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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mixpack/libs/mixpack.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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’ ‘RODBC’ ‘tcltk’ ‘tcltk2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fit.mixtNB: no visible global function definition for ‘dnbinom’
fit.mixtNB: no visible global function definition for ‘nlminb’
wald.test: no visible global function definition for ‘pnorm’
wald.test: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  dnbinom nlminb p.adjust pnorm
Consider adding
  importFrom("stats", "dnbinom", "nlminb", "p.adjust", "pnorm")
to your NAMESPACE file.
computeContourValues: no visible global function definition for
  ‘na.omit’
deselectNonMovementSteps : coOccurProb: no visible global function
  definition for ‘dnorm’
deselectNonMovementSteps: no visible global function definition for
  ‘pnorm’
estVarMKDE: no visible global function definition for ‘na.omit’
estVarMKDE: no visible global function definition for ‘qnorm’
estVarMKDE: no visible global function definition for ‘optimize’
plotMKDE: no visible global function definition for ‘rainbow’
Undefined global functions or variables:
  dnorm na.omit optimize pnorm qnorm rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("stats", "dnorm", "na.omit", "optimize", "pnorm", "qnorm")
to your NAMESPACE file.
File ‘mkde/libs/mkde.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
mkle: no visible global function definition for ‘sd’
mkle: no visible global function definition for ‘density’
mkle: no visible global function definition for ‘optimize’
mkle.ci: no visible global function definition for ‘sd’
mkle.ci: no visible binding for global variable ‘var’
mkle.ci: no visible global function definition for ‘quantile’
mkle.ci: no visible global function definition for ‘qnorm’
opt.bw: no visible global function definition for ‘sd’
opt.bw : mse: no visible global function definition for ‘var’
opt.bw: no visible global function definition for ‘optimize’
opt.bw: no visible global function definition for ‘var’
Undefined global functions or variables:
  density optimize qnorm quantile sd var
Consider adding
  importFrom("stats", "density", "optimize", "qnorm", "quantile", "sd",
             "var")
to your NAMESPACE file.
mkssd: no visible global function definition for ‘txtProgressBar’
mkssd: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘Data-Administration.R’
File ‘mlbench/libs/mlbench.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘GeneSelector’
'library' or 'require' calls in package code:
  ‘cairoDevice’ ‘gplots’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  ‘MASS:::lda.default’ ‘MASS:::qda.default’
  ‘e1071:::naiveBayes.default’ ‘e1071:::svm.default’
  ‘randomForest:::randomForest.default’
  See the note in ?`:::` about the use of this operator.
confusionBarplot: no visible global function definition for ‘par’
confusionBarplot: no visible global function definition for ‘barplot’
confusionBarplot: no visible global function definition for ‘lines’
confusionBarplot: no visible global function definition for ‘text’
confusionBarplot: no visible global function definition for ‘legend’
confusionBarplot: no visible global function definition for ‘axis’
confusionDendrogram: no visible global function definition for ‘plot’
confusionImage: no visible global function definition for ‘par’
confusionImage: no visible global function definition for ‘image’
confusionImage: no visible global function definition for ‘text’
confusionImage: no visible global function definition for ‘abline’
confusionImage: no visible global function definition for ‘axis’
confusionImage: no visible global function definition for ‘plot’
confusionImage: no visible global function definition for ‘mtext’
confusionStars: no visible global function definition for ‘par’
confusionStars: no visible global function definition for ‘stars’
confusionStars: no visible global function definition for ‘rect’
plot.mlearning: no visible global function definition for ‘plot’
Undefined global functions or variables:
  abline axis barplot image legend lines mtext par plot rect stars text
Consider adding
  importFrom("graphics", "abline", "axis", "barplot", "image", "legend",
             "lines", "mtext", "par", "plot", "rect", "stars", "text")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘CONTENTS’
