qnbinom’
modified.cvine.alg: no visible global function definition for ‘cor’
modified.cvine.alg.reg: no visible global function definition for
  ‘qpois’
modified.cvine.alg.reg: no visible global function definition for
  ‘qnbinom’
modified.cvine.alg.reg: no visible global function definition for ‘cor’
rcounts : mysampling: no visible global function definition for ‘runif’
rcounts : mysampling: no visible global function definition for ‘qpois’
rcounts : mysampling: no visible global function definition for
  ‘qnbinom’
rcounts.reg : mysampling: no visible global function definition for
  ‘runif’
rcounts.reg : mysampling: no visible global function definition for
  ‘qpois’
rcounts.reg : mysampling: no visible global function definition for
  ‘qnbinom’
unstructured: no visible global function definition for ‘runif’
Undefined global functions or variables:
  cor pnorm qnbinom qnorm qpois runif
Consider adding
  importFrom("stats", "cor", "pnorm", "qnbinom", "qnorm", "qpois",
             "runif")
to your NAMESPACE file.
File ‘cord/libs/cord.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
binom.pval: no visible global function definition for ‘pbinom’
chisq.pval: no visible global function definition for ‘pchisq’
chisq.pval: no visible global function definition for ‘pnorm’
fisher.pval: no visible global function definition for ‘phyper’
prop.cint: no visible global function definition for ‘qbeta’
prop.cint: no visible global function definition for ‘qnorm’
sample.df: no visible global function definition for ‘is’
simulated.census: no visible global function definition for ‘runif’
simulated.census : height2weight: no visible global function definition
  for ‘rnorm’
simulated.census : height2shoe: no visible global function definition
  for ‘rnorm’
simulated.census: no visible global function definition for ‘rnorm’
simulated.wikipedia: no visible global function definition for ‘runif’
simulated.wikipedia: no visible global function definition for ‘rnorm’
z.score.pval: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  is pbinom pchisq phyper pnorm qbeta qnorm rnorm runif
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "pbinom", "pchisq", "phyper", "pnorm", "qbeta",
             "qnorm", "rnorm", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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.
File ‘CorrBin/libs/CorrBin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘CoSeg/libs/CoSeg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
CosmoPhotoZestimator: no visible global function definition for
  ‘predict’
computeCombPCA: no visible global function definition for ‘prcomp’
computeDiagPhotoZ: no visible global function definition for ‘sd’
computeDiagPhotoZ: no visible global function definition for ‘median’
computeDiagPhotoZ: no visible global function definition for ‘mad’
glmPredictPhotoZ: no visible global function definition for ‘predict’
glmTrainPhotoZ: no visible global function definition for ‘glm’
glmTrainPhotoZ: no visible global function definition for ‘Gamma’
glmTrainPhotoZ: no visible global function definition for
  ‘inverse.gaussian’
plotDiagPhotoZ: no visible global function definition for ‘median’
plotDiagPhotoZ: no visible global function definition for ‘mad’
Undefined global functions or variables:
  Gamma glm inverse.gaussian mad median prcomp predict sd
Consider adding
  importFrom("stats", "Gamma", "glm", "inverse.gaussian", "mad",
             "median", "prcomp", "predict", "sd")
to your NAMESPACE file.
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.
Package in Depends field not imported from: ‘wavethresh’
  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.BootTOS
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Found the following apparent S3 methods exported but not registered:
  cotrend.default print.cotrend
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
cotrend.default: no visible global function definition for ‘coredata’
example_eq3: no visible global function definition for ‘rnorm’
example_eq4: no visible global function definition for ‘rnorm’
example_eq8: no visible global function definition for ‘rnorm’
example_eq9: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  coredata rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
File ‘Countr/libs/Countr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘COUSCOus/libs/COUSCOus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘covBM/libs/covBM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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.
File ‘covr/libs/covr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘CoxBoost/libs/CoxBoost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘coxinterval/libs/coxinterval.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘coxme/libs/coxme.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Coxnet/libs/Coxnet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘coxphf/libs/coxphf.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘coxphw/libs/coxphw.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘CoxPlus/libs/CoxPlus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘coxrobust/libs/coxrobust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘coxsei/libs/coxsei.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable 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.
Packages in Depends field not imported from:
  ‘rms’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
phcpe: no visible global function definition for ‘model.matrix’
phcpe: no visible global function definition for ‘sd’
phcpe2: no visible global function definition for ‘sd’
Undefined global functions or variables:
  model.matrix sd
Consider adding
  importFrom("stats", "model.matrix", "sd")
to your NAMESPACE file.
File ‘CPE/libs/CPE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘cpgen/libs/cpgen.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
CpGFilterICC : f2: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  uniroot
Consider adding
  importFrom("stats", "uniroot")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  plot.CPHshape
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
find.antimodeMLE: no visible global function definition for ‘par’
find.decreasingMLE: no visible global function definition for ‘chull’
find.decreasingMLE: no visible global function definition for ‘points’
find.increasingMLE: no visible global function definition for ‘chull’
find.increasingMLE: no visible global function definition for ‘points’
find.modeMLE: no visible global function definition for ‘par’
plot.CPHshape: no visible global function definition for ‘plot’
plot.CPHshape: no visible global function definition for ‘segments’
plot.CPHshape: no visible global function definition for ‘abline’
plot.CPHshape: no visible global function definition for ‘grey’
plot.CPHshape: no visible global function definition for ‘points’
Undefined global functions or variables:
  abline chull grey par plot points segments
Consider adding
  importFrom("grDevices", "chull", "grey")
  importFrom("graphics", "abline", "par", "plot", "points", "segments")
to your NAMESPACE file.
CPMCGLM: no visible binding for global variable ‘binomial’
CPMCGLM: no visible binding for global variable ‘gaussian’
CPMCGLM: no visible binding for global variable ‘poisson’
CPMCGLM: no visible global function definition for ‘update’
CPMCGLM: no visible global function definition for ‘model.response’
CPMCGLM: no visible global function definition for ‘model.frame’
CPMCGLM: no visible global function definition for ‘is.empty.model’
CPMCGLM: no visible global function definition for ‘model.matrix’
CPMCGLM: no visible binding for global variable ‘contrasts’
CPMCGLM: no visible global function definition for ‘pchisq’
CPMCGLM: no visible global function definition for ‘glm’
CPMCGLM: no visible global function definition for ‘pnorm’
CPMCGLM: no visible global function definition for ‘rnorm’
CPMCGLM: no visible global function definition for ‘sd’
CPMCGLM: no visible global function definition for ‘rbinom’
CPMCGLM: no visible global function definition for ‘rpois’
test.liquet: no visible global function definition for ‘glm’
test.liquet: no visible global function definition for ‘var’
test.score: no visible global function definition for ‘glm’
test.score: no visible global function definition for ‘var’
tmultboot: no visible global function definition for ‘glm’
tmultboot: no visible global function definition for ‘var’
Undefined global functions or variables:
  binomial contrasts gaussian glm is.empty.model model.frame
  model.matrix model.response pchisq pnorm poisson rbinom rnorm rpois
  sd update var
Consider adding
  importFrom("stats", "binomial", "contrasts", "gaussian", "glm",
             "is.empty.model", "model.frame", "model.matrix",
             "model.response", "pchisq", "pnorm", "poisson", "rbinom",
             "rnorm", "rpois", "sd", "update", "var")
to your NAMESPACE file.
File ‘cpm/libs/cpm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package required but not available: ‘tpr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following apparent S3 methods exported but not registered:
  calcInterval.CD calcInterval.Mult calcInterval.Sing crackRmc.CD
  crackRmc.Mult crackRmc.Sing head.CD head.Mult head.Sing
  head.crackRparallel head.crackRresults head.parametersCD
  head.parametersMult head.parametersSing head.stateCD head.stateMult
  head.stateSing inspection.CD inspection.Mult inspection.Sing lines.CD
  lines.Mult lines.Sing lines.crackRparallel lines.crackRresults
  plot.CD plot.Mult plot.Sing plot.crackRparallel plot.crackRresults
  print.CD print.Mult print.Sing print.crackRparallel
  print.crackRresults print.stateCD print.stateMult print.stateSing
  tail.CD tail.Mult tail.Sing tail.crackRparallel tail.crackRresults
  tail.parametersCD tail.parametersMult tail.parametersSing
  tail.stateCD tail.stateMult tail.stateSing
See section ‘Registering S3 methods’ 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.
File ‘crch/libs/crch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘creditr/libs/creditr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘credule/libs/credule.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘CRF/libs/CRF.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
dmZIP: no visible global function definition for ‘flush.console’
dmZIP: no visible global function definition for ‘var’
dmZIPt: no visible global function definition for ‘flush.console’
dmZIPt: no visible global function definition for ‘var’
plot.dmZIP: no visible global function definition for ‘matplot’
plot.dmZIPt: no visible global function definition for ‘matplot’
Undefined global functions or variables:
  flush.console matplot var
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "var")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
File ‘crimCV/libs/crimCV.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
CRMoneIncomplete: no visible global function definition for ‘runif’
CRMoneIncomplete: no visible global function definition for ‘rexp’
CRMsimOne: no visible global function definition for ‘runif’
CRMsimOne: no visible global function definition for ‘rexp’
CRMtwoIncomplete: no visible global function definition for ‘runif’
CRMtwoIncomplete: no visible global function definition for ‘rexp’
Undefined global functions or variables:
  rexp runif
Consider adding
  importFrom("stats", "rexp", "runif")
to your NAMESPACE file.
File ‘CRM/libs/CRM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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.
File ‘Crossover/libs/Crossover.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  Error: GET https://app.crunch.io/api/ (/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/crunch/app.crunch.io/api.json)
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
File ‘crqa/libs/crqa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘crrp/libs/crrp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘crrSC/libs/crrSC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘crskdiag/libs/crskdiag.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(httptest)
  Loading required package: testthat
  > test_check("crunch")
  Loading required package: crunch
  
  Attaching package: 'crunch'
  
  The following object is masked from 'package:base':
  
      table
  
  Error: GET https://app.crunch.io/api/ (/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/crunch/app.crunch.io/api.json)
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
'library' or 'require' call to ‘parallel’ 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:
  ‘car’ ‘ellipse’ ‘rJPSGCS’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘CrypticIBDcheck/libs/CrypticIBDcheck.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.Lapl.cont plot.Lapl.spl
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Laplace.c: no visible global function definition for ‘optim’
Laplace.c: no visible global function definition for ‘spline’
Laplace.cc: no visible global function definition for ‘optim’
Laplace.cs: no visible global function definition for ‘optim’
Laplace.s: no visible global function definition for ‘optim’
Laplace.s: no visible global function definition for ‘spline’
make.sample.data: no visible global function definition for ‘coef’
make.sample.data: no visible global function definition for
  ‘model.matrix’
plot.Lapl.cont: no visible global function definition for ‘contour’
plot.Lapl.spl: no visible global function definition for ‘plot’
rmt: no visible global function definition for ‘rt’
rmt: no visible global function definition for ‘rnorm’
rmt: no visible global function definition for ‘rchisq’
rsm.sample: no visible global function definition for ‘runif’
rsm.sample: no visible global function definition for ‘dweibull’
rsm.sample: no visible global function definition for ‘dt’
rsm.sample: no visible global function definition for ‘dlogis’
Undefined global functions or variables:
  coef contour dlogis dt dweibull model.matrix optim plot rchisq rnorm
  rt runif spline
Consider adding
  importFrom("graphics", "contour", "plot")
  importFrom("stats", "coef", "dlogis", "dt", "dweibull", "model.matrix",
             "optim", "rchisq", "rnorm", "rt", "runif", "spline")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  fitted.cSFM predict.cSFM predict.kpbb print.cSFM
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
D.SN: no visible global function definition for ‘dnorm’
D.SN: no visible global function definition for ‘pnorm’
beta2cp: no visible global function definition for ‘pnorm’
cSFM.est: no visible global function definition for ‘optim’
cSFM.est: no visible global function definition for ‘qnorm’
cSFM.est: no visible global function definition for ‘cor’
case2.b.initial: no visible global function definition for ‘var’
case2.gr: no visible global function definition for ‘pnorm’
case2.gr: no visible global function definition for ‘dnorm’
case2.unmll.optim: no visible global function definition for ‘pnorm’
cp2beta: no visible global function definition for ‘qnorm’
data.generator.y.F: no visible global function definition for ‘cov2cor’
data.generator.y.F: no visible global function definition for ‘rnorm’
data.generator.y.F : <anonymous>: no visible global function definition
  for ‘pnorm’
g: no visible global function definition for ‘dnorm’
g: no visible global function definition for ‘pnorm’
predict.cSFM : <anonymous>: no visible global function definition for
  ‘qnorm’
predict.cSFM: no visible global function definition for ‘qnorm’
predict.cSFM: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  cor cov2cor dnorm optim pnorm qnorm rnorm var
Consider adding
  importFrom("stats", "cor", "cov2cor", "dnorm", "optim", "pnorm",
             "qnorm", "rnorm", "var")
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.
File ‘cstab/libs/cstab.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘csvread/libs/csvread.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  ./ctl.h:38:23: warning: token pasting of ',' and __VA_ARGS__ is a GNU extension [-Wgnu-zero-variadic-macro-arguments]
  ./ctl.h:36:25: warning: token pasting of ',' and __VA_ARGS__ is a GNU extension [-Wgnu-zero-variadic-macro-arguments]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ctl.Rcheck/00install.out’ for details.
File ‘ctl/libs/ctl.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
! Dimension too large.
\fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa 
                                                  \fb@putboxa #1\fb@afterfra...
l.2052 \end{kframe}
                   
! Dimension too large.
\fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa 
                                                  \fb@putboxa #1\fb@afterfra...
l.2052 \end{kframe}
                   
! Dimension too large.
\fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa 
                                                  \fb@putboxa #1\fb@afterfra...
l.2052 \end{kframe}
                   
! Dimension too large.
\fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa 
                                                  \fb@putboxa #1\fb@afterfra...
l.2052 \end{kframe}
                   
! Dimension too large.
\fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa 
                                                  \fb@putboxa #1\fb@a
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘CuCubes/libs/CuCubes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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.
Packages in Depends field not imported from:
  ‘MCMCpack’ ‘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:
  cudia.default plot.cudia print.cudia summary.cudia
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
cudiaDet: no visible global function definition for ‘model.frame’
cudiaDet: no visible global function definition for ‘model.response’
cudiaDet: no visible binding for global variable ‘sd’
cudiaDet: no visible global function definition for ‘rdirichlet’
cudiaDet: no visible global function definition for ‘rnorm’
cudiaDet: no visible global function definition for ‘lm.ridge’
plot.cudia: no visible global function definition for ‘par’
plot.cudia: no visible global function definition for ‘plot’
Undefined global functions or variables:
  lm.ridge model.frame model.response par plot rdirichlet rnorm sd
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "model.frame", "model.response", "rnorm", "sd")
to your NAMESPACE file.
Found the following hidden files and directories:
  .gitignore
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Malformed Title field: should not end in a period.
License components which are templates and need '+ file LICENSE':
  MIT
Non-standard files/directories found at top level:
  ‘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’
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.
'library' or 'require' call to ‘locfit’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘R.methodsS3’ ‘R.oo’ ‘locfit’ ‘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:
  lines.curvefit plot.curvefit print.curvefit print.curvetest
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
curvefit: no visible global function definition for ‘model.frame’
curvefit: no visible global function definition for ‘model.response’
curvefit: no visible global function definition for ‘model.matrix’
curvetest: no visible global function definition for ‘model.frame’
curvetest: no visible global function definition for ‘plot’
curvetest.raw: no visible global function definition for ‘pt’
curvetest.raw: no visible global function definition for ‘pnorm’
getoptimalalpha: no visible global function definition for ‘gcvplot’
getoptimalalpha: no visible global function definition for ‘plot’
lines.curvefit: no visible global function definition for ‘lines’
plot.curvefit: no visible global function definition for ‘plot’
plot.curvefit: no visible global function definition for ‘lines’
plot.curvefit: no visible global function definition for ‘points’
Undefined global functions or variables:
  gcvplot lines model.frame model.matrix model.response plot pnorm
  points pt
Consider adding
  importFrom("graphics", "lines", "plot", "points")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "pnorm", "pt")
to your NAMESPACE file.
Rd file 'alpha2h.Rd':
  \examples lines wider than 100 characters:
         (h=alpha2h(0.3, at=0.5, xseq=x))  ##get the window width h around x=.5 so that 30% data points of xseq fall in the area.  

Rd file 'curvefit.Rd':
  \usage lines wider than 90 characters:
     curvefit(formula, data, kernel = "Quartic", alpha = 0.5, bw = NULL, myx, bcorrect = "simple", getit = F)

Rd file 'curvetest.Rd':
  \usage lines wider than 90 characters:
     curvetest(formula, data1 = NULL, data2 = NULL, equal.var = TRUE, alpha = 0.5, bw = NULL, plotit = TRUE, conf.level = 0.05, kernel = c(" ... [TRUNCATED]
  \examples lines wider than 100 characters:
         curvetest(y~x,data.frame(x=x1,y=y1), data.frame(x=x2,y=y2), alpha =  0.7, equal.var=TRUE,plotit=TRUE) 