File ‘MLEcens/libs/MLEcens.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
dftest: no visible global function definition for ‘slot’
mctest: no visible global function definition for ‘rnorm’
mleurDiag: no visible global function definition for ‘acf’
mleurDiag: no visible global function definition for ‘pchisq’
mleurDiag: no visible global function definition for ‘par’
mleurDiag: no visible global function definition for ‘boxplot’
mleurDiag: no visible global function definition for ‘shapiroTest’
mleurDiag: no visible global function definition for ‘title’
mleurDiag: no visible global function definition for ‘abline’
mleurDiag: no visible global function definition for ‘lines’
simar1: no visible global function definition for ‘rnorm’
simar1: no visible global function definition for ‘rt’
simar1: no visible global function definition for ‘convolve’
Undefined global functions or variables:
  abline acf boxplot convolve lines par pchisq rnorm rt shapiroTest
  slot title
Consider adding
  importFrom("graphics", "abline", "boxplot", "lines", "par", "title")
  importFrom("methods", "slot")
  importFrom("stats", "acf", "convolve", "pchisq", "rnorm", "rt")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Non-standard file/directory found at top level:
  ‘CHANGELOG.txt’
Packages in Depends field not imported from:
  ‘methods’ ‘seqinr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CheckStability: no visible global function definition for ‘cor’
CheckStability: no visible global function definition for ‘var’
PriorNormPCA: no visible global function definition for ‘barplot’
SortModes: no visible global function definition for ‘rnorm’
mlicaMAIN: no visible global function definition for ‘runif’
Undefined global functions or variables:
  barplot cor rnorm runif var
Consider adding
  importFrom("graphics", "barplot")
  importFrom("stats", "cor", "rnorm", "runif", "var")
to your NAMESPACE file.
Rd file 'SortModes.Rd':
  \examples lines wider than 100 characters:
             # A) Computation of relative data power. Store values in vector of size H=ncp. Could use different criterion here.

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mlmmm/libs/mlmmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘BMA’ ‘abind’ ‘maxLik’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘mlogitBMA/libs/mlogitBMA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
listGenoToTable: no visible binding for global variable ‘dummy’
Undefined global functions or variables:
  dummy

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

These lines will be truncated in the PDF manual.
Packages suggested but not available for checking: ‘elmNN’ ‘lqa’
'::' or ':::' imports not declared from:
  ‘lhs’ ‘plyr’
Running ‘testhat.R’ [3s/4s]
Running the tests in ‘tests/testhat.R’ failed.
Complete output:
  > if (packageVersion("testthat") >= "0.7.1.99") {
  +     library(testthat)  
  +     test_check("mlvocab")
  + }
  Loading required package: mlvocab
  ── 1. Failure: Basic tcm works (@test_term_matrices.R#24)  ─────────────────────
  `tcm` not equal to `tcm0`.
  Attributes: < Component "i": Mean relative difference: 1.368421 >
  Attributes: < Component "j": Mean relative difference: 0.7179487 >
  Attributes: < Component "x": Mean relative difference: 0.6666667 >
  
  ── 2. Failure: Basic tcm works (@test_term_matrices.R#38)  ─────────────────────
  `ltcm` not equal to `ltcm0`.
  Attributes: < Component "i": Mean relative difference: 0.6046512 >
  Attributes: < Component "j": Mean relative difference: 0.9047619 >
  Attributes: < Component "x": Mean relative difference: 0.7692308 >
  
  ── 3. Failure: Basic tcm works (@test_term_matrices.R#51)  ─────────────────────
  `rtcm` not equal to `rtcm0`.
  Attributes: < Component "i": Mean relative difference: 0.7272727 >
  Attributes: < Component "j": Mean relative difference: 0.5405405 >
  Attributes: < Component "x": Mean relative difference: 1 >
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 136 SKIPPED: 0 FAILED: 3
  1. Failure: Basic tcm works (@test_term_matrices.R#24) 
  2. Failure: Basic tcm works (@test_term_matrices.R#38) 
  3. Failure: Basic tcm works (@test_term_matrices.R#51) 
  
  Error: testthat unit tests failed
  Execution halted
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/MM2Sdata.Rnw’
(Is a VignetteBuilder field missing?)