These lines will be truncated in the PDF manual.
File ‘cusp/libs/cusp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘CUSUMdesign/libs/CUSUMdesign.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
path.plot: no visible global function definition for ‘plot’
path.plot: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines plot
Consider adding
  importFrom("graphics", "lines", "plot")
to your NAMESPACE file.
File ‘cvplogistic/libs/cvplogistic.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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').
Packages in Depends field not imported from:
  ‘Matrix’ ‘kernlab’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.klogreg: no visible global function definition for ‘Matrix’
.klogreg: no visible global function definition for ‘kernelMatrix’
.klogreg: no visible global function definition for ‘Diagonal’
.klogreg.predict: no visible global function definition for
  ‘kernelMult’
.krr: no visible global function definition for ‘kernelMatrix’
.krr: no visible global function definition for ‘Matrix’
.krr.predict: no visible global function definition for ‘kernelMatrix’
cochranq.test: no visible global function definition for ‘pchisq’
constructSVMLearner : learn.svm: no visible global function definition
  for ‘ksvm’
constructSVMLearner : predict.svm: no visible global function
  definition for ‘predict’
constructSVRLearner : learn.svr: no visible global function definition
  for ‘ksvm’
constructSVRLearner : predict.svr: no visible global function
  definition for ‘predict’
fastCV: no visible binding for global variable ‘sd’
fastCV: no visible global function definition for ‘qnorm’
fastCV: no visible global function definition for ‘friedman.test’
noisyDonoho: no visible global function definition for ‘runif’
noisyDonoho: no visible global function definition for ‘rnorm’
noisySinc: no visible global function definition for ‘runif’
noisySinc: no visible global function definition for ‘rnorm’
noisySine: no visible global function definition for ‘runif’
noisySine: no visible global function definition for ‘rnorm’
plotSequence: no visible global function definition for ‘plot’
plotSequence: no visible global function definition for ‘abline’
plotSequence: no visible global function definition for ‘title’
Undefined global functions or variables:
  Diagonal Matrix abline friedman.test kernelMatrix kernelMult ksvm
  pchisq plot predict qnorm rnorm runif sd title
Consider adding
  importFrom("graphics", "abline", "plot", "title")
  importFrom("stats", "friedman.test", "pchisq", "predict", "qnorm",
             "rnorm", "runif", "sd")
to your NAMESPACE file.
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.
File ‘cvxbiclustr/libs/cvxbiclustr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘cvxclustr/libs/cvxclustr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.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').
File ‘cycleRtools/libs/cycleRtools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Cyclops/libs/Cyclops.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘D3M/libs/D3M.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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.
y.stand: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
File ‘dagbag/libs/dagbag.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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.
Found the following apparent S3 methods exported but not registered:
  roc.area
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘Daim/libs/Daim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘DALY/libs/DALY.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ 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.
File ‘darch/libs/darch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘darts/libs/darts.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
get_temporary_file_name: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
File ‘DatABEL/libs/DatABEL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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’.
File ‘datamap/libs/datamap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘Datasmith/libs/Datasmith.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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’.
Found the following apparent S3 methods exported but not registered:
  [.timeline [<-.timepoint [[.timeline
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
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:
  print.list.pairs
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
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.
File ‘dblcens/libs/dblcens.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ 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.
File ‘dcemriS4/libs/dcemriS4.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘DCluster/libs/DCluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
DrawAlphas: no visible global function definition for ‘rmultinom’
DrawClasses: no visible global function definition for ‘runif’
GetGammaNames: no visible global function definition for ‘combn’
GetLambdaNamesForItem: no visible global function definition for
  ‘combn’
SampleParameterEstimates: no visible global function definition for
  ‘rnorm’
plot,attribute.class-missing: no visible binding for global variable
  ‘attr.number’
plot,attribute.class-missing: no visible binding for global variable
  ‘mean.attr’
plot,attribute.profile.class-missing: no visible binding for global
  variable ‘attr.profile.number’
plot,attribute.profile.class-missing: no visible binding for global
  variable ‘mean.attr.profile’
summary,attribute.class: no visible binding for global variable ‘value’
summary,attribute.profile.class: no visible binding for global variable
  ‘max.class’
Undefined global functions or variables:
  attr.number attr.profile.number combn max.class mean.attr
  mean.attr.profile rmultinom rnorm runif value
Consider adding
  importFrom("stats", "rmultinom", "rnorm", "runif")
  importFrom("utils", "combn")
to your NAMESPACE file.
test.LM: no visible global function definition for ‘lm’
Undefined global functions or variables:
  lm
Consider adding
  importFrom("stats", "lm")
to your NAMESPACE file.
File ‘ddalpha/libs/ddalpha.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘DDHFm/libs/DDHFm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘ddR/libs/ddR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.network plot.networkfamily plot.node print.network
  print.networkfamily print.node prob.network prob.node score.network
  score.node unique.networkfamily
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘deal/libs/deal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘debug.Recall’ ‘debug.eval’ ‘debug.eval.guts’ ‘debug.fun.name’
  ‘evaluator’ ‘find.debug.HQ’ ‘mvb.sys.on.exit’ ‘stepping’
Rd file 'debug.eval.Rd':
  \usage lines wider than 90 characters:
     debug.eval(expr, envir = parent.frame(), enclos = if (is.list(envir) ||  is.pairlist(envir)) parent.frame() else baseenv())

Rd file 'mtrace.Rd':
  \usage lines wider than 90 characters:
     mtrace( fname, tracing=TRUE, char.fname, from=mvb.sys.parent(), update.tracees=TRUE, return.envs=FALSE)

These lines will be truncated in the PDF manual.
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.
File ‘decon/libs/decon.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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').
File ‘deepboost/libs/deepboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘deformula/libs/deformula.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘degreenet/libs/degreenet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  [.triang.list
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Found the following apparent S3 methods exported but not registered:
  print.deltaPlot
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
deltaPlot : internalDelta: no visible global function definition for
  ‘qnorm’
deltaPlot : internalDelta: no visible global function definition for
  ‘cov’
deltaPlot: no visible global function definition for ‘capture.output’
diagPlot : internalDP: no visible global function definition for ‘plot’
diagPlot : internalDP: no visible global function definition for
  ‘abline’
diagPlot : internalDP: no visible global function definition for
  ‘points’
diagPlot : internalDP: no visible global function definition for ‘cor’
diagPlot : internalDP: no visible global function definition for
  ‘legend’
diagPlot: no visible global function definition for ‘pdf’
diagPlot: no visible global function definition for ‘dev.off’
diagPlot: no visible global function definition for ‘jpeg’
print.deltaPlot: no visible global function definition for ‘symnum’
Undefined global functions or variables:
  abline capture.output cor cov dev.off jpeg legend pdf plot points
  qnorm symnum
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "pdf")
  importFrom("graphics", "abline", "legend", "plot", "points")
  importFrom("stats", "cor", "cov", "qnorm", "symnum")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
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.
File ‘delt/libs/delt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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’.
Non-standard file/directory found at top level:
  ‘configure-build’
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.
File ‘DendSer/libs/DendSer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘denpro/libs/denpro.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘densityClust/libs/densityClust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  densregion.default densregion.normal
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘DEoptim/libs/DEoptim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘DEploid/libs/DEploid.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘Rdonlp2’
File ‘depmix/libs/depmix.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘depmixS4/libs/depmixS4.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘DepthProc/libs/DepthProc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘depth/libs/depth.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘dequer/libs/dequer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘descr/libs/descr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘desire/libs/desire.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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').
File ‘deSolve/libs/deSolve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking: ‘Rmosek’ ‘gurobi’
File ‘DESP/libs/libscsdir.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
File ‘DESP/libs/scsSolveSOCP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘deTestSet/libs/deTestSet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘DetMCD/libs/DetMCD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘DetR/libs/DetR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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.
File ‘DetSel/libs/DetSel.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘dexter/libs/dexter.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘dfphase1/libs/dfphase1.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘dgof/libs/dgof.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  beadsplot.character beadsplot.data.frame beadsplot.default
  beadsplot.formula beadsplot.numeric
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
beadsplot.formula: no visible global function definition for
  ‘model.frame’
calc.stats: no visible global function definition for ‘str’
do.call.with.par: no visible global function definition for
  ‘modifyList’
make.colors: no visible global function definition for ‘rainbow’
make.colors : <anonymous>: no visible global function definition for
  ‘adjustcolor’
make.scale: no visible global function definition for ‘modifyList’
only.graphic.pars: no visible global function definition for ‘par’
plt.diamond: no visible global function definition for ‘polygon’
plt.diamond: no visible global function definition for ‘lines’
plt.gridline: no visible global function definition for ‘abline’
plt.gridline: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  abline adjustcolor lines model.frame modifyList mtext par polygon
  rainbow str
Consider adding
  importFrom("grDevices", "adjustcolor", "rainbow")
  importFrom("graphics", "abline", "lines", "mtext", "par", "polygon")
  importFrom("stats", "model.frame")
  importFrom("utils", "modifyList", "str")
to your NAMESPACE file.
File ‘DiceDesign/libs/DiceDesign.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘DiceKriging/libs/DiceKriging.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘DiceOptim/libs/DiceOptim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘diffIRT/libs/diffIRT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘diffobj/libs/diffobj.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
exber.maxwdth: no visible global function definition for ‘median’
exber.maxwdth: no visible global function definition for ‘mad’
fcnst: no visible global function definition for ‘median’
fcnst: no visible global function definition for ‘plot’
fcnst: no visible global function definition for ‘lines’
fnpregm: no visible global function definition for ‘median’
fnpregm: no visible global function definition for ‘plot’
fnpregm: no visible global function definition for ‘lines’
frunmed: no visible global function definition for ‘median’
mrqsim: no visible global function definition for ‘rnorm’
mrqsim: no visible global function definition for ‘quantile’
pkdecomp: no visible global function definition for ‘mad’
pkdecompint: no visible global function definition for ‘runif’
pkdecompint: no visible global function definition for ‘optim’
wsspoiss: no visible global function definition for ‘mad’
Undefined global functions or variables:
  lines mad median optim plot quantile rnorm runif
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "mad", "median", "optim", "quantile", "rnorm",
             "runif")
to your NAMESPACE file.
File ‘diffractometry/libs/diffractometry.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘diffrprojects/libs/diffrprojects.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.dmap print.dmap
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
adapreg: no visible global function definition for ‘optimize’
adapreg: no visible global function definition for ‘runif’
adapreg.m: no visible global function definition for ‘lm’
epsilonCompute: no visible global function definition for ‘median’
plot.dmap: no visible global function definition for ‘plot’
plot.dmap: no visible global function definition for ‘stripchart’
Undefined global functions or variables:
  lm median optimize plot runif stripchart
Consider adding
  importFrom("graphics", "plot", "stripchart")
  importFrom("stats", "lm", "median", "optimize", "runif")
to your NAMESPACE file.
File ‘DiffusionRgqd/libs/DiffusionRgqd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘DiffusionRimp/libs/DiffusionRimp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘DiffusionRjgqd/libs/DiffusionRjgqd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘diffusr/libs/diffusr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ 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.
File ‘dils/libs/dils.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘DIME/libs/DIME.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘DIRECT/libs/DIRECT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘DirichletReg/libs/DirichletReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
kf: no visible global function definition for ‘dbinom’
Undefined global functions or variables:
  dbinom
Consider adding
  importFrom("stats", "dbinom")
to your NAMESPACE file.
File ‘disclapmix/libs/disclapmix.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
rdisclap: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
DiscML : midpoint : allAncestors: no visible global function definition
  for ‘reorder’
DiscML : midpoint : reroot: no visible global function definition for
  ‘reorder’
DiscML : midpoint : node2root: no visible global function definition
  for ‘reorder’
DiscML : midpoint: no visible global function definition for ‘reorder’
DiscML: no visible global function definition for ‘reorder’
DiscML : DiscML2 : dev: no visible global function definition for
  ‘qgamma’
DiscML : DiscML2 : dev: no visible global function definition for ‘is’
DiscML : DiscML2: no visible global function definition for ‘nlminb’
DiscML : DiscML2: no visible global function definition for ‘nlm’
DiscML: no visible global function definition for ‘par’
DiscML: no visible global function definition for ‘plot’
DiscML: no visible global function definition for ‘axis’
DiscML: no visible global function definition for ‘axTicks’
DiscML: no visible global function definition for ‘text’
Undefined global functions or variables:
  axTicks axis is nlm nlminb par plot qgamma reorder text
Consider adding
  importFrom("graphics", "axTicks", "axis", "par", "plot", "text")
  importFrom("methods", "is")
  importFrom("stats", "nlm", "nlminb", "qgamma", "reorder")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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’
Package unavailable to check Rd xrefs: ‘INLA’
File ‘dismo/libs/dismo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following hidden files and directories:
  .directory
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
distSegment: no visible global function definition for ‘dist’
distShape: no visible global function definition for ‘dist’
distTriangle: no visible global function definition for ‘dist’
exactHausdorff: no visible global function definition for ‘aggregate’
Undefined global functions or variables:
  aggregate dist
Consider adding
  importFrom("stats", "aggregate", "dist")
to your NAMESPACE file.
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.
Non-standard file/directory found at top level:
  ‘Misc’
Found the following apparent S3 methods exported but not registered:
  summary.dispmod
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
glm.binomial.disp: no visible global function definition for ‘family’
glm.binomial.disp : pearson.X2: no visible global function definition
  for ‘residuals’
glm.binomial.disp: no visible global function definition for
  ‘model.matrix’
glm.binomial.disp: no visible global function definition for
  ‘lm.influence’
glm.poisson.disp: no visible global function definition for ‘family’
glm.poisson.disp : pearson.X2: no visible global function definition
  for ‘residuals’
glm.poisson.disp: no visible global function definition for
  ‘lm.influence’
lm.disp: no visible global function definition for ‘glm.control’
lm.disp: no visible binding for global variable ‘na.omit’
lm.disp: no visible global function definition for ‘as.formula’
lm.disp: no visible global function definition for ‘model.response’
lm.disp: no visible global function definition for ‘model.offset’
lm.disp: no visible global function definition for ‘is.empty.model’
lm.disp: no visible global function definition for ‘model.matrix’
lm.disp: no visible global function definition for ‘model.extract’
lm.disp: no visible global function definition for ‘glm.fit’
lm.disp: no visible global function definition for ‘gaussian’
lm.disp: no visible global function definition for ‘Gamma’
summary.dispmod: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  Gamma as.formula family gaussian glm.control glm.fit is.empty.model
  lm.influence model.extract model.matrix model.offset model.response
  na.omit pchisq residuals
Consider adding
  importFrom("stats", "Gamma", "as.formula", "family", "gaussian",
             "glm.control", "glm.fit", "is.empty.model", "lm.influence",
             "model.extract", "model.matrix", "model.offset",
             "model.response", "na.omit", "pchisq", "residuals")
to your NAMESPACE file.
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.
File ‘dissUtils/libs/dissUtils.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard file/directory found at top level:
  ‘Distance.Rproj’
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.
Found the following apparent S3 methods exported but not registered:
  plot.distfree.cr
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
distfree.cr: no visible global function definition for ‘plot’
linescrosspoint: no visible global function definition for ‘na.exclude’
plot.distfree.cr: no visible global function definition for ‘plot’
plot.distfree.cr: no visible global function definition for ‘points’
plot.distfree.cr: no visible global function definition for ‘polygon’
plot.distfree.cr: no visible global function definition for ‘legend’
xy.quantile: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  legend na.exclude plot points polygon quantile
Consider adding
  importFrom("graphics", "legend", "plot", "points", "polygon")
  importFrom("stats", "na.exclude", "quantile")
to your NAMESPACE file.
Rd file 'distfree.cr.Rd':
  \usage lines wider than 90 characters:
     distfree.cr(x, y, alpha = 0.05, alpha.min.diff = alpha/10, nknots = 40, xlab = deparse(substitute(x)), ylab = deparse(substitute(y)), c ... [TRUNCATED]
  \examples lines wider than 100 characters:
     dat=data.frame(x=c(rnorm(3000), rnorm(3000, mean=1, sd=2.5)), y=c(rnorm(3000), rnorm(3000, mean=1, sd=2.5)))

These lines will be truncated in the PDF manual.
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.
File ‘distory/libs/distory.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.rd
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
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.
File ‘DistributionUtils/libs/DistributionUtils.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
prepare_Rd: extract.val.Rd:25-26: Dropping empty section \note
prepare_Rd: extract.val.Rd:27: Dropping empty section \seealso
Found the following apparent S3 methods exported but not registered:
  DiveMaster.default divsamplenum.default divsubsamples.default
  fitsinglemod.default format.input plot.fitsingleMod
  print.DiversityMaster print.divsubsamples print.fitsingleMod
  print.scoresingleMod print.summary.DiversityMaster
  print.summary.divsubsamples print.summary.fitsingleMod
  print.summary.scoresingleMod scoresinglemod.default
  summary.DiversityMaster summary.divsubsamples summary.fitsingleMod
  summary.scoresingleMod
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Curvature: no visible global function definition for ‘tail’
gen.rarefac.div: no visible global function definition for ‘sd’
plot.fitsingleMod: no visible global function definition for ‘points’
plot.fitsingleMod: no visible global function definition for ‘lines’
ref.area: no visible global function definition for ‘integrate’
simm: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate lines points sd tail
Consider adding
  importFrom("graphics", "lines", "points")
  importFrom("stats", "integrate", "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
Rd file 'H.sampler.Rd':
  \usage lines wider than 90 characters:
     H.sampler(x = "community matrix (spp=col,obs=row)", n = "sample size vector", nit = "number of iterations to use", base = exp(1), corr  ... [TRUNCATED]

These lines will be truncated in the PDF manual.
'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.
dixon: no visible global function definition for ‘pnorm’
mNNtest: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq pnorm
Consider adding
  importFrom("stats", "pchisq", "pnorm")
to your NAMESPACE file.
File ‘dixon/libs/dixon.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘dkDNA/libs/dkDNA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘magick’
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.
'library' or 'require' calls in package code:
  ‘FKF’ ‘dlm’
  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:
  %%.dlmodeler *.dlmodeler +.dlmodeler
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
dlmodeler.extract: no visible global function definition for ‘qnorm’
dlmodeler.fit.MAD: no visible global function definition for ‘optim’
dlmodeler.fit.MAPE: no visible global function definition for ‘optim’
dlmodeler.fit.MLE: no visible global function definition for ‘optim’
dlmodeler.fit.MSE: no visible global function definition for ‘optim’
dlmodeler.fit.sigma : fit.fun: no visible global function definition
  for ‘var’
dlmodeler.fit.sigma: no visible global function definition for ‘optim’
dlmodeler.forecast: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  optim qnorm var
Consider adding
  importFrom("stats", "optim", "qnorm", "var")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  dlmSmooth.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘dlm/libs/dlm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package in Depends field not imported from: ‘magic’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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
File ‘dna/libs/dna.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘DNAtools/libs/DNAtools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘dnc/libs/dnc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘docopulae/libs/docopulae.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘documair/libs/documair.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.AccSampPlan plot.CurtSampPlan plot.SeqSampPlan print.AccSampPlan
  print.CurtSampPlan print.SeqSampPlan
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
.ccd.1.41: no visible global function definition for ‘rnorm’
.ccd.1.41: no visible global function definition for ‘formula’
.ccd.1.41: no visible global function definition for ‘coef’
.ccd.1.41: no visible global function definition for ‘runif’
.ccd.1.41 : <anonymous>: no visible global function definition for
  ‘as.formula’
.gen.des.old.way: no visible global function definition for ‘runif’
.randomize: no visible global function definition for ‘[.coded.data’
Dopt.augment: no visible global function definition for ‘rnorm’
Dopt.augment: no visible global function definition for ‘as.formula’
Dopt.augment: no visible global function definition for ‘model.matrix’
Dopt.design: no visible global function definition for ‘as.formula’
Dopt.design: no visible global function definition for ‘model.matrix’
Scalc: no visible global function definition for ‘dist’
bbd.design: no visible global function definition for ‘model.matrix’
ccd.augment: no visible global function definition for ‘as.formula’
ccd.augment: no visible global function definition for ‘model.matrix’
ccd.augment: no visible global function definition for ‘model.frame’
ccd.augment: no visible binding for global variable ‘na.pass’
generators.from.design: no visible global function definition for
  ‘formula’
generators.from.design : <anonymous>: no visible global function
  definition for ‘as.formula’
lhs.design: no visible global function definition for ‘cor’
rsm.design: no visible global function definition for ‘as.formula’
rsmformula: no visible global function definition for ‘formula’
Undefined global functions or variables:
  [.coded.data as.formula coef cor dist formula model.frame
  model.matrix na.pass rnorm runif
Consider adding
  importFrom("stats", "as.formula", "coef", "cor", "dist", "formula",
             "model.frame", "model.matrix", "na.pass", "rnorm", "runif")
to your NAMESPACE file.
BugReports field should be the URL of a single webpage
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.
File ‘doRedis/libs/doRedis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘DoseFinding/libs/DoseFinding.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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').
File ‘dotCall64/libs/dotCall64.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
hazard.LL: no visible global function definition for ‘integrate’
hazard.LL: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  integrate qnorm
Consider adding
  importFrom("stats", "integrate", "qnorm")
to your NAMESPACE file.
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.
File ‘dpglasso/libs/dpglasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [8s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  There are 3 series
  1    	TST14A  	 1906	 1914	0.01
  2    	TST14B  	 1905	 1913	0.01
  3    	TST14C  	 1906	 1913	0.01
  There does not appear to be a header in the rwl file
  There are 3 series
  1    	TST14A  	 1908	 1914	0.01
  2    	TST14B  	 1905	 1911	0.01
  3    	TST14C  	 1907	 1912	0.01
  testthat results ================================================================
  OK: 470 SKIPPED: 0 FAILED: 1
  1. Failure: read.tucson stops on overlapping data (@test-io.R#110) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘dplyr/libs/dplyr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [9s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  testthat results ================================================================
  OK: 1499 SKIPPED: 1 FAILED: 10
  1.  Failure: duplicated column name is explicit about which column (#996) (@test-arrange.r#139) 
  2.  Failure: duplicated column name is explicit about which column (#996) (@test-arrange.r#143) 
  3.  Failure: filter uses the white list (#566) (@test-filter.r#193) 
  4.  Failure: ungrouped output (@test-output.R#10) 
  5.  Failure: ungrouped output (@test-output.R#10) 
  6.  Failure: ungrouped output (@test-output.R#10) 
  7.  Failure: ungrouped output (@test-output.R#10) 
  8.  Failure: ungrouped output (@test-output.R#10) 
  9.  Failure: summarise gives proper errors (#153) (@test-summarise.r#61) 
  10. Failure: summarise gives proper errors (#153) (@test-summarise.r#62) 
  