File which contains pragma(s) suppressing diagnostics:
  ‘src/lemon/core.h’
mmm2: no visible global function definition for ‘model.frame’
mmm2: no visible global function definition for ‘model.matrix’
mmm2: no visible global function definition for ‘model.response’
mmm2: no visible global function definition for ‘as.formula’
Undefined global functions or variables:
  as.formula model.frame model.matrix model.response
Consider adding
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response")
to your NAMESPACE file.
mmm: no visible global function definition for ‘model.frame’
mmm: no visible global function definition for ‘model.matrix’
mmm: no visible global function definition for ‘model.response’
mmm: no visible global function definition for ‘as.formula’
mmm: no visible global function definition for ‘gee’
Undefined global functions or variables:
  as.formula gee model.frame model.matrix model.response
Consider adding
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response")
to your NAMESPACE file.
get.score: no visible global function definition for ‘sd’
get.score: no visible global function definition for ‘coef’
get.score: no visible global function definition for ‘as’
get.score.main: no visible global function definition for ‘sd’
get.score.main: no visible global function definition for ‘coef’
get.subgroup: no visible global function definition for ‘sd’
sample.tte: no visible global function definition for ‘runif’
Undefined global functions or variables:
  as coef runif sd
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "coef", "runif", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘mnlogit/libs/mnlogit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
sadmvng: no visible global function definition for ‘cov2cor’
sadmvng: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  cov2cor pnorm
Consider adding
  importFrom("stats", "cov2cor", "pnorm")
to your NAMESPACE file.
File ‘mnormpow/libs/mnormpow.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
bin.by.date: no visible binding for global variable ‘quantile’
bin.by.date: no visible global function definition for ‘na.omit’
biplot: no visible global function definition for ‘na.omit’
biplot.character: no visible global function definition for ‘runif’
biplot.character: no visible global function definition for ‘opts’
biplot.character: no visible global function definition for
  ‘theme_blank’
distributionplot: no visible global function definition for ‘na.omit’
distributionplot.character: no visible global function definition for
  ‘head’
distributionplot.factor: no visible global function definition for
  ‘opts’
distributionplot.factor: no visible global function definition for
  ‘theme_text’
mapmobility: no visible global function definition for ‘lines’
responseplot: no visible global function definition for ‘na.omit’
scatterplot: no visible global function definition for ‘na.omit’
scatterplot: no visible global function definition for ‘opts’
scatterplot: no visible global function definition for ‘theme_text’
sharedtimeplot: no visible global function definition for ‘na.omit’
timeplot: no visible global function definition for ‘na.omit’
timeplot: no visible global function definition for ‘opts’
timeplot.character: no visible global function definition for ‘runif’
timeplot.character: no visible global function definition for ‘rnorm’
timeplot.character: no visible binding for global variable ‘text’
userplot: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  head lines na.omit opts quantile rnorm runif text theme_blank
  theme_text
Consider adding
  importFrom("graphics", "lines", "text")
  importFrom("stats", "na.omit", "quantile", "rnorm", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
'library' or 'require' call not declared from: ‘R6’
File ‘modeest/libs/modeest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘SparseM’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘glmnet’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
File ‘ModelGood/libs/ModelGood.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘date’ ‘raster’ ‘rgdal’ ‘sfsmisc’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘date’ ‘raster’ ‘rgdal’ ‘sfsmisc’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.clustOrder: no visible global function definition for ‘hclust’
.clustOrder: no visible global function definition for ‘as.dist’
consensusMEDissimilarity: no visible global function definition for
  ‘cor’
mergeCloseModules: no visible global function definition for ‘cor’
mergeCloseModules: no visible global function definition for ‘hclust’
mergeCloseModules: no visible global function definition for ‘as.dist’
moduleEigengenes: no visible global function definition for ‘cor’
moduleEigengenes: no visible global function definition for ‘cov’
moduleNumber: no visible global function definition for ‘cutree’
orderMEs: no visible global function definition for ‘cor’
orderMEs: no visible global function definition for ‘as.dist’
plotHclustColors: no visible global function definition for ‘barplot’
plotHclustColors: no visible global function definition for ‘strwidth’
plotHclustColors: no visible global function definition for ‘rect’
plotHclustColors: no visible global function definition for ‘text’
plotHclustColors: no visible global function definition for ‘lines’
Undefined global functions or variables:
  as.dist barplot cor cov cutree hclust lines rect strwidth text
Consider adding
  importFrom("graphics", "barplot", "lines", "rect", "strwidth", "text")
  importFrom("stats", "as.dist", "cor", "cov", "cutree", "hclust")
to your NAMESPACE file.
agostino.test: no visible global function definition for
  ‘complete.cases’
agostino.test: no visible global function definition for ‘pnorm’
anscombe.test: no visible global function definition for
  ‘complete.cases’
anscombe.test: no visible global function definition for ‘pnorm’
bonett.test: no visible global function definition for ‘complete.cases’
bonett.test: no visible global function definition for ‘pnorm’
jarque.test: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  complete.cases pchisq pnorm
Consider adding
  importFrom("stats", "complete.cases", "pchisq", "pnorm")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from ‘mondate’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
.date.to.mondate: no visible global function definition for ‘new’
as.character.mondate: no visible global function definition for ‘slot’
Arith,array-mondate: no visible global function definition for
  ‘callGeneric’
Arith,mondate-array: no visible global function definition for
  ‘callGeneric’
Arith,mondate-mondate: no visible global function definition for
  ‘callGeneric’
Arith,mondate-numeric: no visible global function definition for
  ‘callGeneric’
Arith,numeric-mondate: no visible global function definition for
  ‘callGeneric’
Compare,mondate-ANY: no visible global function definition for
  ‘callGeneric’
Compare,mondate-ANY: no visible global function definition for
  ‘getDataPart’
Summary,mondate: no visible global function definition for
  ‘callGeneric’
[,mondate: no visible global function definition for ‘callNextMethod’
[,mondate: no visible global function definition for ‘new’
array,mondate: no visible global function definition for
  ‘callNextMethod’
as.numeric,mondate: no visible global function definition for ‘slot’
c,mondate: no visible global function definition for ‘new’
c,mondate: no visible binding for global variable ‘getDataPart’
c,mondate: no visible global function definition for ‘getDataPart’
matrix,mondate: no visible global function definition for
  ‘callNextMethod’
mondate,Date: no visible global function definition for ‘new’
mondate,POSIXt: no visible global function definition for ‘new’
mondate,missing: no visible global function definition for ‘new’
mondate,mondate: no visible global function definition for ‘new’
mondate,numeric: no visible global function definition for ‘new’
Undefined global functions or variables:
  callGeneric callNextMethod getDataPart new slot
Consider adding
  importFrom("methods", "callGeneric", "callNextMethod", "getDataPart",
             "new", "slot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Missing or unexported objects:
  ‘dplyr::base_agg’ ‘dplyr::base_scalar’ ‘dplyr::build_sql’
  ‘dplyr::is.ident’ ‘dplyr::sql_infix’ ‘dplyr::sql_prefix’
  ‘dplyr::sql_translator’ ‘dplyr::sql_variant’ ‘dplyr::src_sql’
  ‘dplyr::tbl_sql’
File ‘MonetDB.R/libs/MonetDB.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 ‘monomvn/libs/monomvn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘monreg/libs/monreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  format.dms format.jd format.time plot.apos plot.rst print.eqc
  print.jd print.time
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.apos: no visible global function definition for ‘plot’
plot.apos: no visible global function definition for ‘abline’
plot.apos: no visible global function definition for ‘text’
plot.rst: no visible global function definition for ‘matplot’
plot.rst: no visible global function definition for ‘abline’
plot.rst: no visible global function definition for ‘text’
track : background: no visible global function definition for ‘par’
track : background: no visible global function definition for ‘plot’
track : background: no visible global function definition for ‘axTicks’
track : background: no visible global function definition for ‘abline’
track : background: no visible global function definition for ‘box’