  Error: testthat unit tests failed
  Execution halted
Packages in Depends field not imported from:
  ‘cluster’ ‘oro.nifti’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dpmixsim: no visible global function definition for ‘runif’
dpmixsim: no visible global function definition for ‘clara’
postdpmixciz: no visible global function definition for ‘par’
postdpmixciz: no visible global function definition for ‘barplot’
postdpmixciz: no visible global function definition for ‘dnorm’
postdpmixciz: no visible global function definition for ‘hist’
postdpmixciz: no visible global function definition for ‘lines’
postdpmixciz: no visible global function definition for ‘axis’
postdpmixciz: no visible global function definition for ‘dev.cur’
postdpmixciz: no visible global function definition for ‘points’
postdpmixciz: no visible global function definition for ‘dev.set’
postimgclgrp: no visible global function definition for ‘par’
postimgclgrp: no visible global function definition for ‘image’
postimgclgrp: no visible global function definition for ‘gray’
postimgcomps: no visible global function definition for ‘par’
postimgcomps: no visible global function definition for ‘image’
postimgcomps: no visible global function definition for ‘gray’
postkcluster: no visible global function definition for ‘clara’
postkcluster: no visible global function definition for ‘par’
postkcluster: no visible global function definition for ‘image’
postkcluster: no visible global function definition for ‘gray’
readsliceimg: no visible global function definition for ‘readNIfTI’
Undefined global functions or variables:
  axis barplot clara dev.cur dev.set dnorm gray hist image lines par
  points readNIfTI runif
Consider adding
  importFrom("grDevices", "dev.cur", "dev.set", "gray")
  importFrom("graphics", "axis", "barplot", "hist", "image", "lines",
             "par", "points")
  importFrom("stats", "dnorm", "runif")
to your NAMESPACE file.
File ‘dpmixsim/libs/dpmixsim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Symbol ‘nsave’ is used before it is typed at (1)
  Warning: GNU Extension: Different type kinds at (1)
  Warning: GNU Extension: Nonstandard type declaration INTEGER*4 at (1)
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/DPpackage.Rcheck/00install.out’ for details.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘nlme’ ‘survival’
  Please remove these calls from your code.
Found the following apparent S3 methods exported but not registered:
  BDPdensity.default CSDPbinary.default DPMdencens.default
  DPMglmm.default DPMlmm.default DPMmeta.default DPMolmm.default
  DPMrandom.default DPMrasch.default DPMraschpoisson.default
  DPbetabinom.default DPbinary.default DPcdensity.default
  DPdensity.default DPelicit.default DPglmm.default DPlmm.default
  DPmeta.default DPmultmeta.default DPolmm.default DPrandom.default
  DPrasch.default DPraschpoisson.default DProc.default
  DPsurvint.default FPTbinary.default FPTrasch.default
  FPTraschpoisson.default HDPMcdensity.default HDPMdensity.default
  LDBDPdensity.default LDDPdensity.default LDDPrasch.default
  LDDPraschpoisson.default LDDProc.default LDDPsurvival.default
  LDDPtwopl.default LDPDdoublyint.default LDTFPdensity.default
  LDTFPglmm.default LDTFPsurvival.default PSgam.default
  PTdensity.default PTglmm.default PTlm.default PTlmm.default
  PTmeta.default PTolmm.default PTrandom.default PTsampler.default
  Pbinary.default Plm.default TDPdensity.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘DPpackage/libs/DPpackage.so’:
  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’
File ‘DPpackage/libs/DPpackage.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘dprep/libs/dprep.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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').
File ‘drgee/libs/drgee.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘DRIP/libs/DRIP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘drmdel/libs/drmdel.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.depratio print.depratio print.drm print.summary.drm summary.drm
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
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.
File ‘dse/libs/dse.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘dslice/libs/dslice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘DSL/libs/DSL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘DStree/libs/DStree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘dti/libs/dti.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘dtw/libs/dtw.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.ds print.ds summary.ds
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
dsCHECK: no visible global function definition for ‘na.omit’
dsFC: no visible global function definition for ‘cor’
dsMC: no visible global function definition for ‘cor’
plot.ds: no visible global function definition for ‘plot’
plot.ds: no visible global function definition for ‘par’
plot.ds: no visible global function definition for ‘points’
plot.ds: no visible global function definition for ‘text’
Undefined global functions or variables:
  cor na.omit par plot points text
Consider adding
  importFrom("graphics", "par", "plot", "points", "text")
  importFrom("stats", "cor", "na.omit")
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:
  ‘Read-and-delete-me’
'library' or 'require' call to ‘wmtsa’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘wmtsa’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
perturbFBM: warning in circFBM(n, H, plot = FALSE): partial argument
  match of ‘plot’ to ‘plotfBm’
circFBM: no visible global function definition for ‘fft’
circFBM: no visible global function definition for ‘rnorm’
circFBM: no visible global function definition for ‘par’
circFBM: no visible global function definition for ‘plot’
dvFBM: no visible global function definition for ‘filter’
dvFBM: no visible global function definition for ‘quantile’
dvFBM: no visible global function definition for ‘lm’
dvFBM: no visible global function definition for ‘plot’
dvFBM: no visible global function definition for ‘abline’
filt: no visible global function definition for ‘wavDaubechies’
perturbFBM: no visible global function definition for ‘rnorm’
perturbFBM: no visible global function definition for ‘rbinom’
perturbFBM: no visible global function definition for ‘par’
perturbFBM: no visible global function definition for ‘segments’
perturbFBM: no visible global function definition for ‘points’
Undefined global functions or variables:
  abline fft filter lm par plot points quantile rbinom rnorm segments
  wavDaubechies
Consider adding
  importFrom("graphics", "abline", "par", "plot", "points", "segments")
  importFrom("stats", "fft", "filter", "lm", "quantile", "rbinom",
             "rnorm")
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.
File ‘dynamichazard/libs/dynamichazard.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Package in Depends field not imported from: ‘lpridge’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
bootstrapCI: no visible global function definition for ‘lpepa’
bootstrapCI: no visible global function definition for ‘var’
bootstrapCI: no visible global function definition for ‘quantile’
dynamicCorrelation: no visible global function definition for ‘lpepa’
dynamicCorrelation: no visible global function definition for ‘var’
Undefined global functions or variables:
  lpepa quantile var
Consider adding
  importFrom("stats", "quantile", "var")
to your NAMESPACE file.

Found the following calls to attach():
File ‘dynCorr/R/bootstrapCI.r’:
  attach(dataFrame)
File ‘dynCorr/R/dynamicCorrelation.r’:
  attach(dataFrame)
See section ‘Good practice’ in ‘?attach’.
Rd file 'bootstrapCI.rd':
  \usage lines wider than 90 characters:
        bootstrapCI(dataFrame, depVar, indepVar, subjectVar, function.choice, width.range, width.place, boundary.trunc, byOrder, max.dynCorr ... [TRUNCATED]

Rd file 'dynamicCorrelation.rd':
  \usage lines wider than 90 characters:
        dynamicCorrelation(dataFrame, depVar, indepVar, subjectVar, function.choice, width.range, width.place, boundary.trunc, lag.input, by ... [TRUNCATED]
  \examples lines wider than 100 characters:
           ##            for all three pairs of responses, for both original function and the first derivative 
           ## note: output includes zero lag correlations, as well as maximum correlation (in absolute value)

These lines will be truncated in the PDF manual.
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.
File ‘dynpred/libs/dynpred.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  $.dyn
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘dynsurv/libs/dynsurv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  eafplot.data.frame eafplot.default eafplot.formula eafplot.list
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘eaf/libs/eaf.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘EasyABC/libs/EasyABC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
beta.cauchy: no visible global function definition for ‘dnorm’
beta.laplace: no visible global function definition for ‘pnorm’
beta.laplace: no visible global function definition for ‘dnorm’
cauchy.medzero: no visible global function definition for ‘dnorm’
cauchy.medzero: no visible global function definition for ‘pnorm’
cauchy.threshzero: no visible global function definition for ‘pnorm’
cauchy.threshzero: no visible global function definition for ‘dnorm’
ebayesthresh: no visible global function definition for ‘mad’
ebayesthresh.wavelet.dwt: no visible global function definition for
  ‘mad’
ebayesthresh.wavelet.splus: no visible global function definition for
  ‘mad’
ebayesthresh.wavelet.wd: no visible global function definition for
  ‘mad’
laplace.threshzero: no visible global function definition for ‘pnorm’
laplace.threshzero: no visible global function definition for ‘dnorm’
postmean.laplace: no visible global function definition for ‘pnorm’
postmean.laplace: no visible global function definition for ‘dnorm’
postmed.laplace: no visible global function definition for ‘dnorm’
postmed.laplace: no visible global function definition for ‘qnorm’
wandafromx: no visible global function definition for ‘optim’
wandafromx: no visible global function definition for ‘nlminb’
wfromt: no visible global function definition for ‘pnorm’
wfromt: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm mad nlminb optim pnorm qnorm
Consider adding
  importFrom("stats", "dnorm", "mad", "nlminb", "optim", "pnorm",
             "qnorm")
to your NAMESPACE file.
File ‘ebdbNet/libs/ebdbNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘EBEN/libs/EBEN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘EBglmnet/libs/EBglmnet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘EBMAforecast/libs/EBMAforecast.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
ebSNP: no visible global function definition for ‘optim’
Undefined global functions or variables:
  optim
Consider adding
  importFrom("stats", "optim")
to your NAMESPACE file.
File ‘EBS/libs/EBS.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘GeneralFunctions.o’
File ‘EBS/libs/EBS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ecespa/libs/ecespa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘ecodist/libs/ecodist.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘ecolMod/libs/ecolMod.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘eco/libs/eco.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ecp/libs/ecp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘edci/libs/edci.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘edesign/libs/edesign.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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').
File ‘EditImputeCont/libs/EditImputeCont.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
as.character.cateditmatrix: no visible global function definition for
  ‘str’
datamodel: no visible global function definition for ‘stack’
localize: no visible global function definition for ‘flush.console’
perturbWeights: no visible global function definition for ‘runif’
plot.errorLocation: no visible global function definition for ‘par’
plot.errorLocation: no visible global function definition for ‘barplot’
plot.errorLocation: no visible global function definition for ‘plot’
plot.errorLocation: no visible global function definition for ‘grid’
plot.errorLocation: no visible global function definition for ‘mtext’
plot.errorLocation: no visible global function definition for ‘density’
plot.errorLocation: no visible global function definition for ‘lines’
plot.errorLocation: no visible global function definition for ‘axis’
plot.violatedEdits: no visible global function definition for ‘par’
plot.violatedEdits: no visible global function definition for ‘barplot’
plot.violatedEdits: no visible global function definition for ‘plot’
plot.violatedEdits: no visible global function definition for ‘mtext’
plotEditGraph: no visible global function definition for ‘plot’
print.backtracker: no visible global function definition for ‘ls.str’
removeRedundantDummies: no visible global function definition for
  ‘dist’
summary.errorLocation: no visible global function definition for
  ‘quantile’
summary.errorLocation : <anonymous>: no visible global function
  definition for ‘quantile’
Undefined global functions or variables:
  axis barplot density dist flush.console grid lines ls.str mtext par
  plot quantile runif stack str
Consider adding
  importFrom("graphics", "axis", "barplot", "grid", "lines", "mtext",
             "par", "plot")
  importFrom("stats", "density", "dist", "quantile", "runif")
  importFrom("utils", "flush.console", "ls.str", "stack", "str")
to your NAMESPACE file.
File ‘eDMA/libs/eDMA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘edrGraphicalTools/libs/edrGraphicalTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘EDR/libs/EDR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
geteegdata: no visible global function definition for ‘untar’
geteegdata: no visible global function definition for ‘read.table’
geteegdata: no visible global function definition for ‘write.csv’
geteegdata: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  read.table untar write.csv write.table
Consider adding
  importFrom("utils", "read.table", "untar", "write.csv", "write.table")
to your NAMESPACE file.
Running ‘test-all.R’ [12s/11s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  Loading required package: ggplot2
  > 
  > test_check("eeptools")
  Loading required package: MASS
  1. Error: Function works for multiple types of inputs (@test-utils.R#140) ------
  invalid format '%04d'; use format %f, %e, %g or %a for numeric objects
  1: leading_zero(a, digits = 3) at testthat/test-utils.R:140
  2: sprintf(formatter, x)
  
  testthat results ================================================================
  OK: 526 SKIPPED: 0 FAILED: 1
  1. Error: Function works for multiple types of inputs (@test-utils.R#140) 
  
  Error: testthat unit tests failed
  Execution halted
.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').
File ‘eggCounts/libs/eggCounts.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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.
Found the following apparent S3 methods exported but not registered:
  plot.eigenmodel_post
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
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.
File ‘eiPack/libs/eiPack.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
eive.cga : f: no visible global function definition for ‘lm.fit’
eive.cga: no visible global function definition for ‘lm’
generate.eive.data: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  lm lm.fit rnorm
Consider adding
  importFrom("stats", "lm", "lm.fit", "rnorm")
to your NAMESPACE file.
File ‘eive/libs/eive.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ 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.
File ‘eiwild/libs/eiwild.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.enet predict.enet print.arrayspc print.enet print.spca
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
cv.enet: no visible global function definition for ‘predict’
cv.enet: no visible binding for global variable ‘var’
cv.enet: no visible global function definition for ‘plot’
plot.enet: no visible global function definition for ‘plot’
plot.enet: no visible global function definition for ‘lines’
plot.enet: no visible global function definition for ‘axis’
plot.enet: no visible global function definition for ‘abline’
predict.enet: no visible global function definition for ‘approx’
Undefined global functions or variables:
  abline approx axis lines plot predict var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "plot")
  importFrom("stats", "approx", "predict", "var")
to your NAMESPACE file.
Rd file 'enet.Rd':
  \usage lines wider than 90 characters:
     enet(x, y, lambda, max.steps, normalize=TRUE, intercept=TRUE, trace = FALSE, eps = .Machine$double.eps)

Rd file 'spca.Rd':
  \usage lines wider than 90 characters:
     spca(x,K,para,type=c("predictor","Gram"),sparse=c("penalty","varnum"),use.corr=FALSE,lambda=1e-6,max.iter=200,trace=FALSE,eps.conv=1e-3 ... [TRUNCATED]

These lines will be truncated in the PDF manual.
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
File ‘elec.strat/libs/elec.strat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  ellipseplot.data.frame ellipseplot.default ellipseplot.list
  ellipseplot.matrix ellipseplot.numeric
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
anellipse: no visible global function definition for ‘str’
anellipse: no visible global function definition for ‘polygon’
ellipseplot.data.frame: no visible global function definition for ‘par’
ellipseplot.default: no visible global function definition for ‘par’
ellipses: no visible global function definition for ‘text’
ellipses: no visible global function definition for ‘mtext’
many.ellipses: no visible global function definition for ‘modifyList’
many.ellipses: no visible global function definition for ‘hasArg’
many.ellipses: no visible global function definition for ‘rainbow’
sheer.color: no visible global function definition for ‘adjustcolor’
Undefined global functions or variables:
  adjustcolor hasArg modifyList mtext par polygon rainbow str text
Consider adding
  importFrom("grDevices", "adjustcolor", "rainbow")
  importFrom("graphics", "mtext", "par", "polygon", "text")
  importFrom("methods", "hasArg")
  importFrom("utils", "modifyList", "str")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Rd file 'ellipse.profile.nls.Rd':
  \usage lines wider than 90 characters:
     ellipse(x, which = c(1, 2), level = 0.95, t = sqrt(2 * qf(level, 2, attr(x, "summary")$df[2])), 

Rd file 'plotcorr.Rd':
  \usage lines wider than 90 characters:
     plotcorr(corr, outline = TRUE, col = 'grey', numbers = FALSE, type = c("full","lower","upper"),

These lines will be truncated in the PDF manual.
Found the following apparent S3 methods exported but not registered:
  elmtrain.default elmtrain.formula
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
elmtrain.default: no visible global function definition for ‘runif’
elmtrain.formula: no visible global function definition for
  ‘model.frame’
elmtrain.formula: no visible global function definition for
  ‘model.matrix’
elmtrain.formula: no visible global function definition for
  ‘model.response’
predict.elmNN: no visible global function definition for ‘fitted’
predict.elmNN: no visible global function definition for ‘model.matrix’
print.elmNN: no visible global function definition for ‘head’
print.elmNN: no visible global function definition for ‘fitted’
randomMatrix: no visible global function definition for ‘runif’
Undefined global functions or variables:
  fitted head model.frame model.matrix model.response runif
Consider adding
  importFrom("stats", "fitted", "model.frame", "model.matrix",
             "model.response", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
File ‘EloChoice/libs/EloChoice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘EL/libs/EL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.elrm summary.elrm update.elrm
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
elrm: no visible global function definition for ‘write.table’
plot.elrm: no visible global function definition for ‘dev.new’
progress: no visible global function definition for ‘flush.console’
update.elrm: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  dev.new flush.console write.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
File ‘elrm/libs/elrm.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Objects: ‘binomMCMC.o’, ‘functions.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘binomMCMC.o’
File ‘elrm/libs/elrm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ 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').
File ‘ELYP/libs/ELYP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘EMbC/libs/EMbC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘EMC/libs/EMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘emdist/libs/emdist.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  image.plot.ts
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘EMD/libs/EMD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘emil/libs/emil.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘emIRT/libs/emIRT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘EmiStatR/libs/EmiStatR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ 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.
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.
File ‘EMMIXuskew/libs/EMMIXuskew.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
nondominated_ordering: no visible binding for global variable ‘par’
rsbxbeta: no visible global function definition for ‘runif’
Undefined global functions or variables:
  par runif
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "runif")
to your NAMESPACE file.
File ‘emoa/libs/emoa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
el2.cen.EMm: no visible global function definition for ‘pchisq’
el2.cen.EMs: no visible global function definition for ‘pchisq’
el2.test.wts: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  pchisq uniroot
Consider adding
  importFrom("stats", "pchisq", "uniroot")
to your NAMESPACE file.
File ‘emplik/libs/emplik.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
makeinputfiles: no visible global function definition for ‘qnorm’
makeinputfiles: no visible global function definition for ‘qunif’
makeinputfiles: no visible global function definition for ‘write.table’
optimal.scale: no visible global function definition for ‘optimize’
optimal.scales: no visible global function definition for ‘optim’
sample.from.exp.est: no visible global function definition for ‘qnorm’
sample.n.fit: no visible global function definition for ‘plot’
sample.n.fit: no visible global function definition for ‘lines’
sample.n.fit: no visible global function definition for ‘points’
sample.n.fit: no visible global function definition for ‘legend’
Undefined global functions or variables:
  legend lines optim optimize plot points qnorm qunif write.table
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("stats", "optim", "optimize", "qnorm", "qunif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  cbind.trackdata rbind.trackdata
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘endogMNP/libs/endogMNP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘energy/libs/energy.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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.
Non-standard file/directory found at top level:
  ‘desktop.ini’
Packages in Depends field not imported from:
  ‘FactoMineR’ ‘MASS’ ‘Rcmdr’ ‘SensoMineR’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'ENMCA.Rd':
  \usage lines wider than 90 characters:
     ENMCA(dataset,ind.sup = NULL, quanti.sup = NULL, quali.sup = NULL, axes = c(1, 2), row.w = NULL,level.ventil = 0,signif=FALSE,proba=0.0 ... [TRUNCATED]

Rd file 'ENellipse.Rd':
  \usage lines wider than 90 characters:
     ENellipse(matP, cluster, resampling="population", iter=500, alpha = 0.05, coord = c(1, 2), eig, cex = 1, color = NULL)
  \examples lines wider than 100 characters:
     ENellipse(matP=x, cluster=b, resampling="population", iter=500, alpha = 0.05, coord = c(1, 2), eig=res.enmca$MCA$eig, cex = 1, color =  ... [TRUNCATED]

These lines will be truncated in the PDF manual.
File ‘enRich/libs/enRich.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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.
'library' or 'require' call to ‘chron’ which was already attached by Depends.
  Please remove these calls from your code.
Found the following apparent S3 methods exported but not registered:
  cdf.ensembleMOSnormal cdf.fitMOSnormal crps.ensembleMOSnormal
  crps.fitMOSnormal ensembleMemberLabels.ensembleData
  ensembleNobs.ensembleData ensembleObsLabels.ensembleData
  ensembleVerifObs.ensembleData matchEnsembleMembers.ensembleMOSnormal
  matchEnsembleMembers.fitMOSnormal matchITandFH.default
  quantileForecast.ensembleMOSnormal quantileForecast.fitMOSnormal
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
cdf.ensembleMOSnormal: no visible global function definition for ‘var’
cdf.ensembleMOSnormal: no visible global function definition for
  ‘pnorm’
cdf.fitMOSnormal: no visible binding for global variable ‘var’
cdf.fitMOSnormal: no visible global function definition for ‘pnorm’
crps.ensembleMOSnormal : crpsFunc: no visible global function
  definition for ‘pnorm’
crps.ensembleMOSnormal : crpsFunc: no visible global function
  definition for ‘dnorm’
crps.ensembleMOSnormal: no visible global function definition for ‘var’
crps.fitMOSnormal : crpsFunc: no visible global function definition for
  ‘pnorm’
crps.fitMOSnormal : crpsFunc: no visible global function definition for
  ‘dnorm’
crps.fitMOSnormal: no visible global function definition for ‘var’
fitMOSnormal: no visible global function definition for ‘lm’
fitMOSnormal : objectiveFUN: no visible global function definition for
  ‘pnorm’
fitMOSnormal : objectiveFUN: no visible global function definition for
  ‘dnorm’
fitMOSnormal: no visible global function definition for ‘optim’
quantileForecast.ensembleMOSnormal: no visible global function
  definition for ‘var’
quantileForecast.ensembleMOSnormal: no visible global function
  definition for ‘qnorm’
quantileForecast.fitMOSnormal: no visible binding for global variable
  ‘var’
quantileForecast.fitMOSnormal: no visible global function definition
  for ‘qnorm’
Undefined global functions or variables:
  dnorm lm optim pnorm qnorm var
Consider adding
  importFrom("stats", "dnorm", "lm", "optim", "pnorm", "qnorm", "var")
to your NAMESPACE file.
File ‘EntropyEstimation/libs/EntropyEstimation.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘enviPat/libs/enviPat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘enviPick/libs/enviPick.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘EnviroStat/libs/EnviroStat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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.
File ‘EPGLM/libs/EPGLM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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.
File ‘EpiContactTrace/libs/EpiContactTrace.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘epiDisplay-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pyramid
> ### Title: Population pyramid
> ### Aliases: pyramid
> ### Keywords: aplot
> 
> ### ** Examples
> 
> data(Oswego)
> .data <- Oswego
> attach(.data)
> pyramid(age, sex)
> pyramid(age, sex, bar.label = TRUE)
> pyramid(age, sex, printTable=TRUE)

 Tabulation of age by sex (frequency). 
Error in print.default(xx, quote = quote, right = TRUE, ...) : 
  formal argument "right" matched by multiple actual arguments
Calls: pyramid -> print.noquote -> print -> print.table -> print
Execution halted
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.
File ‘epifit/libs/epifit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘epinet/libs/epinet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Found the following apparent S3 methods exported but not registered:
  plot.bootsize
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Package in Depends field not imported from: ‘car’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.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 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 image par r
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.
File ‘equivalence/libs/equivalence.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘erboost/libs/erboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ergm.count/libs/ergm.count.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  [.egodata
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘ergm.graphlets/libs/ergm.graphlets.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ergm.rank/libs/ergm.rank.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ergm/libs/ergm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ergm.userterms/libs/ergm.userterms.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘eRm/libs/eRm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ 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.
File ‘esaddle/libs/esaddle.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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').
File ‘ESGtoolkit/libs/ESGtoolkit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
cv.ES: no visible binding for global variable ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
File ‘EstHer/libs/EstHer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable 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:
  ‘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.
File ‘etasFLP/libs/etasFLP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ETAS/libs/ETAS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
avec.cov: no visible global function definition for ‘qnorm’
closPseudo: no visible global function definition for ‘terms’
etmCIF: no visible global function definition for ‘model.extract’
lines.etm: no visible global function definition for ‘lines’
phiPseudo: no visible global function definition for ‘terms’
plot.clos.etm: no visible global function definition for ‘par’
plot.clos.etm: no visible global function definition for ‘split.screen’
plot.clos.etm: no visible global function definition for ‘screen’
plot.clos.etm: no visible global function definition for ‘plot’
plot.clos.etm: no visible global function definition for ‘axis’
plot.clos.etm: no visible global function definition for ‘box’
plot.clos.etm: no visible global function definition for ‘lines’
plot.clos.etm: no visible global function definition for ‘close.screen’
plot.etm: no visible global function definition for ‘plot’
plot.etm: no visible global function definition for ‘lines’
plot.etmCIF: no visible global function definition for ‘plot’
plot.etmCIF: no visible global function definition for ‘lines’
plot.etmCIF: no visible global function definition for ‘segments’
print.summary.etm: no visible global function definition for ‘quantile’
print.summary.etmCIF: no visible global function definition for
  ‘quantile’
Undefined global functions or variables:
  axis box close.screen lines model.extract par plot qnorm quantile
  screen segments split.screen terms
Consider adding
  importFrom("graphics", "axis", "box", "close.screen", "lines", "par",
             "plot", "screen", "segments", "split.screen")
  importFrom("stats", "model.extract", "qnorm", "quantile", "terms")
to your NAMESPACE file.
File ‘etm/libs/etm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘eulerr/libs/eulerr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Unknown package ‘DNAprofiles’ in Rd xrefs
File ‘euroMix/libs/euroMix.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
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 ‘http://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 13543 bytes (13 KB)
==================================================
downloaded 13 KB

Table ten00081 cached at /tmp/RtmpkoQ72x/eurostat/ten00081_date_code_TF.rds
trying URL ‘http://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 5933 bytes
==================================================
downloaded 5933 bytes

Quitting from lines 366-378 (eurostat_tutorial.Rmd) 
Error: processing vignette ‘eurostat_tutorial.Rmd’ failed with diagnostics:
HTTP request failed with status: 500 Internal Server Error
Execution halted
Missing or unexported object: ‘purrr::by_row’
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.
File ‘evdbayes/libs/evdbayes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘evd/libs/evd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘event/libs/event.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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').
Packages in Depends field not imported from:
  ‘boot’ ‘xts’ ‘zoo’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'eesPlot.Rd':
  \examples lines wider than 100 characters:
     eesPlot(z=eesData, response.series.name="nifty", event.series.name="sp500",titlestring="S&P500", ylab="(Cum.) change in NIFTY")

These lines will be truncated in the PDF manual.
Found the following apparent S3 methods exported but not registered:
  plot.gev plot.gpd plot.gpdbiv plot.potd
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘evolqg/libs/evolqg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
LRI.test : LRI.statistic: no visible global function definition for
  ‘integrate’
MLEst: no visible global function definition for ‘optimize’
MLEst_c: no visible global function definition for ‘optimize’
WLK.test : LK.statistic: no visible global function definition for
  ‘optimize’
WLK.test: no visible global function definition for ‘sd’
WNS.test : MLE: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  integrate optimize sd
Consider adding
  importFrom("stats", "integrate", "optimize", "sd")
to your NAMESPACE file.
File ‘EWGoF/libs/EWGoF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘exactLoglinTest/libs/exactLoglinTest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘lars’ ‘ncvreg’
  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.path print.path
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.path: no visible global function definition for ‘par’
plot.path: no visible global function definition for ‘plot’
plot.path: no visible global function definition for ‘axis’
plot.path: no visible global function definition for ‘points’
plot.path: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline axis par plot points
Consider adding
  importFrom("graphics", "abline", "axis", "par", "plot", "points")
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.
File ‘excursions/libs/excursions.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘exif/libs/exif.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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').
File ‘ExomeDepth/libs/ExomeDepth.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard file/directory found at top level:
  ‘ExpDes.pt-Ex.R’
Non-standard file/directory found at top level:
  ‘ExpDes-Ex.R’
'library' or 'require' call to ‘fields’ 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: ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package in Depends field not imported from: ‘boot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘experiment/libs/experiment.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
expv,CsparseMatrix-vector: no visible global function definition for
  ‘callGeneric’
expv,CsparseMatrix-vector: no visible global function definition for
  ‘as’
expv,matrix-vector: no visible global function definition for
  ‘callGeneric’
expv,matrix-vector: no visible global function definition for ‘as’
Undefined global functions or variables:
  as callGeneric
Consider adding
  importFrom("methods", "as", "callGeneric")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘expoRkit/libs/expoRkit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘expoTree/libs/expoTree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘spatstat’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
eppSimDat: no visible global function definition for ‘rnorm’
eppSimDat: no visible global function definition for ‘rpois’
DirichletPolygons,SpatialPointsBreeding-missing: no visible global
  function definition for ‘ripras’
barplot,epp: no visible global function definition for ‘axis’
barplot,epp: no visible global function definition for ‘par’
plot,SpatialPointsBreeding-eppMatrix: no visible global function
  definition for ‘points’
plot,SpatialPointsBreeding-eppMatrix: no visible global function
  definition for ‘text’
plot,SpatialPointsBreeding-eppMatrix: no visible global function
  definition for ‘arrows’
plot,SpatialPointsBreeding-missing: no visible global function
  definition for ‘points’
plot,SpatialPointsBreeding-missing: no visible global function
  definition for ‘text’
Undefined global functions or variables:
  arrows axis par points ripras rnorm rpois text
Consider adding
  importFrom("graphics", "arrows", "axis", "par", "points", "text")
  importFrom("stats", "rnorm", "rpois")
to your NAMESPACE 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.
File ‘extracat/libs/extracat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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').
File ‘extRemes/libs/extRemes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘extWeibQuant/libs/extWeibQuant.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘ezglm/libs/ezglm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
pandoc: Could not fetch http://ropensci.org/public_images/github_footer.png
TlsExceptionHostPort (HandshakeFailed Error_EOF) "ropensci.org" 80
Error: processing vignette ‘ezknitr.Rmd’ failed with diagnostics:
pandoc document conversion failed with error 67
Execution halted
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.
File ‘FactoClass/libs/FactoClass.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘factorcpt/libs/factorcpt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘factorQR/libs/factorQR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘factorstochvol/libs/factorstochvol.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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.
'library' or 'require' calls in package code:
  ‘Rgraphviz’ ‘corpcor’ ‘energy’ ‘mvnmle’ ‘mvnormtest’ ‘nFactors’
  ‘polycor’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Calls with DUP:
   .C(FAiR_QD_sum, sum = numeric(1), x = x, middle = middle, length = length(x), 
       DUP = FALSE, NAOK = TRUE)
   .C(FAiR_QD_grad, grad = numeric(length_x), x = x, middle = middle, 
       length = length_x, holder = numeric(length_x), DUP = FALSE, 
       NAOK = TRUE)
   .C("exhaustive_mve", number = as.integer(0), combos = combos, 
       lengthcombos = length(combos), Xdata = as.double(X), Xrow = nrow(X), 
       Xcol = ncol(X), DUP = FALSE, PACKAGE = "FAiR")
DUP is no longer supported and will be ignored.
File ‘FAiR/libs/FAiR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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.
File ‘falcon/libs/falcon.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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'.
File ‘fame/libs/fame.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Familias/libs/Familias.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘FAmle/libs/FAmle.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘fanc/libs/fanc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ 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.
File ‘farff/libs/farff.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
':::' call which should be '::': ‘fBasics:::.sliderMenu’
  See the note in ?`:::` about the use of this operator.
Found the following apparent S3 methods exported but not registered:
  .plot.arma.1 .plot.arma.2 .plot.arma.3 .plot.arma.4
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Functions or methods with usage in documentation object 'LrdModelling' but not in code:
  whittleFit
Found the following Makefile(s) without a final LF:
  inst/unitTests/Makefile
Some ‘make’ programs ignore lines not ending in LF.
File ‘fArma/libs/fArma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘far/libs/far.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  Ops.farsi as.character.farsi as.numeric.farsi farsi.default
  farsi.farsi farsi.numeric print.farsi sort.farsi
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: ‘i’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/fAsianOptions.Rcheck/00install.out’ for details.
File ‘fAsianOptions/libs/fAsianOptions.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fastAdaboost/libs/fastAdaboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘FastBandChol/libs/FastBandChol.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fastclime/libs/fastclime.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fastcluster/libs/fastcluster.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fastcmh/libs/fastcmh.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fastdigest/libs/fastdigest.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fastGHQuad/libs/fastGHQuad.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘FastGP/libs/FastGP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
FHCSpsdo: no visible global function definition for ‘is’
FastHCS: no visible global function definition for ‘complete.cases’
compPcaParams: no visible global function definition for ‘quantile’
compPcaParams: no visible global function definition for ‘qchisq’
compPcaParams: no visible global function definition for ‘qnorm’
compPcaParams: no visible global function definition for ‘sd’
plot.FastHCS: no visible global function definition for ‘plot’
plot.FastHCS: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline complete.cases is plot qchisq qnorm quantile sd
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("methods", "is")
  importFrom("stats", "complete.cases", "qchisq", "qnorm", "quantile",
             "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘FastHCS/libs/FastHCS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘fastHorseshoe/libs/fastHorseshoe.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
fastICA: 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: ‘coxKM’
File ‘fastmatch/libs/fastmatch.so’:
  Found non-API call to R: ‘match5’
File ‘fastmatch/libs/fastmatch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
MVTMLE_symm: no visible global function definition for ‘cov’
MVTMLE_symm: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn cov
Consider adding
  importFrom("stats", "cov")
  importFrom("utils", "combn")
to your NAMESPACE file.
File ‘fastM/libs/fastM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.FastPCS
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
FastPCS: no visible global function definition for ‘complete.cases’
FastPCS: no visible global function definition for ‘cov’
FastPCS: no visible global function definition for ‘mahalanobis’
FastPCS: no visible global function definition for ‘qchisq’
FastPCS: no visible global function definition for ‘quantile’
plot.FastPCS: no visible global function definition for ‘plot’
plot.FastPCS: no visible global function definition for ‘abline’
plot.FastPCS: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  abline complete.cases cov mahalanobis plot qchisq quantile
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("stats", "complete.cases", "cov", "mahalanobis", "qchisq",
             "quantile")
to your NAMESPACE file.
File ‘FastPCS/libs/FastPCS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘FastRCS/libs/FastRCS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

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
File ‘FastRWeb/libs/null.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fastSOM/libs/fastSOM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fasttime/libs/fasttime.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls in package code:
  ‘akima’ ‘spatial’ ‘tcltk’
  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.histogram .print.ssd .summary.gel .summary.gmm getModel.default
  print.control stdev.default termPlot.default volatility.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘fBasics/libs/fBasics.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fbati/libs/fbati.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘FBFsearch/libs/FBFsearch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
NelsonSiegel: no visible global function definition for ‘nlminb’
NelsonSiegel: no visible global function definition for ‘grid’
Svensson: no visible global function definition for ‘persp’
Svensson: no visible global function definition for ‘title’
Svensson: no visible global function definition for ‘image’
Svensson: no visible global function definition for ‘contour’
Svensson: no visible global function definition for ‘nlminb’
Svensson: no visible global function definition for ‘grid’
Undefined global functions or variables:
  contour grid image nlminb persp title
Consider adding
  importFrom("graphics", "contour", "grid", "image", "persp", "title")
  importFrom("stats", "nlminb")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘RCurl’ ‘RJSONIO’ ‘XML’ ‘glmnet’ ‘httr’ ‘speedglm’ ‘tcltk’ ‘xtable’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
File ‘fbroc/libs/fbroc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable 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').
File ‘FCNN4R/libs/FCNN4R.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fdapace/libs/fdapace.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fdaPDE/libs/fdaPDE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls in package code:
  ‘R.matlab’ ‘RCurl’ ‘nlme’ ‘quadprog’
  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:
  fRegress.CV fRegress.stderr norder.bspline plot.cca.fd plot.pca.fd
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘fda.usc/libs/fda.usc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘FDGcopulas/libs/FDGcopulas.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘FD/libs/FD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
CountsNormalizerInEdgeR: no visible global function definition for ‘is’
DGEList_adjusted: no visible global function definition for ‘new’
GeneralizedEstimatorsGrouped: no visible global function definition for
  ‘quantile’
GeneralizedEstimatorsGrouped: no visible global function definition for
  ‘kmeans’
GeneralizedFDREstimators : <anonymous>: no visible global function
  definition for ‘fisher.test’
GeneralizedFDREstimators: no visible global function definition for
  ‘median’
estimateCommonDisp_adjusted: no visible global function definition for
  ‘is’
estimateCommonDisp_adjusted: no visible global function definition for
  ‘optimize’
pvalueByBinoSupport: no visible global function definition for ‘dbinom’
pvalueByNegativeBinoSupport: no visible global function definition for
  ‘dnbinom’
pvalueByNegativeBinoSupportApp: no visible global function definition
  for ‘dnbinom’
q2qnbinom_notadjusted: no visible global function definition for
  ‘pnorm’
q2qnbinom_notadjusted: no visible global function definition for
  ‘pgamma’
q2qnbinom_notadjusted: no visible global function definition for
  ‘qnorm’
q2qnbinom_notadjusted: no visible global function definition for
  ‘qgamma’
Undefined global functions or variables:
  dbinom dnbinom fisher.test is kmeans median new optimize pgamma pnorm
  qgamma qnorm quantile
Consider adding
  importFrom("methods", "is", "new")
  importFrom("stats", "dbinom", "dnbinom", "fisher.test", "kmeans",
             "median", "optimize", "pgamma", "pnorm", "qgamma", "qnorm",
             "quantile")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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.
File ‘FDRreg/libs/FDRreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fdrtool/libs/fdrtool.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
FeaLect: no visible global function definition for ‘plot’
compute.logistic.score: no visible global function definition for
  ‘coef’
ignore.redundant: no visible global function definition for ‘var’
train.doctor: no visible global function definition for ‘coef’
train.doctor: no visible global function definition for ‘predict’
Undefined global functions or variables:
  coef plot predict var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "predict", "var")
to your NAMESPACE file.
File ‘feather/libs/feather.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘FeatureHashing/libs/FeatureHashing.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fechner/libs/fechner.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  print.express.certificate
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘ffbase/libs/ffbase.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘FFD/libs/FFD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ 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.
Found the following significant warnings:
  ff.cpp:256:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ff.cpp:256:54: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ff.Rcheck/00install.out’ for details.
Found the following apparent S3 methods exported but not registered:
  as.hi.logical keyorder.default keysort.default mergeorder.default
  mergesort.default radixorder.default radixsort.default
  ramorder.default ramsort.default shellorder.default shellsort.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
bigsample.default: no visible global function definition for ‘runif’
cmedian: no visible binding for global variable ‘median’
cquantile: no visible binding for global variable ‘quantile’
read.table.ffdf: no visible binding for global variable ‘read.fwf’
read.table.ffdf: no visible binding for global variable ‘read.table’
regtest.fforder: no visible global function definition for ‘runif’
str.ff: no visible global function definition for ‘str’
str.ffdf: no visible global function definition for ‘str’
str.hi: no visible global function definition for ‘str’
write.csv: no visible binding for global variable ‘write.table’
write.csv2: no visible binding for global variable ‘write.table’
Undefined global functions or variables:
  median quantile read.fwf read.table runif str write.table
Consider adding
  importFrom("stats", "median", "quantile", "runif")
  importFrom("utils", "read.fwf", "read.table", "str", "write.table")
to your NAMESPACE file.
File ‘ff/libs/ff.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ffstream/libs/ffstream.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
garchFit: no visible binding for global variable ‘dem2gbp’
fitted,fGARCH: no visible binding for global variable ‘fit’
Undefined global functions or variables:
  dem2gbp fit
File ‘fGarch/libs/fGarch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  Boot.FitFGN predict.FitFGN
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘FGN/libs/FGN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ 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.
File ‘FGSG/libs/FGSG.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘tcltk’
A package should be listed in only one of these fields.
'library' or 'require' call to ‘tcltk’ 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: ‘tools’
  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: ‘tools:::fetchRdDB’
  See the note in ?`:::` about the use of this operator.
parseHelp: no visible global function definition for ‘help’
parseHelp: no visible global function definition for ‘unzip’
Undefined global functions or variables:
  help unzip
Consider adding
  importFrom("utils", "help", "unzip")
to your NAMESPACE file.
Rd file 'gui.Rd':
  \examples lines wider than 100 characters:
     gui( summaryStats, helps=list(data="Enter the data as an R vector, e.g. 'c(13,66,44,27)' or enter the text 'rivers' to use a builtin da ... [TRUNCATED]
     ## If you want it modal though, do not do so until the last mgui call, or it will be modal inbetween additions to the menu!
     guiv( lmgui, argFilename=list(csvFilename=NULL), argList=list(response=NULL,explanatory=NULL), callback=lmguiCallback )
         data <- data.frame( mvrnorm( n=100, mu=c(0,0,0), Sigma=matrix(c(1,0.3,0, 0.3,1,0.3, 0,0.3,1),nrow=3) ) )

These lines will be truncated in the PDF manual.
File ‘FIACH/libs/FIACH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fICA/libs/fICA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
fieldsim: no visible global function definition for ‘rnorm’
midpoint: no visible global function definition for ‘rnorm’
setAtlas_under: no visible global function definition for ‘runif’
setCovf_under : Ibeta: no visible global function definition for
  ‘pbeta’
visualize: no visible global function definition for ‘colorRampPalette’
Undefined global functions or variables:
  colorRampPalette pbeta rnorm runif
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "pbeta", "rnorm", "runif")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  [.spatial.design
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘filehash’ ‘DBI’
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  ‘RSQLite’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
createSQLite: no visible global function definition for ‘dbDriver’
createSQLite: no visible global function definition for ‘dbConnect’
createSQLite: no visible global function definition for
  ‘dbUnloadDriver’
createSQLite: no visible global function definition for ‘dbGetQuery’
initializeSQLite: no visible global function definition for ‘dbDriver’
initializeSQLite: no visible global function definition for ‘dbConnect’
initializeSQLite: no visible global function definition for ‘new’
dbDelete,filehashSQLite-character: no visible global function
  definition for ‘dbGetQuery’
dbDisconnect,filehashSQLite: no visible global function definition for
  ‘dbUnloadDriver’
dbFetch,filehashSQLite-character: no visible global function definition
  for ‘dbGetQuery’
dbInsert,filehashSQLite-character: no visible global function
  definition for ‘dbGetQuery’
dbList,filehashSQLite: no visible global function definition for
  ‘dbGetQuery’
dbMultiFetch,filehashSQLite-character: no visible global function
  definition for ‘dbGetQuery’
Undefined global functions or variables:
  dbConnect dbDriver dbGetQuery dbUnloadDriver new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Attributes: < Length mismatch: comparison on first 2 components >
  
  
  2. Failure: MergeTablesOnDisk works (@test_files.R#82) -------------------------
  readr::read_csv("merged.csv") not equal to tibble::tibble(x = c(1.5, 1.5), y = c(2.5, 29.5)).
  Attributes: < Length mismatch: comparison on first 2 components >
  
  
  testthat results ================================================================
  OK: 141 SKIPPED: 0 FAILED: 2
  1. Failure: MergeTablesOnDisk works (@test_files.R#80) 
  2. Failure: MergeTablesOnDisk works (@test_files.R#82) 
  
  Error: testthat unit tests failed
  Execution halted
.getYahooData: no visible global function definition for
  ‘flush.console’
.getYahooData: no visible global function definition for ‘read.table’
.read.xls: no visible global function definition for ‘read.csv’
.xls2csv: no visible global function definition for ‘download.file’
fredImport: no visible global function definition for ‘download.file’
fredImport: no visible global function definition for ‘write.table’
oandaImport: no visible global function definition for ‘download.file’
oandaImport: no visible global function definition for ‘write.table’
yahooBriefing: no visible global function definition for
  ‘download.file’
yahooImport: no visible global function definition for ‘download.file’
yahooImport: no visible global function definition for ‘read.table’
yahooImport: no visible global function definition for ‘write.table’
yahooKeystats: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file flush.console read.csv read.table write.table
Consider adding
  importFrom("utils", "download.file", "flush.console", "read.csv",
             "read.table", "write.table")
to your NAMESPACE file.
Package suggested but not available for checking: ‘its’
'library' or 'require' calls in package code:
  ‘XML’ ‘foreach’ ‘its’ ‘timeSeries’ ‘utils’
  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.cf plot.tvm print.cf print.tvm summary.cf summary.tvm update.cf
  update.tvm
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.cf: no visible global function definition for ‘barplot’
plot.cf: no visible global function definition for ‘lines’
plot.cf: no visible global function definition for ‘abline’
plot.cf: no visible global function definition for ‘axis’
plot.cf: no visible global function definition for ‘curve’
plot.tvm: no visible global function definition for ‘barplot’
plot.tvm: no visible global function definition for ‘lines’
tvm: no visible global function definition for ‘uniroot’
update.tvm: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  abline axis barplot curve lines uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "barplot", "curve", "lines")
  importFrom("stats", "uniroot")
to your NAMESPACE file.
File ‘FindIt/libs/FindIt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  FindMinIC.default FindMinIC.formula fmi.default fmi.formula
  formula.cm print.summary.cm print.summary.cmList summary.cm
  summary.cmList
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘fingerprint/libs/fingerprint.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘fUnitRoots’
'library' or 'require' calls in package code:
  ‘e1071’ ‘fUnitRoots’ ‘polynom’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unknown package ‘fUnitRoots’ in Rd xrefs
Running examples in ‘FinTS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Unitroot
> ### Title: unit root tests
> ### Aliases: Unitroot summary.fHTEST
> ### Keywords: ts
> 
> ### ** Examples
> 
> ##
> ## Tsay, pp. 69-71
> ##
> data(q.gdp4703)
> adft.gdp <- Unitroot(log(q.gdp4703), trend='c', method='adf', lags=10)
Loading required package: fUnitRoots
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘fUnitRoots’
Error in Unitroot(log(q.gdp4703), trend = "c", method = "adf", lags = 10) : 
  require(fUnitRoots);  not available.
Execution halted
Packages in Depends field not imported from:
  ‘MASS’ ‘elasticnet’
  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 ‘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.
File ‘FisHiCal/libs/FisHiCal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fishMod/libs/fishMod.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘FitARMA/libs/FitARMA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘FitAR/libs/FitAR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  CDF.distribution CDFinv.distribution Fl.drclass FlInv.drclass
  Fu.drclass FuInv.drclass Kappa.drclass Lambda.drclass
  MEAN.distribution MEDIAN.distribution MODE.distribution
  PDF.distribution RANGE.distribution SD.distribution
  TRANS.BACKW.transformation TRANS.DERIV.transformation
  TRANS.FORW.transformation TRANS.RANGE.X.transformation
  TRANS.RANGE.Y.transformation metric.ci.drclass metric.mode.drclass
  metric.shape.drclass metric.width.drclass metrics.drclass
  plot.distribution plot.drclass plot.transformation print.distribution
  print.drclass print.transformation summary.distribution
  summary.drclass summary.transformation
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘FIT/libs/FIT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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.
plot.fkf: no visible global function definition for ‘rainbow’
plot.fkf: no visible global function definition for ‘qnorm’
plot.fkf: no visible global function definition for ‘qqnorm’
plot.fkf: no visible global function definition for ‘qchisq’
plot.fkf: no visible global function definition for ‘ppoints’
plot.fkf: no visible global function definition for ‘qqplot’
plot.fkf: no visible global function definition for ‘acf’
plot.fkf: no visible global function definition for ‘ccf’
Undefined global functions or variables:
  acf ccf ppoints qchisq qnorm qqnorm qqplot rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("stats", "acf", "ccf", "ppoints", "qchisq", "qnorm",
             "qqnorm", "qqplot")
to your NAMESPACE file.
File ‘FKF/libs/FKF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘flam/libs/flam.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘flare/libs/flare.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘flars/libs/flars.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘flashClust/libs/flashClust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘clue’ in package code.
  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:
  ‘getData’ ‘newKccaObject’
File ‘flexclust/libs/flexclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.flim plot.flimList plot.flimboot print.flim print.flimList
  print.flimboot summary.flim summary.flimList
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
FlimFormula: no visible global function definition for ‘is’
FlimFormula: no visible global function definition for ‘terms’
FlimFormula: no visible global function definition for ‘reformulate’
ImputateMissingValues : RegFun: no visible global function definition
  for ‘lm’
ImputateMissingValues : RegFun: no visible binding for global variable
  ‘na.omit’
ImputateMissingValues: no visible global function definition for
  ‘predict’
ImputateMissingValues: no visible global function definition for
  ‘model.matrix’
ImputateMissingValues: no visible global function definition for ‘coef’
flimList: no visible global function definition for ‘coef’
flimSD: no visible binding for global variable ‘sd’
plot.flim: no visible global function definition for ‘plot’
plot.flim: no visible global function definition for ‘lines’
plot.flim: no visible global function definition for ‘points’
plot.flimList: no visible global function definition for ‘par’
plot.flimList: no visible global function definition for ‘plot’
plot.flimboot: no visible global function definition for ‘plot’
plot.flimboot: no visible global function definition for ‘points’
plot.flimboot: no visible global function definition for ‘lines’
spaplot: no visible global function definition for ‘plot’
spaplot: no visible global function definition for ‘lines’
Undefined global functions or variables:
  coef is lines lm model.matrix na.omit par plot points predict
  reformulate sd terms
Consider adding
  importFrom("graphics", "lines", "par", "plot", "points")
  importFrom("methods", "is")
  importFrom("stats", "coef", "lm", "model.matrix", "na.omit", "predict",
             "reformulate", "sd", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘flip/libs/flip.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘flock/libs/flock.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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.
File ‘flsa/libs/flsa.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘FLSSS/libs/FLSSS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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.
File ‘FME/libs/FME.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fmri/libs/fmri.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fmrs/libs/fmrs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘FMStable/libs/FMStable.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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.
Found the following apparent S3 methods exported but not registered:
  contour.gridData persp.gridData plot.hexBinning plot.squareBinning
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Calls with DUP:
   .C("KL_dist", t(X), t(Y), as.integer(k), d, n, m, KLD = double(k), 
       DUP = FALSE)
   .C("KL_divergence", t(X), t(Y), as.integer(k), d, n, m, KL = double(k), 
       DUP = FALSE)
   .C(Cname, t(X), as.integer(k), p, n, MLD = double(k), DUP = FALSE)
   .C(Cname, t(data), as.integer(k), d, n, nn.index = integer(n * 
       k), nn.dist = double(n * k), DUP = FALSE)
   .C(Cname, t(data), t(query), as.integer(k), d, n, m, nn.index = integer(m * 
       k), nn.dist = double(m * k), DUP = FALSE)
   .C("mdmutinfo", t(X), t(Y), as.integer(p1), as.integer(p2), as.integer(k), 
       n, nx = integer(n), ny = integer(n), DUP = FALSE)
DUP is no longer supported and will be ignored.
File ‘FNN/libs/FNN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.lyapunovFit: no visible global function definition for ‘lm’
bdsTest: no visible global function definition for ‘sd’
bdsTest: no visible global function definition for ‘pnorm’
falsennPlot: no visible global function definition for ‘sd’
henonSim: no visible global function definition for ‘runif’
henonSim: no visible global function definition for ‘ts’
ikedaSim: no visible global function definition for ‘runif’
ikedaSim: no visible global function definition for ‘ts’
logisticSim: no visible global function definition for ‘runif’
logisticSim: no visible global function definition for ‘ts’
lorentzSim: no visible global function definition for ‘ts’
lyapunovPlot: no visible global function definition for ‘ts’
roesslerSim: no visible global function definition for ‘ts’
runsTest : runs.test: no visible global function definition for ‘pnorm’
tentSim: no visible global function definition for ‘runif’
tentSim: no visible global function definition for ‘ts’
tnnTest: no visible global function definition for ‘embed’
tnnTest: no visible global function definition for ‘as.formula’
tnnTest: no visible global function definition for ‘lm’
tnnTest: no visible global function definition for ‘pchisq’
tnnTest: no visible global function definition for ‘pf’
wnnTest: no visible global function definition for ‘embed’
wnnTest: no visible global function definition for ‘as.formula’
wnnTest: no visible global function definition for ‘lm’
wnnTest: no visible global function definition for ‘runif’
wnnTest: no visible global function definition for ‘prcomp’
wnnTest: no visible global function definition for ‘pchisq’
wnnTest: no visible global function definition for ‘pf’
Undefined global functions or variables:
  as.formula embed lm pchisq pf pnorm prcomp runif sd ts
Consider adding
  importFrom("stats", "as.formula", "embed", "lm", "pchisq", "pf",
             "pnorm", "prcomp", "runif", "sd", "ts")
to your NAMESPACE file.
File ‘fNonlinear/libs/fNonlinear.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘fOptions/libs/fOptions.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘forecastSNSTS/libs/forecastSNSTS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘forega/libs/forega.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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'.
File ‘forensim/libs/forensim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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').
Functions or methods with usage in documentation object 'formula.parts' but not in code:
  \S4method{lhs}{<-} \S4method{op}{<-} \S4method{rhs}{<-}

Functions or methods with usage in documentation object '.is.one.sided' but not in code:
  \S4method{is.one.sided}{<-} \S4method{is.two.sided}{<-}

Functions or methods with usage in documentation object 'op.type' but not in code:
  \S4method{op.type}{<-}
Non-standard file/directory found at top level:
  ‘scripts’
Found the following apparent S3 methods exported but not registered:
  plot.fwdglm plot.fwdlm plot.fwdsco print.fwdglm print.fwdlm
  print.fwdsco print.summary.fwdglm print.summary.fwdlm
  print.summary.fwdsco summary.fwdglm summary.fwdlm summary.fwdsco
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'lmsglm.Rd':
  \usage lines wider than 90 characters:
     lmsglm(x, y, family, weights, offset, n.samples = 100, max.samples = 200, epsilon = 1e-04, maxit = 50, trace = FALSE)

These lines will be truncated in the PDF manual.
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.
FourScores : getPlayerNames: no visible global function definition for
  ‘plot’
FourScores : getPlayerNames: no visible global function definition for
  ‘mtext’
FourScores : getPlayerNames: no visible global function definition for
  ‘getGraphicsEvent’
FourScores : getPlayerNames: no visible global function definition for
  ‘text’
FourScores : clicking: no visible global function definition for
  ‘grconvertX’
FourScores : preview: no visible global function definition for
  ‘grconvertX’
FourScores : preview: no visible global function definition for
  ‘points’
FourScores : FieldPlot: no visible global function definition for ‘par’
FourScores : FieldPlot: no visible global function definition for
  ‘plot’
FourScores : FieldPlot: no visible global function definition for
  ‘points’
FourScores: no visible global function definition for
  ‘getGraphicsEvent’
FourScores: no visible global function definition for ‘plot’
FourScores: no visible global function definition for ‘text’
Undefined global functions or variables:
  getGraphicsEvent grconvertX mtext par plot points text
Consider adding
  importFrom("grDevices", "getGraphicsEvent")
  importFrom("graphics", "grconvertX", "mtext", "par", "plot", "points",
             "text")
to your NAMESPACE file.
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’
'library' or 'require' calls in package code:
  ‘Rdonlp2’ ‘Rnlminb2’ ‘bcp’ ‘dplR’ ‘fGarch’ ‘mvoutlier’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
File ‘fpow/libs/fpow.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
q.mle.emg.estimate: no visible global function definition for ‘median’
q.mle.emg.estimate: no visible global function definition for ‘sd’
q.mle.norm.estimate: no visible global function definition for ‘sd’
q.rates : q.rates.inner : f: no visible global function definition for
  ‘integrate’
q.rates : q.rates.inner: no visible global function definition for
  ‘uniroot’
Undefined global functions or variables:
  integrate median sd uniroot
Consider adding
  importFrom("stats", "integrate", "median", "sd", "uniroot")
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.
File ‘fractional/libs/fractional.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘fragilityindex-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: logisticfragility
> ### Title: Logistic fragility function
> ### Aliases: logisticfragility
> 
> ### ** Examples
> 
> # Import and format example data
> mydata <- read.csv("http://www.ats.ucla.edu/stat/data/binary.csv")
> mydata$rank <- factor(mydata$rank)
Error in `$<-.data.frame`(`*tmp*`, rank, value = integer(0)) : 
  replacement has 0 rows, data has 528
Calls: $<- -> $<-.data.frame
Execution halted
'library' or 'require' calls to packages already attached by Depends:
  ‘Matrix’ ‘numDeriv’ ‘survival’
  Please remove these calls from your code.
FrailtyFrames: no visible global function definition for
  ‘model.response’
FrailtyFrames: no visible global function definition for
  ‘is.empty.model’
FrailtyFrames: no visible global function definition for ‘model.matrix’
FrailtyFrames: no visible global function definition for
  ‘model.weights’
FrailtyFrames: no visible global function definition for ‘model.offset’
HGLMFactorList : <anonymous>: no visible global function definition for
  ‘as’
HGLMFactorList : <anonymous>: no visible global function definition for
  ‘validObject’
HGLMFactorList : <anonymous>: no visible global function definition for
  ‘as.formula’
HGLMFactorList : <anonymous>: no visible global function definition for
  ‘model.matrix’
expandSlash : <anonymous>: no visible global function definition for
  ‘makeInteraction’
frailtyHL: no visible global function definition for ‘terms’
frailtyHL: no visible global function definition for ‘model.extract’
frailtyHL: no visible binding for global variable ‘contrasts’
frailtyHL: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as as.formula contrasts is.empty.model makeInteraction model.extract
  model.matrix model.offset model.response model.weights pnorm terms
  validObject
Consider adding
  importFrom("methods", "as", "validObject")
  importFrom("stats", "as.formula", "contrasts", "is.empty.model",
             "model.extract", "model.matrix", "model.offset",
             "model.response", "model.weights", "pnorm", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘frailtySurv/libs/frailtySurv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  FRBhotellingMM.default FRBhotellingMM.formula FRBhotellingS.default
  FRBhotellingS.formula FRBmultiregGS.default FRBmultiregGS.formula
  FRBmultiregMM.default FRBmultiregMM.formula FRBmultiregS.default
  FRBmultiregS.formula FRBpcaMM.default FRBpcaMM.formula
  FRBpcaS.default FRBpcaS.formula GSest_multireg.default
  GSest_multireg.formula MMest_multireg.default MMest_multireg.formula
  Sest_multireg.default Sest_multireg.formula diagplot.FRBhot
  diagplot.FRBmultireg diagplot.FRBpca plot.FRBhot plot.FRBmultireg
  plot.FRBpca predict.FRBmultireg print.FRBmultireg print.FRBpca
  print.summary.FRBhot print.summary.FRBmultireg print.summary.FRBpca
  summary.FRBhot summary.FRBmultireg summary.FRBpca vcov.FRBmultireg
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
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.
Packages in Depends field not imported from:
  ‘methods’ ‘splines’
  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:
  AIC.freekt BIC.freekt coef.freekt fitted.freekt plot.freekt
  residuals.freekt summary.freekt
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
AIC.freekt: no visible global function definition for ‘residuals’
AICc.freekt: no visible global function definition for ‘residuals’
BIC.freekt: no visible global function definition for ‘residuals’
adjAIC.freekt: no visible global function definition for ‘residuals’
adjGCV.freekt: no visible global function definition for ‘residuals’
chgbasismat: no visible global function definition for ‘splineDesign’
coef.freekt: no visible global function definition for ‘splineDesign’
fit.search.numknots: no visible global function definition for ‘AIC’
fit.search.numknots: no visible global function definition for ‘BIC’
fitted.freekt: no visible global function definition for ‘splineDesign’
freelsgen: no visible global function definition for ‘new’
freelsgold: no visible global function definition for ‘new’
freepsgen: no visible global function definition for ‘new’
freepsgold: no visible global function definition for ‘new’
plot.freekt: no visible global function definition for ‘plot’
plot.freekt: no visible global function definition for ‘lines’
summary.freekt: no visible global function definition for ‘residuals’
Undefined global functions or variables:
  AIC BIC lines new plot residuals splineDesign
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("methods", "new")
  importFrom("stats", "AIC", "BIC", "residuals")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘freeknotsplines/libs/freeknotsplines.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Found the following apparent S3 methods exported but not registered:
  termPlot.fREG
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Found the following apparent S3 methods exported but not registered:
  plot.freqMAP print.freqMAP summary.freqMAP
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
add.p.value.legend: no visible global function definition for ‘legend’
cat.freq.post: no visible global function definition for ‘quantile’
draw.signif.post.boxes: no visible global function definition for
  ‘polygon’
plot.freqMAP: no visible global function definition for ‘layout’
plot.freqMAP: no visible global function definition for ‘plot’
plot.freqMAP: no visible global function definition for ‘points’
plot.freqMAP: no visible global function definition for ‘lines’
plot.freqMAP: no visible global function definition for ‘abline’
plot.freqMAP: no visible global function definition for ‘axTicks’
posterior.comparison.freqMAP: no visible global function definition for
  ‘quantile’
rdirichlet: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  abline axTicks layout legend lines plot points polygon quantile
  rgamma
Consider adding
  importFrom("graphics", "abline", "axTicks", "layout", "legend",
             "lines", "plot", "points", "polygon")
  importFrom("stats", "quantile", "rgamma")
to your NAMESPACE file.
File ‘FRESA.CAD/libs/FRESA.CAD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Package suggested but not available for checking: ‘INLA’

Package which this enhances but not available for checking: ‘dggrids’
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.
File ‘fromo/libs/fromo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘frontiles/libs/frontiles.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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
Running ‘testthat.R’ [4s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > library(entropy)
  
  Attaching package: 'entropy'
  
  The following object is masked from 'package:FSelectorRcpp':
  
      discretize
  
  > 
  > test_check("FSelectorRcpp")
  Segmentation fault
Found the following apparent S3 methods exported but not registered:
  boxplot.fso boxplot.mfso chullord.fso chullord.mfso fso.default
  fso.formula hilight.fso hilight.mfso mfso.default mfso.formula
  plot.fso plot.mfso plotid.fso plotid.mfso points.fso points.mfso
  summary.fso summary.mfso thull.mfso
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘fso/libs/fso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fst/libs/fst.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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.
File ‘ftnonpar/libs/ftnonpar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
ohlcPlot: no visible global function definition for ‘par’
ohlcPlot: no visible global function definition for ‘is.mts’
ohlcPlot: no visible global function definition for ‘plot.new’
ohlcPlot: no visible global function definition for ‘plot.window’
ohlcPlot: no visible global function definition for ‘segments’
ohlcPlot: no visible global function definition for ‘title’
ohlcPlot: no visible global function definition for ‘axis’
ohlcPlot: no visible global function definition for ‘box’
rollVar: no visible binding for global variable ‘var’
sharpeRatio: no visible global function definition for ‘sd’
Undefined global functions or variables:
  axis box is.mts par plot.new plot.window sd segments title var
Consider adding
  importFrom("graphics", "axis", "box", "par", "plot.new", "plot.window",
             "segments", "title")
  importFrom("stats", "is.mts", "sd", "var")
to your NAMESPACE file.
File ‘FTRLProximal/libs/FTRLProximal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  [<-.fts as.data.frame.fts as.fts.data.frame as.fts.default as.fts.zoo
  as.matrix.fts cbind.fts diff.fts lead.fts rbind.fts
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
cor.by.row: no visible global function definition for ‘cor’
plot.fts: no visible global function definition for ‘plot’
plot.fts: no visible global function definition for ‘xy.coords’
plot.fts: no visible binding for global variable ‘plot.xy’
read.csv.fts: no visible global function definition for ‘read.csv’
write.csv.fts: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  cor plot plot.xy read.csv write.csv xy.coords
Consider adding
  importFrom("grDevices", "xy.coords")
  importFrom("graphics", "plot", "plot.xy")
  importFrom("stats", "cor")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
File ‘fts/libs/fts.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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.
File ‘fugeR/libs/fugeR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘Funclustering/libs/Funclustering.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘FunctionalNetworks/libs/FunctionalNetworks.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘funcy/libs/funcy.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.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.
funHDDC: no visible global function definition for ‘kmeans’
funHDDC: no visible global function definition for ‘rmultinom’
funHDDC: no visible global function definition for ‘cutree’
funHDDC: no visible global function definition for ‘hclust’
funHDDC: no visible global function definition for ‘dist’
Undefined global functions or variables:
  cutree dist hclust kmeans rmultinom
Consider adding
  importFrom("stats", "cutree", "dist", "hclust", "kmeans", "rmultinom")
to your NAMESPACE file.
Package in Depends field not imported from: ‘genlasso’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dualpathFusedX.mod: no visible global function definition for
  ‘graph.adjacency’
dualpathFusedX.mod: no visible global function definition for
  ‘clusters’
dualpathFusedX.mod: no visible global function definition for ‘ginv’
dualpathFusedX.mod: no visible global function definition for
  ‘subcomponent’
dualpathFusedX.mod: no visible global function definition for ‘rBind’
fpca.nonscore.cluster: no visible global function definition for
  ‘kmeans’
fpca.score.cluster: no visible global function definition for ‘kmeans’
gen.dcbm: no visible global function definition for ‘rbinom’
gen.sbm: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  clusters ginv graph.adjacency kmeans rBind rbinom subcomponent
Consider adding
  importFrom("stats", "kmeans", "rbinom")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  resetOptions.character resetOptions.default updateOptions.character
  updateOptions.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
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.
File ‘futureheatwaves/libs/futureheatwaves.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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
Found the following significant warnings:
  Warning: replacing previous import ‘FuzzyNumbers::maximum’ by ‘ROI::maximum’ when loading ‘FuzzyLP’
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/FuzzyLP.Rcheck/00install.out’ for details.
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.
fwsim: no visible global function definition for ‘is’
fwsim_fixed: no visible global function definition for ‘is’
plot.fwsim: no visible global function definition for ‘is’
plot.fwsim: no visible global function definition for ‘plot’
plot.fwsim: no visible global function definition for ‘axis’
plot.fwsim: no visible global function definition for ‘points’
plot.fwsim: no visible global function definition for ‘legend’
print.fwsim: no visible global function definition for ‘is’
print.mutmodel: no visible global function definition for ‘is’
summary.fwsim: no visible global function definition for ‘is’
summary.fwsim: no visible global function definition for ‘head’
Undefined global functions or variables:
  axis head is legend plot points
Consider adding
  importFrom("graphics", "axis", "legend", "plot", "points")
  importFrom("methods", "is")
  importFrom("utils", "head")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘fwsim/libs/fwsim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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.
GA4StratificationP1: no visible global function definition for
  ‘flush.console’
GA4StratificationP1m: no visible global function definition for ‘runif’
GA4StratificationP2: no visible global function definition for
  ‘flush.console’
GA4StratificationP2m: no visible global function definition for ‘runif’
GA4StratificationP3: no visible global function definition for
  ‘flush.console’
GA4StratificationP3m: no visible global function definition for ‘runif’
GA4StratificationP4: no visible global function definition for ‘runif’
GA4StratificationP4: no visible global function definition for
  ‘flush.console’
GA4StratificationP4m: no visible global function definition for ‘runif’
GA4StratificationSelection: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  flush.console runif
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "flush.console")
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.
File ‘gafit/libs/gafit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
gains : ci.gains: no visible global function definition for ‘qnorm’
gains : ci.gains: no visible global function definition for ‘sd’
gains : ci.gains: no visible global function definition for ‘qt’
gains : ci.gains: no visible global function definition for ‘quantile’
plot.gains: no visible global function definition for ‘plot’
plot.gains: no visible global function definition for ‘axTicks’
plot.gains: no visible global function definition for ‘axis’
plot.gains: no visible global function definition for ‘points’
Undefined global functions or variables:
  axTicks axis plot points qnorm qt quantile sd
Consider adding
  importFrom("graphics", "axTicks", "axis", "plot", "points")
  importFrom("stats", "qnorm", "qt", "quantile", "sd")
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.
ga.lts: no visible global function definition for ‘model.matrix’
ga.lts: no visible global function definition for ‘model.frame’
ga.lts : cstep: no visible global function definition for ‘lm’
medmad: no visible global function definition for ‘model.matrix’
medmad: no visible global function definition for ‘model.frame’
medmad : cstep: no visible global function definition for ‘lm’
medmad: no visible binding for global variable ‘median’
medmad: no visible global function definition for ‘mahalanobis’
medmad: no visible global function definition for ‘lm’
medmad.cov: no visible binding for global variable ‘median’
medmad.cov: no visible global function definition for ‘median’
Undefined global functions or variables:
  lm mahalanobis median model.frame model.matrix
Consider adding
  importFrom("stats", "lm", "mahalanobis", "median", "model.frame",
             "model.matrix")
to your NAMESPACE file.
Rd file 'ga.lts.Rd':
  \usage lines wider than 90 characters:
     ga.lts(formula, h = NULL, iters = 2, popsize = 50, lower, upper, csteps = 2, method = "ga", verbose = FALSE)

These lines will be truncated in the PDF manual.
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.
File ‘GAMBoost/libs/GAMBoost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gamlr/libs/gamlr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Unexported object imported by a ':::' call: ‘gamlss:::numeric.deriv’
  See the note in ?`:::` about the use of this operator.
File ‘gamlss.dist/libs/gamlss.dist.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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’.
Error in re-building vignettes:
  ...
  no polygon information is given, null plot is produced
Warning in term.plot(m2, what = "mu", ylim = "free") :
  no polygon information is given, null plot is produced
Warning in if (scheme == "lines") { :
  the condition has length > 1 and only the first element will be used
Warning in if (scheme == "lines") { :
  the condition has length > 1 and only the first element will be used
Warning in if (scheme == "lines") { :
  the condition has length > 1 and only the first element will be used
Warning in panel(x[id], y[id], col = col[id], pch = pch[id], ...) :
  Some points are missed out 
increase the y limits using ylim.worm
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running ‘texi2dvi’ on ‘GAMLSS_GMRF.tex’ failed.
BibTeX errors:
The top-level auxiliary file: GAMLSS_GMRF.aux
The style file: plainnat.bst
I couldn't open database file Book-2016.bib
---line 144 of file GAMLSS_GMRF.aux
 : \bibdata{Book-2016
 :                   }
I'm skipping whatever remains of this command
I found no database files---while reading file GAMLSS_GMRF.aux
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
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.
Found the following apparent S3 methods exported but not registered:
  plot.gSlc summary.gSlc
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘gammSlice/libs/gammSlice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gamreg/libs/gamreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
basis.gen: no visible global function definition for ‘poly’
cv.gamsel: no visible global function definition for ‘predict’
error.bars: no visible global function definition for ‘segments’
gendata: no visible global function definition for ‘rnorm’
gendata: no visible global function definition for ‘poly’
gendata: no visible global function definition for ‘rbinom’
mypoly: no visible global function definition for ‘polym’
plot.cv.gamsel: no visible global function definition for ‘points’
plot.cv.gamsel: no visible global function definition for ‘axis’
plot.cv.gamsel: no visible global function definition for ‘abline’
plot.gamsel: no visible global function definition for ‘plot’
plot.gamsel: no visible global function definition for ‘rug’
summary.gamsel: no visible global function definition for ‘rainbow’
summary.gamsel : nzlines: no visible global function definition for
  ‘lines’
summary.gamsel: no visible global function definition for ‘plot’
summary.gamsel: no visible global function definition for ‘abline’
summary.gamsel: no visible global function definition for ‘text’
summaryplot: no visible global function definition for ‘rainbow’
summaryplot : nzlines: no visible global function definition for
  ‘lines’
summaryplot: no visible global function definition for ‘plot’
summaryplot: no visible global function definition for ‘abline’
summaryplot: no visible global function definition for ‘text’
Undefined global functions or variables:
  abline axis lines plot points poly polym predict rainbow rbinom rnorm
  rug segments text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "axis", "lines", "plot", "points",
             "rug", "segments", "text")
  importFrom("stats", "poly", "polym", "predict", "rbinom", "rnorm")
to your NAMESPACE file.
File ‘gamsel/libs/gamsel.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Found the following apparent S3 methods exported but not registered:
  plot.GAPerm plot.GAReal print.GAPerm print.GAReal print.summaryGAPerm
  print.summaryGAReal summary.GAPerm summary.GAReal
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
GAPerm : pmxCrossover: no visible global function definition for
  ‘runif’
GAReal : twoPointsCrossover: no visible global function definition for
  ‘runif’
GAReal : blendCrossover: no visible global function definition for
  ‘runif’
GAReal : mutateNoise: no visible global function definition for ‘runif’
GAReal : initPopulation: no visible global function definition for
  ‘runif’
plot.GAPerm: no visible global function definition for ‘plot’
plot.GAPerm: no visible global function definition for ‘grid’
plot.GAPerm: no visible global function definition for ‘lines’
plot.GAPerm: no visible global function definition for ‘legend’
plot.GAReal: no visible global function definition for ‘plot’
plot.GAReal: no visible global function definition for ‘grid’
plot.GAReal: no visible global function definition for ‘lines’
plot.GAReal: no visible global function definition for ‘legend’
Undefined global functions or variables:
  grid legend lines plot runif
Consider adding
  importFrom("graphics", "grid", "legend", "lines", "plot")
  importFrom("stats", "runif")
to your NAMESPACE file.
Rd file 'plot_perm.Rd':
  \usage lines wider than 90 characters:
         legend.pos = c("bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right", "center"),

Rd file 'plot_real.Rd':
  \usage lines wider than 90 characters:
         legend.pos = c("bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right", "center"),

These lines will be truncated in the PDF manual.
File ‘gapfill/libs/gapfill.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘run-all.R’ [12s/12s]
Running the tests in ‘tests/run-all.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > test_check('gapfill')
  Loading required package: gapfill
  Loading required package: ggplot2
  1. Failure: Score_errors (@test-Score.R#40) ------------------------------------
  error$message does not match "not a matrix".
  Actual value: "Not a matrix."
  
  
  testthat results ================================================================
  OK: 866 SKIPPED: 0 FAILED: 1
  1. Failure: Score_errors (@test-Score.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘gaselect/libs/gaselect.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘GauPro/libs/GauPro.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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.
File ‘gbp/libs/gbp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  lines.gld plot.egld plot.gld print.egld print.gld
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
.bincount: no visible global function definition for ‘sd’
.mom: no visible global function definition for ‘sd’
.mop: no visible global function definition for ‘quantile’
degld: no visible global function definition for ‘dbeta’
fit.egld: no visible global function definition for ‘sd’
fit.egld: no visible global function definition for ‘var’
fit.egld: no visible global function definition for ‘pchisq’
fit.gld: no visible global function definition for ‘sd’
fit.gld: no visible global function definition for ‘pchisq’
gboot: no visible global function definition for ‘boot’
lines.gld: no visible global function definition for ‘lines.default’
pegld: no visible global function definition for ‘pbeta’
plot.egld: no visible global function definition for ‘plot.default’
plot.egld: no visible global function definition for ‘abline’
plot.gld: no visible global function definition for ‘plot.default’
plot.gld: no visible global function definition for ‘abline’
qegld: no visible global function definition for ‘qbeta’
regld: no visible global function definition for ‘rbeta’
rrsgld: no visible global function definition for ‘runif’
Undefined global functions or variables:
  abline boot dbeta lines.default pbeta pchisq plot.default qbeta
  quantile rbeta runif sd var
Consider adding
  importFrom("graphics", "abline", "lines.default", "plot.default")
  importFrom("stats", "dbeta", "pbeta", "pchisq", "qbeta", "quantile",
             "rbeta", "runif", "sd", "var")
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.
File ‘gCat/libs/gCat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  coef.hsvmpath coef.logitpath coef.lspath coef.sqsvmpath
  predict.hsvmpath predict.logitpath predict.lspath predict.sqsvmpath
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
coef.cv.gcdnet: no visible global function definition for ‘coef’
cv.gcdnet: no visible global function definition for ‘coef’
cv.hsvmpath: no visible global function definition for ‘predict’
cv.logitpath: no visible global function definition for ‘predict’
cv.lspath: no visible global function definition for ‘predict’
cv.sqsvmpath: no visible global function definition for ‘predict’
error.bars: no visible global function definition for ‘segments’
getoutput: no visible global function definition for ‘new’
lambda.interp: no visible global function definition for ‘approx’
plot.cv.gcdnet: no visible global function definition for ‘points’
plot.cv.gcdnet: no visible global function definition for ‘axis’
plot.cv.gcdnet: no visible global function definition for ‘abline’
plot.gcdnet: no visible global function definition for ‘matplot’
plot.gcdnet: no visible global function definition for ‘gray.colors’
plot.gcdnet: no visible global function definition for ‘approx’
plot.gcdnet: no visible global function definition for ‘axis’
plot.gcdnet: no visible global function definition for ‘text’
predict.cv.gcdnet: no visible global function definition for ‘predict’
zeromat: no visible global function definition for ‘new’
Undefined global functions or variables:
  abline approx axis coef gray.colors matplot new points predict
  segments text
Consider adding
  importFrom("grDevices", "gray.colors")
  importFrom("graphics", "abline", "axis", "matplot", "points",
             "segments", "text")
  importFrom("methods", "new")
  importFrom("stats", "approx", "coef", "predict")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘gcdnet/libs/gcdnet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘gconcord/libs/gconcord.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘GCPM/libs/GCPM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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’.
Files in the 'vignettes' directory newer than same file in 'inst/doc':
  ‘Rnews.sty’
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.
File ‘gdmp/libs/gdmp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘gdns-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bulk_query
> ### Title: Vectorized query, returning only answers in a data frame
> ### Aliases: bulk_query
> 
> ### ** Examples
> 
> hosts <- c("rud.is", "dds.ec", "r-project.org", "rstudio.com", "apple.com")
> gdns::bulk_query(hosts)
Error: `map_df()` requires dplyr
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(gdns)
  > 
  > test_check("gdns")
  1. Error: we can do something (@test-gdns.R#7) ---------------------------------
  `map_df()` requires dplyr
  1: gdns::bulk_query(doms) at testthat/test-gdns.R:7
  2: map_df(results, "Answer")
  3: stop("`map_df()` requires dplyr", call. = FALSE)
  
  testthat results ================================================================
  OK: 1 SKIPPED: 0 FAILED: 1
  1. Error: we can do something (@test-gdns.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘GEEaSPU/libs/GEEaSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘geepack/libs/geepack.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard files/directories found at top level:
  ‘README.too’ ‘blurb’
File ‘geiger/libs/geiger.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gelnet/libs/gelnet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gemtc/libs/gemtc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Warning: no function found corresponding to methods exports from ‘GenABEL’ 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:
  ‘DatABEL’ ‘genetics’ ‘haplo.stats’ ‘hglm’ ‘qvalue’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘GenABEL.data’ ‘MASS’ ‘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.character.snp.coding as.character.snp.strand merge.gwaa.data
  merge.snp.data summary.snp.data_old
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘GenABEL/libs/GenABEL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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’
'library' or 'require' call to ‘mmap’ 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:
  format.GRtime plot.AccData print.VirtAccData
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
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.
File ‘GeneFeST/libs/GeneFeST.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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').
File ‘genepi/libs/genepi.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard files/directories found at top level:
  ‘Todo’ ‘regressionTests’
'library' or 'require' call to ‘MASS’ 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:
  ‘DistributionUtils’ ‘RUnit’
  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.hyperblm
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
'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.
File ‘GenKern/libs/GenKern.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkrows: no visible global function definition for ‘rnorm’
cv.trendfilter: no visible binding for global variable ‘sd’
plot.cv.trendfilter: no visible global function definition for ‘plot’
plot.cv.trendfilter: no visible global function definition for ‘lines’
plot.cv.trendfilter: no visible global function definition for ‘points’
plot.cv.trendfilter: no visible global function definition for ‘legend’
plot.gcv.genlasso: no visible global function definition for ‘plot’
plot.gcv.genlasso: no visible global function definition for ‘points’
plot.genlasso: no visible global function definition for ‘par’
plot.genlasso: no visible global function definition for ‘rainbow’
plot.genlasso: no visible global function definition for ‘plot’
plot.genlasso: no visible global function definition for ‘matplot’
plot.genlasso: no visible global function definition for ‘abline’
plot.genlasso: no visible global function definition for ‘text’
plot.genlasso: no visible global function definition for ‘lines’
plot.trendfilter: no visible global function definition for ‘plot’
plot.trendfilter: no visible global function definition for ‘matplot’
predict.genlasso: no visible global function definition for ‘coef’
softthresh: no visible global function definition for ‘coef’
Undefined global functions or variables:
  abline coef legend lines matplot par plot points rainbow rnorm sd
  text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "legend", "lines", "matplot", "par",
             "plot", "points", "text")
  importFrom("stats", "coef", "rnorm", "sd")
to your NAMESPACE file.
File ‘genlasso/libs/genlasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
error.bar: no visible global function definition for ‘arrows’
gen.completenessVar: no visible binding for global variable ‘var’
gen.graph: no visible global function definition for ‘plot’
gen.implexVar: no visible binding for global variable ‘var’
gen.phiCI : FUN: no visible global function definition for ‘quantile’
genlibDLLTest: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  arrows plot quantile rnorm var
Consider adding
  importFrom("graphics", "arrows", "plot")
  importFrom("stats", "quantile", "rnorm", "var")
to your NAMESPACE file.
File ‘GENLIB/libs/GENLIB.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘genMOSSplus/libs/genMOSSplus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘genMOSS/libs/genMOSS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘GenSA/libs/GenSA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘genSurv/libs/genSurv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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.
File ‘geoBayes/libs/geoBayes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘geoCount/libs/geoCount.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘GeoGenetix/libs/GeoGenetix.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘geohash/libs/geohash.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘geometry/libs/geometry.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
getJson: no visible global function definition for ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
Unexported objects imported by ':::' calls:
  ‘maps:::makepoly’ ‘maps:::mapgetg’ ‘maps:::mapgetl’ ‘maps:::mapname’
  See the note in ?`:::` about the use of this operator.
File ‘geo/libs/geo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
image.glm.krige.bayes: no visible global function definition for
  ‘heat.colors’
Undefined global functions or variables:
  heat.colors
Consider adding
  importFrom("grDevices", "heat.colors")
to your NAMESPACE file.
File ‘geoRglm/libs/geoRglm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘geoR/libs/geoR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘geosphere/libs/geosphere.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘geostatsp/libs/geostatsp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
getopt: 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.
File ‘getPass/libs/getPass.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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.
example.alpha: no visible global function definition for ‘rnorm’
example.quadratic.approx: no visible global function definition for
  ‘rnorm’
generate_nnm: no visible global function definition for ‘rnorm’
generate_nnm: no visible global function definition for ‘rgamma’
generate_nnm: no visible global function definition for ‘dnorm’
plot_nnm: no visible global function definition for ‘stack’
testmatrix: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  dnorm rgamma rnorm stack
Consider adding
  importFrom("stats", "dnorm", "rgamma", "rnorm")
  importFrom("utils", "stack")
to your NAMESPACE file.
File ‘gettz/libs/gettz.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Missing or unexported object: ‘stable::dstable.quick’
'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.
File ‘ggforce/libs/ggforce.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: GNU Extension: Different type kinds at (1)
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/gglasso.Rcheck/00install.out’ for details.
coef.cv.gglasso: no visible global function definition for ‘coef’
coef.gglasso: no visible global function definition for ‘rbind2’
cv.hsvm: no visible global function definition for ‘predict’
cv.logit: no visible global function definition for ‘predict’
cv.ls: no visible global function definition for ‘predict’
cv.sqsvm: no visible global function definition for ‘predict’
error.bars: no visible global function definition for ‘segments’
lambda.interp: no visible global function definition for ‘approx’
plot.cv.gglasso: no visible global function definition for ‘points’
plot.cv.gglasso: no visible global function definition for ‘axis’
plot.cv.gglasso: no visible global function definition for ‘abline’
plot.gglasso: no visible global function definition for ‘par’
plot.gglasso: no visible binding for global variable ‘plot.default’
plot.gglasso: no visible global function definition for ‘gray.colors’
plot.gglasso: no visible global function definition for ‘abline’
predict.cv.gglasso: no visible global function definition for ‘predict’
predict.gglasso: no visible global function definition for ‘rbind2’
predict.gglasso: no visible global function definition for ‘cbind2’
Undefined global functions or variables:
  abline approx axis cbind2 coef gray.colors par plot.default points
  predict rbind2 segments
Consider adding
  importFrom("grDevices", "gray.colors")
  importFrom("graphics", "abline", "axis", "par", "plot.default",
             "points", "segments")
  importFrom("methods", "cbind2", "rbind2")
  importFrom("stats", "approx", "coef", "predict")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘gglasso/libs/gglasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ggrepel/libs/ggrepel.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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
Namespace with empty importFrom: ‘statmod’
File ‘ghyp/libs/ghyp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘GIGrvg/libs/GIGrvg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
g.ipf: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
File ‘GiRaF/libs/GiRaF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard file/directory found at top level:
  ‘changes.txt’
Warning: no function found corresponding to methods exports from ‘giRaph’ for: ‘coerce’, ‘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.
'library' or 'require' call to ‘mathgraph’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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').
File ‘git2r/libs/git2r.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘gkmSVM/libs/gkmSVM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘glamlasso/libs/glamlasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘glasso/libs/glasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘glcm/libs/glcm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘GLDEX/libs/GLDEX.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gld/libs/gld.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘glinternet/libs/glinternet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘gllm/libs/gllm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
glm.fit2: no visible global function definition for ‘gaussian’
glm.fit2: no visible global function definition for ‘lm.fit’
glm.fit2: no visible binding for global variable ‘n’
glm2: no visible binding for global variable ‘gaussian’
glm2: no visible global function definition for ‘model.response’
glm2: no visible global function definition for ‘is.empty.model’
glm2: no visible global function definition for ‘model.matrix’
glm2: no visible global function definition for ‘model.weights’
glm2: no visible global function definition for ‘model.offset’
glm2: no visible global function definition for ‘model.extract’
glm2: no visible global function definition for ‘.getXlevels’
Undefined global functions or variables:
  .getXlevels gaussian is.empty.model lm.fit model.extract model.matrix
  model.offset model.response model.weights n
Consider adding
  importFrom("stats", ".getXlevels", "gaussian", "is.empty.model",
             "lm.fit", "model.extract", "model.matrix", "model.offset",
             "model.response", "model.weights")
to your NAMESPACE file.
File ‘GLMaSPU/libs/GLMaSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  dataStructure.cpp:146:13: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  dataStructure.cpp:148:70: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  dataStructure.cpp:149:27: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/glmBfp.Rcheck/00install.out’ for details.
File ‘glmBfp/libs/glmBfp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘glmgraph/libs/glmgraph.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ 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.
File ‘glmlep/libs/glmlep.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘glmm/libs/glmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘glmmsr/libs/glmmsr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package in Depends field not imported from: ‘glmnet’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
glmnet.cr: no visible global function definition for ‘glmnet’
plot.glmnet.cr: no visible binding for global variable ‘sd’
plot.glmnet.cr: no visible global function definition for ‘predict’
plot.glmnet.cr: no visible global function definition for ‘plot’
plot.glmnet.cr: no visible global function definition for ‘title’
plot.glmnet.cr: no visible global function definition for ‘matplot’
plot.glmnet.cr: no visible global function definition for ‘abline’
plot.glmnet.cr: no visible global function definition for ‘axis’
Undefined global functions or variables:
  abline axis glmnet matplot plot predict sd title
Consider adding
  importFrom("graphics", "abline", "axis", "matplot", "plot", "title")
  importFrom("stats", "predict", "sd")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘glmpath’ ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
coef.glmpath.cr: no visible global function definition for ‘approx’
fitted.glmpath.cr: no visible global function definition for ‘coef’
glmpath.cr: no visible global function definition for ‘glmpath’
glmpath.cr: no visible binding for global variable ‘binomial’
nonzero.coef: no visible global function definition for ‘coef’
plot.glmpath.cr: no visible global function definition for ‘par’
plot.glmpath.cr: no visible global function definition for ‘plot’
plot.glmpath.cr: no visible global function definition for ‘title’
plot.glmpath.cr: no visible global function definition for ‘matplot’
plot.glmpath.cr: no visible global function definition for ‘abline’
plot.glmpath.cr: no visible global function definition for ‘axis’
plot.glmpath.cr: no visible global function definition for ‘segments’
predict.glmpath.cr: no visible global function definition for ‘coef’
summary.glmpath.cr: no visible global function definition for ‘coef’
Undefined global functions or variables:
  abline approx axis binomial coef glmpath matplot par plot segments
  title
Consider adding
  importFrom("graphics", "abline", "axis", "matplot", "par", "plot",
             "segments", "title")
  importFrom("stats", "approx", "binomial", "coef")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  plot.bootpath plot.coxpath plot.glmpath predict.coxpath
  predict.glmpath print.coxpath print.glmpath summary.coxpath
  summary.glmpath
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘glmpath/libs/glmpath.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Found the following apparent S3 methods exported but not registered:
  $.GlobalOptionsFun $<-.GlobalOptionsFun
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘globalOptTests/libs/globalOptTests.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘fxregime’ 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:
  glogisfit.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
refit.breakpoints.glogisfit: no visible binding for global variable
  ‘head’
refit.breakpoints.glogisfit: no visible binding for global variable
  ‘tail’
summary.glogisfit: no visible global function definition for ‘tail’
Undefined global functions or variables:
  head tail
Consider adding
  importFrom("utils", "head", "tail")
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.
File ‘GMCM/libs/GMCM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gMCP/libs/gMCP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.elbow plot.gmdm plot.gmdp plot.mhist plot.mhist.summary
  print.gmdm print.gmdp summary.gmdp
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘GMD/libs/GMD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Gmedian/libs/Gmedian.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gmeta/libs/gmeta.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Gmisc/libs/Gmisc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
estfun.gmmFct: no visible global function definition for ‘is’
getModel.baseGel: no visible global function definition for ‘is’
getModel.baseGmm: no visible global function definition for ‘is’
getModel.constGmm: no visible global function definition for ‘is’
plot.gel: no visible binding for global variable ‘panel.smooth’
plot.gel: no visible binding for global variable ‘points’
plot.gel: no visible global function definition for ‘par’
plot.gel: no visible global function definition for ‘dev.interactive’
plot.gel: no visible global function definition for ‘plot’
plot.gmm: no visible binding for global variable ‘panel.smooth’
plot.gmm: no visible binding for global variable ‘points’
plot.gmm: no visible global function definition for ‘par’
plot.gmm: no visible global function definition for ‘dev.interactive’
plot.gmm: no visible global function definition for ‘devAskNewPage’
plot.gmm: no visible global function definition for ‘extendrange’
plot.gmm: no visible global function definition for ‘plot’
plot.gmm: no visible global function definition for ‘abline’
plot.gmm: no visible global function definition for ‘lines’
plot.gmm: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline dev.interactive devAskNewPage extendrange is legend lines
  panel.smooth par plot points
Consider adding
  importFrom("grDevices", "dev.interactive", "devAskNewPage",
             "extendrange")
  importFrom("graphics", "abline", "legend", "lines", "panel.smooth",
             "par", "plot", "points")
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
r2gmt: no visible global function definition for ‘read.table’
r2gmt: 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.
File ‘gmum.r/libs/gmum.r.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gMWT/libs/gMWT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘GNE/libs/GNE.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gnlm/libs/gnlm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gnmf/libs/gnmf.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘FactorMatrix.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘FactorMatrix.o’
File ‘gnmf/libs/gnmf.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gnm/libs/gnm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

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.
File ‘gof/libs/gof.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gogamer/libs/gogamer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘GPareto/libs/GPareto.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Random.Start: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
File ‘GPB/libs/GPB.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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').
File ‘gpclib/libs/gpclib.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.GPCE.lar plot.GPCE.quad plot.GPCE.sparse predict.GPCE.lar
  predict.GPCE.quad predict.GPCE.sparse print.GPCE.lar print.GPCE.quad
  print.GPCE.sparse tell.GPCE.lar tell.GPCE.quad tell.GPCE.sparse
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
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.
.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.
File ‘gplm/libs/gplm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Warning: parse error in file ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/GPoM/doc/II_PreProcessing.R’:
invalid multibyte character in parser at line 59
Warning: parse error in file ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/GPoM/doc/IV_VisualizeOutputs.R’:
invalid multibyte character in parser at line 30
Non-standard files/directories found at top level:
  ‘doc’ ‘scr’
calc_chisq_statistic: no visible global function definition for ‘dpois’
generalized_poisson_likelihood: no visible global function definition
  for ‘var’
perform_permutation_de: no visible binding for global variable ‘rbinom’
perform_permutation_de: no visible global function definition for ‘var’
perform_permutation_ds: no visible binding for global variable ‘rbinom’
perform_permutation_ds: no visible global function definition for ‘var’
Undefined global functions or variables:
  dpois rbinom var
Consider adding
  importFrom("stats", "dpois", "rbinom", "var")
to your NAMESPACE file.
File ‘gpuR/libs/gpuR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package in Depends field not imported from: ‘dismo’
  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.graf predict.graf print.graf
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘gRain/libs/gRain.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘GrammR/libs/GrammR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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.
Namespace with empty importFrom: ‘methods’
Found the following apparent S3 methods exported but not registered:
  plot.gRapHD print.gRapHD summary.gRapHD
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘gRapHD/libs/gRapHD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘graphscan/libs/graphscan.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable 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.
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.
Package suggested but not available for checking: ‘taxstats’
Non-standard files/directories found at top level:
  ‘TODO.txt’ ‘Wishlist.txt’
Found the following apparent S3 methods exported but not registered:
  K2theta.rcon K2theta.rcor as.cc.default as.cc.list findKinModel.rcox
  formula2names.NULL formula2names.default formula2names.formula
  formula2names.list formula2string.default formula2string.list
  getIndex.character getIndex.default getIndex.list getScore.rcon
  getScore.rcor listOrder.atom listOrder.cc listOrder.default
  listOrder.list listOrder.numeric names2formula.default
  names2formula.list theta2K.rcon theta2K.rcor toLisp.cc toLisp.default
  toLisp.list
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘gRc/libs/gRc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  cbind.printCrudeAndAdjusted rbind.printCrudeAndAdjusted
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'printCrudeAndAdjustedModel':
  ‘rbind.printCrudeAndAdjusted’ ‘cbind.printCrudeAndAdjusted’

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.
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.
File ‘Grid2Polygons/libs/Grid2Polygons.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  cbind.gtable rbind.gtable
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'cbind.gtable':
  ‘cbind.gtable’

S3 methods shown with full name in documentation object 'rbind.gtable':
  ‘rbind.gtable’

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.
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.
pictureHull: no visible global function definition for ‘chull’
picturePaths: no visible global function definition for ‘n2mfrow’
readPicture : funPath: no visible global function definition for ‘rgb’
drawPath,PictureChar: no visible global function definition for
  ‘polypath’
drawPath,PictureFill: no visible global function definition for
  ‘polypath’
drawPath,PictureStroke: no visible global function definition for
  ‘xinch’
drawPath,PictureStroke: no visible global function definition for
  ‘lines’
drawPath,PictureText: no visible global function definition for ‘text’
Undefined global functions or variables:
  chull lines n2mfrow polypath rgb text xinch
Consider adding
  importFrom("grDevices", "chull", "n2mfrow", "rgb")
  importFrom("graphics", "lines", "polypath", "text", "xinch")
to your NAMESPACE file.
File ‘groc/libs/groc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.drBootSpline plot.drFit plot.drFitSpline plot.gcBootSpline
  plot.gcFit plot.gcFitModel plot.gcFitSpline summary.drBootSpline
  summary.drFit summary.drFitSpline summary.gcBootSpline summary.gcFit
  summary.gcFitModel summary.gcFitSpline
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘groupRemMap/libs/groupRemMap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘grove/libs/grove.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘growcurves/libs/growcurves.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘growfunctions/libs/growfunctions.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘GrowingSOM/libs/GrowingSOM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘growthrates/libs/growthrates.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘growth/libs/growth.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
cv.plot: no visible global function definition for ‘plot’
cv.plot: no visible global function definition for ‘lines’
cv.plot: no visible global function definition for ‘legend’
path.plot: no visible global function definition for ‘par’
path.plot: no visible global function definition for ‘plot’
path.plot: no visible global function definition for ‘lines’
Undefined global functions or variables:
  legend lines par plot
Consider adding
  importFrom("graphics", "legend", "lines", "par", "plot")
to your NAMESPACE file.
File ‘grppenalty/libs/grppenalty.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘grr/libs/grr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  extractAIC.gcjc extractAIC.grg mcovs.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
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
File ‘gsDesign/libs/gsDesign.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gsEasy/libs/gsEasy.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘GSE/libs/GSE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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’
File ‘gsl/libs/gsl.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gsmoothr/libs/gsmoothr.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘brassicaData’
File ‘gsscopu/libs/gsscopu.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  [.gstat
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Found the following apparent S3 methods exported but not registered:
  $.fn as.function.formula
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
read.pattern: 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.
File ‘gsw/libs/gsw.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘gte/libs/gte.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following possibly unsafe calls:
File ‘gtools/R/unByteCode.R’:
  unlockBinding(name, env = env)

checkReverseDependencies: no visible global function definition for
  ‘available.packages’
getDependencies: no visible global function definition for
  ‘installed.packages’
getDependencies: no visible global function definition for
  ‘available.packages’
getDependencies: no visible global function definition for
  ‘flush.console’
keywords: no visible global function definition for ‘na.omit’
keywords : topics: no visible global function definition for
  ‘help.search’
loadedPackages : <anonymous>: no visible global function definition for
  ‘packageVersion’
quantcut: no visible global function definition for ‘quantile’
rdirichlet: no visible global function definition for ‘rgamma’
running: no visible global function definition for ‘new’
smartbind: no visible global function definition for ‘head’
stars.pval: no visible global function definition for ‘symnum’
Undefined global functions or variables:
  available.packages flush.console head help.search installed.packages
  na.omit new packageVersion quantile rgamma symnum
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "na.omit", "quantile", "rgamma", "symnum")
  importFrom("utils", "available.packages", "flush.console", "head",
             "help.search", "installed.packages", "packageVersion")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘gtools/libs/gtools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘GUILDS/libs/GUILDS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
PermanovaG: no visible global function definition for ‘as.dist’
PermanovaG: no visible global function definition for ‘as.formula’
Undefined global functions or variables:
  as.dist as.formula
Consider adding
  importFrom("stats", "as.dist", "as.formula")
to your NAMESPACE file.
Running ‘testthat.R’ [5s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(gutenbergr)
  > 
  > test_check("gutenbergr")
  1. Failure: read_zip_url can download and read a zip file (@test-utils.R#7) ----
  any(z == "Congress shall make no law respecting an establishment of religion,") isn't true.
  
  
  testthat results ================================================================
  OK: 46 SKIPPED: 0 FAILED: 1
  1. Failure: read_zip_url can download and read a zip file (@test-utils.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘GUTS/libs/GUTS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘GWASExactHW/libs/GWASExactHW.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ 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.
File ‘gwfa/libs/gwfa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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’.
Running ‘run-tests.R’ [1s/1s]
Running the tests in ‘tests/run-tests.R’ failed.
Last 13 lines of output:
  > f <- list.files(system.file("tests", package="gWidgets2"), full=T)
  > f <- Filter(function(x) !grepl("README", x), f)
  > f <- Filter(function(x) !grepl("html", x), f)
  > 
  > sapply(f, function(i) {
  +   message("testing ", i)
  +   source(i)
  + })
  testing /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/gWidgets2/tests/button.R
  Loading required package: gWidgets2RGtk2
  Loading required package: memoise
  Loading required package: RGtk2
  Error in `[.enums`(GtkIconSize, 4) : Enum values must be strings
  Calls: sapply ... <Anonymous> -> <Anonymous> -> method -> .RGtkCall -> [ -> [.enums
  Execution halted
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.
GWLelast.est: no visible global function definition for ‘dist’
GWLelast.inner: no visible global function definition for ‘predict’
GWLelast.inner.parallel: no visible global function definition for
  ‘predict’
GWLelast.sel.bw: no visible global function definition for ‘dist’
GWLelast.sel.bw: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  dist optimize predict
Consider adding
  importFrom("stats", "dist", "optimize", "predict")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘fields’ ‘lars’
  Please remove these calls from your code.
Package in Depends field not imported from: ‘lars’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gwl.beta: no visible global function definition for ‘lars’
gwl.cv.err: no visible global function definition for ‘lars’
gwl.est: no visible global function definition for ‘lm’
gwr.bw.est: no visible global function definition for ‘lm’
gwr.est: no visible global function definition for ‘lm’
gwr.rsquare: no visible global function definition for ‘cor’
gwrr.est: no visible global function definition for ‘lm’
Undefined global functions or variables:
  cor lars lm
Consider adding
  importFrom("stats", "cor", "lm")
to your NAMESPACE file.
GxMestimator: no visible global function definition for ‘na.omit’
initialization_chol: no visible global function definition for ‘cov’
initialization_corr: no visible global function definition for ‘cov’
initialization_nlmain: no visible global function definition for
  ‘lm.fit’
print.summaryGxMclass: no visible global function definition for
  ‘pnorm’
print.summaryGxMclass: no visible global function definition for
  ‘printCoefmat’
Undefined global functions or variables:
  cov lm.fit na.omit pnorm printCoefmat
Consider adding
  importFrom("stats", "cov", "lm.fit", "na.omit", "pnorm",
             "printCoefmat")
to your NAMESPACE file.
File ‘gyriq/libs/gyriq.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘h5/libs/h5.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘Hankel/libs/Hankel.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘hapassoc/libs/hapassoc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘HapEstXXR/libs/HapEstXXR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Found the following apparent S3 methods exported but not registered:
  AIC.haplo.ccs anova.haplo.ccs coef.haplo.ccs fitted.haplo.ccs
  logLik.haplo.ccs print.haplo.ccs print.summary.haplo.ccs
  residuals.haplo.ccs summary.haplo.ccs vcov.haplo.ccs
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
haplo.ccs: no visible global function definition for ‘terms’
haplo.ccs: no visible global function definition for ‘model.response’
haplo.ccs: no visible global function definition for ‘model.matrix’
haplo.ccs.fit: no visible global function definition for ‘glm’
haplo.ccs.fit: no visible global function definition for
  ‘quasibinomial’
haplo.ccs.fit: no visible binding for global variable ‘logit’
haplo.ccs.fit: no visible global function definition for ‘coef’
print.summary.haplo.ccs: no visible global function definition for ‘pt’
sandcov: no visible global function definition for ‘coef’
sandcov: no visible global function definition for ‘model.matrix’
sandcov: no visible global function definition for ‘residuals’
Undefined global functions or variables:
  coef glm logit model.matrix model.response pt quasibinomial residuals
  terms
Consider adding
  importFrom("stats", "coef", "glm", "model.matrix", "model.response",
             "pt", "quasibinomial", "residuals", "terms")
to your NAMESPACE file.
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.
File ‘haplo.stats/libs/haplo.stats.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Found the following significant warnings:
  SNPHWEX.cpp:50:31: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  SNPHWEX.cpp:51:65: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/HardyWeinberg.Rcheck/00install.out’ for details.
Namespace with empty importFrom: ‘utils’
Found the following significant warnings:
  ./City.h:82:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:93:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:94:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:95:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:96:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:87:8: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:89:8: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:267:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:268:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ./Spooky.h:285:36: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/hashFunction.Rcheck/00install.out’ for details.
File ‘hashFunction/libs/hashFunction.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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').
File ‘hashr/libs/hashr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘haven/libs/haven.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hawkes/libs/hawkes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘hbmem/libs/hbmem.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
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.
Rd file 'CARsimu.Rd':
  \usage lines wider than 90 characters:
     CARsimu(level = 5, row1 = 0.2499999, row2 = 0, col1 = 0.2499999, col2 = 0, rc1 = 0, cr1 = 0)

Rd file 'hdeco.Rd':
  \usage lines wider than 90 characters:
     hdeco(BE1 = demoimage1, BE2 = demoimage2, MICIKE = decomppath, MSK = FALSE, MASK = NULL, fnev = "", AutoDecoPath = FALSE, JPG = FALSE,  ... [TRUNCATED]

Rd file 'sigplot.Rd':
  \usage lines wider than 90 characters:
     sigplot(mat = .HPROFIL, column = 5, sigcol = 7, tit = "Title of Graph", xtit = "Step", ytit = "Uncertainty Coefficient", override = FAL ... [TRUNCATED]
  \examples lines wider than 100 characters:
     sigplot(mat = HPROFIL, column = 5, sigcol = 7, tit = "Title of Graph", xtit = "Step", ytit = "Uncertainty Coefficient", override = FALS ... [TRUNCATED]

These lines will be truncated in the PDF manual.
File ‘HDGLM/libs/HDGLM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hdlm/libs/hdlm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘HDPenReg/libs/HDPenReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hdrcde/libs/hdrcde.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘HDtest/libs/HDtest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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').
File ‘HDtweedie/libs/HDtweedie.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Found the following apparent S3 methods exported but not registered:
  plot.threshpt print.summary.threshpt print.threshpt summary.threshpt
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.threshpt: no visible global function definition for ‘glm’
plot.threshpt: no visible global function definition for ‘predict’
plot.threshpt: no visible global function definition for ‘plot’
plot.threshpt: no visible global function definition for ‘lines’
plot.threshpt: no visible global function definition for ‘abline’
plot.threshpt: no visible global function definition for ‘points’
print.summary.threshpt: no visible global function definition for
  ‘printCoefmat’
threshpt: no visible global function definition for ‘as.formula’
threshpt: no visible global function definition for ‘glm’
threshpt: no visible global function definition for ‘vcov’
threshpt: no visible global function definition for ‘pnorm’
threshpt: no visible global function definition for ‘predict’
Undefined global functions or variables:
  abline as.formula glm lines plot pnorm points predict printCoefmat
  vcov
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "points")
  importFrom("stats", "as.formula", "glm", "pnorm", "predict",
             "printCoefmat", "vcov")
to your NAMESPACE file.
File ‘hergm/libs/hergm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘glmmADMB’
Warning: no function found corresponding to methods exports from ‘het.test’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
Packages in Depends field not imported from:
  ‘methods’ ‘vars’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
whites.htest: no visible global function definition for ‘residuals’
whites.htest: no visible global function definition for ‘lm’
whites.htest: no visible global function definition for ‘pchisq’
whites.htest: no visible global function definition for ‘new’
Undefined global functions or variables:
  lm new pchisq residuals
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "lm", "pchisq", "residuals")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following apparent S3 methods exported but not registered:
  print.summary.tlm print.tlm print.tsum summary.tlm
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘hexbin/libs/hexbin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘HHG/libs/HHG.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘HiClimR/libs/HiClimR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘HiCseg/libs/HiCseg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘HiddenMarkov/libs/HiddenMarkov.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘HiDimDA/libs/HiDimDA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
build.clusters.spatial: no visible global function definition for
  ‘kmeans’
build.clusters.spatial: no visible global function definition for
  ‘points’
mubz.copula: no visible global function definition for ‘integrate’
perspcolor: no visible global function definition for ‘terrain.colors’
rCMS: no visible global function definition for ‘runif’
rSchlatherExcess: no visible global function definition for ‘runif’
simul.maxlik.maxstable: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  integrate kmeans points runif terrain.colors
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "points")
  importFrom("stats", "integrate", "kmeans", "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.
File ‘hierarchicalSets/libs/hierarchicalSets.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘hierband/libs/hierband.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Found the following apparent S3 methods exported but not registered:
  plot.hierNet.cv predict.hierNet predict.hierNet.logistic
  predict.hierNet.path print.hierNet print.hierNet.cv
  print.hierNet.path
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Calls with DUP:
   .C("compute_phat_zz_R", xnum, as.integer(n), as.integer(p), zz, 
       as.integer(aa$diagonal), as.double(aa$b0), as.double(aa$th), 
       aa$bp, aa$bn, phat = rep(0, n), DUP = FALSE, PACKAGE = "hierNet")
   .C("compute_yhat_zz_R", xnum, as.integer(n), as.integer(p), zz, 
       as.integer(aa$diagonal), as.double(aa$th), aa$bp, aa$bn, 
       yhat = rep(0, n), DUP = FALSE, PACKAGE = "hierNet")
   .C("ggdescent_R", xnum, as.integer(n), as.integer(p), zz, as.integer(diagonal), 
       y, as.double(lam.l1), as.double(lam.l2), as.double(rho), 
       as.double(V), as.integer(maxiter), as.double(aa$th), aa$bp, 
       aa$bn, stepsize, as.integer(stepwindow), backtrack, tol, 
       as.integer(trace), th = rep(0, p * p), bp = rep(0, p), bn = rep(0, 
           p), DUP = FALSE, PACKAGE = "hierNet")
   .C("ggdescent_logistic_R", xnum, as.integer(n), as.integer(p), 
       zz, as.integer(diagonal), as.double(y), as.double(lam.l1), 
       as.double(lam.l2), as.double(rho), as.double(V), as.integer(maxiter), 
       as.double(aa$b0), as.double(aa$th), aa$bp, aa$bn, as.double(stepsize), 
       as.integer(stepwindow), as.double(backtrack), as.double(tol), 
       as.integer(trace), b0 = as.double(0), th = rep(0, p * p), 
       bp = rep(0, p), bn = rep(0, p), DUP = FALSE, PACKAGE = "hierNet")
DUP is no longer supported and will be ignored.
error.bars: no visible global function definition for ‘segments’
hierNet.cv: no visible binding for global variable ‘var’
hierNet.varimp: no visible global function definition for ‘predict’
permute.rows: no visible global function definition for ‘runif’
plot.hierNet.cv: no visible global function definition for ‘par’
plot.hierNet.cv: no visible global function definition for ‘plot’
plot.hierNet.cv: no visible global function definition for ‘axis’
plot.hierNet.cv: no visible global function definition for ‘mtext’
plot.hierNet.cv: no visible global function definition for ‘points’
plot.hierNet.cv: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline axis mtext par plot points predict runif segments var
Consider adding
  importFrom("graphics", "abline", "axis", "mtext", "par", "plot",
             "points", "segments")
  importFrom("stats", "predict", "runif", "var")
to your NAMESPACE file.
File ‘hierNet/libs/hierNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘hier.part/libs/hier.part.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘highD2pop/libs/highD2pop.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘hillmakeR/libs/hillmakeR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘hint/libs/hint.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard files/directories found at top level:
  ‘InstallScript’ ‘Installation.html’
Unexported object imported by a ':::' call: ‘Matrix:::copyClass’
  See the note in ?`:::` about the use of this operator.
OptimiseChol2invDtr: no visible global function definition for ‘rnorm’
OptimiseLU: no visible global function definition for ‘rnorm’
OptimiseSolveDge: no visible global function definition for ‘rnorm’
OptimiseSolveDgemat: no visible global function definition for ‘rnorm’
OptimiseSolveDpoDge: no visible global function definition for ‘rnorm’
OptimiseSolveDpomat: no visible global function definition for ‘rnorm’
OptimiseSolveDtr: no visible global function definition for ‘rnorm’
OptimiseSolveDtrmat: no visible global function definition for ‘rnorm’
OptimisecrossprodDge: no visible global function definition for ‘rnorm’
OptimisecrossprodDgeDge: no visible global function definition for
  ‘rnorm’
OptimisecrossprodDgemat: no visible global function definition for
  ‘rnorm’
OptimisedetDge: no visible global function definition for ‘rnorm’
OptimisematmulDgeDge: no visible global function definition for ‘rnorm’
OptimisematmulDgemat: no visible global function definition for ‘rnorm’
OptimisematmulDtrDtr: no visible global function definition for ‘rnorm’
OptimisematmulDtrmat: no visible global function definition for ‘rnorm’
OptimisenormDge: no visible global function definition for ‘rnorm’
OptimisercondDge: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Functions or methods with usage in documentation object 'chol' but not in code:
  chol

Functions or methods with usage in documentation object 'crossprod' but not in code:
  crossprod

Functions or methods with usage in documentation object 'lu' but not in code:
  lu

Functions or methods with usage in documentation object 'tcrossprod' but not in code:
  tcrossprod
Package has both ‘src/Makevars.in’ and ‘src/Makevars’.
Installation with --no-configure' is unlikely to work.  If you intended
‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’
otherwise remove it.  If ‘configure’ created ‘src/Makevars’, you need a
‘cleanup’ script.
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.
File ‘HI/libs/HI.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘histmdl/libs/histmdl.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hitandrun/libs/hitandrun.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hit/libs/hit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hkevp/libs/hkevp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘HKprocess/libs/HKprocess.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘HLMdiag/libs/HLMdiag.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘HLSM/libs/HLSM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Found the following apparent S3 methods exported but not registered:
  [.Cbind [.describe [.discrete [.impute [.mChoice [.pBlock [.roundN
  [.special.miss [.substi [.summary.formula.response [.transcan
  [.ynbind [<-.discrete [[.discrete
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
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.
File ‘hmm.discnp/libs/hmm.discnp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
deal1: no visible global function definition for ‘runif’
hand1: no visible global function definition for ‘runif’
hand1: no visible global function definition for ‘text’
hand1: no visible global function definition for ‘locator’
hand1: no visible binding for global variable ‘name1’
mygraphics1: no visible global function definition for ‘plot’
mygraphics1: no visible global function definition for ‘text’
mygraphics1: no visible global function definition for ‘locator’
timemachine: no visible global function definition for ‘runif’
tourn1: no visible global function definition for ‘plot’
tourn1: no visible global function definition for ‘text’
william: no visible global function definition for ‘runif’
writebets1: no visible global function definition for ‘text’
writebets1: no visible global function definition for ‘locator’
xena: no visible global function definition for ‘runif’
zelda: no visible global function definition for ‘runif’
Undefined global functions or variables:
  locator name1 plot runif text
Consider adding
  importFrom("graphics", "locator", "plot", "text")
  importFrom("stats", "runif")
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.
File ‘HotDeckImputation/libs/HotDeckImputation.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.hotspots print.hotspots print.summary.hotspots summary.hotspots
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
print.summary.hotspots: warning in sort(x$data, dec = TRUE): partial
  argument match of ‘dec’ to ‘decreasing’
print.summary.hotspots: warning in sort(x$disprop$positive, dec =
  TRUE): partial argument match of ‘dec’ to ‘decreasing’
print.summary.hotspots: warning in sort(x$disprop$negative, dec =
  TRUE): partial argument match of ‘dec’ to ‘decreasing’
Lchs: no visible global function definition for ‘plot’
Lchs: no visible global function definition for ‘points’
disprop: no visible global function definition for ‘median’
hotspots: no visible global function definition for ‘median’
hotspots: no visible global function definition for ‘qnorm’
hotspots: no visible global function definition for ‘qt’
plot.hotspots: no visible global function definition for ‘par’
summary.hotspots: no visible global function definition for ‘median’
Undefined global functions or variables:
  median par plot points qnorm qt
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "median", "qnorm", "qt")
to your NAMESPACE file.
Rd file 'hotspots.Rd':
  \usage lines wider than 90 characters:
     outliers(x, p = 0.99, tail = "positive", distribution = "t", var.est = "mad", center.est = "mean")

These lines will be truncated in the PDF manual.
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.
File ‘HSAR/libs/HSAR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Missing or unexported object: ‘pracma::nelder_mead’
Missing link or links in documentation object 'PROSPECT2R.Rd':
  ‘[pracma]{nelder_mead}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
Functions or methods with usage in documentation object 'Clman' but not in code:
  Clman
File ‘hsdar/libs/hsdar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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’
File ‘hSDM/libs/hSDM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
It is good practice to register native routines and to disable symbol
search.

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.
File ‘hsmm/libs/hsmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hsm/libs/hsm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hsphase/libs/hsphase.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘HSROC/libs/HSROC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘htdp/libs/htdp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘htmltidy/libs/htmltidy.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘hts/libs/hts.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘httpuv/libs/httpuv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘huge/libs/huge.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘humaniformat/libs/humaniformat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘HUM/libs/HUM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

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