track : tracks: no visible global function definition for ‘lines’
track : magselect: no visible global function definition for ‘na.omit’
track : add.stars: no visible global function definition for ‘points’
track : addlab.eqc: no visible global function definition for ‘points’
track : addlab.eqc: no visible global function definition for ‘text’
track : add.planet: no visible global function definition for ‘text’
track : add.planet: no visible global function definition for ‘points’
track : add.ecliptic: no visible global function definition for ‘lines’
track : add.brightlab: no visible global function definition for ‘text’
track: no visible global function definition for ‘par’
track: no visible binding for global variable ‘axis’
track: no visible global function definition for ‘title’
Undefined global functions or variables:
  abline axTicks axis box lines matplot na.omit par plot points text
  title
Consider adding
  importFrom("graphics", "abline", "axTicks", "axis", "box", "lines",
             "matplot", "par", "plot", "points", "text", "title")
  importFrom("stats", "na.omit")
to your NAMESPACE file.
mopsocd : initialize_pop: no visible global function definition for
  ‘runif’
mopsocd : compute_velocity: no visible global function definition for
  ‘runif’
mopsocd : mutate: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
checkTH: no visible global function definition for ‘pchisq’
getOrderPval: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
ametrine : <anonymous>: no visible global function definition for
  ‘approx’
ametrine: no visible global function definition for ‘rgb’
isolum : <anonymous>: no visible global function definition for
  ‘approx’
isolum: no visible global function definition for ‘rgb’
morgenstemning : <anonymous>: no visible global function definition for
  ‘approx’
morgenstemning: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  approx rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "approx")
to your NAMESPACE file.
cor.gen: no visible global function definition for ‘rnorm’
cor.gen: no visible global function definition for ‘resid’
cor.gen: no visible global function definition for ‘lm’
cor.gen: no visible binding for global variable ‘sd’
cor.gen: no visible global function definition for ‘cor’
cor.gen: no visible global function definition for ‘write.table’
stat.gen: no visible global function definition for ‘rexp’
stat.gen: no visible global function definition for ‘rnorm’
stat.gen: no visible binding for global variable ‘sd’
stat.gen: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  cor lm resid rexp rnorm sd write.table
Consider adding
  importFrom("stats", "cor", "lm", "resid", "rexp", "rnorm", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Rd file 'cor.gen.Rd':
  \usage lines wider than 90 characters:
     cor.gen(num.subj, x.mean, x.sd, y.mean, y.sd, correlation, data.dec = 2, x.name = "Variable X", y.name = "Variable Y")

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

These lines will be truncated in the PDF manual.
Mort1Dsmooth: no visible global function definition for ‘time’
Mort1Dsmooth: no visible global function definition for ‘glm’
Mort1Dsmooth: no visible binding for global variable ‘poisson’
Mort1Dsmooth_optimize: no visible global function definition for
  ‘median’
Mort2Dsmooth: no visible global function definition for ‘glm’
Mort2Dsmooth: no visible binding for global variable ‘poisson’
Mort2Dsmooth: no visible global function definition for ‘median’
Mort2Dsmooth_optimize: no visible global function definition for
  ‘median’
plot.HMDdata: no visible global function definition for ‘plot’
plot.Mort1Dsmooth: no visible global function definition for ‘matplot’
plot.Mort2Dsmooth: no visible global function definition for ‘quantile’
predict.Mort1Dsmooth: no visible global function definition for ‘glm’
predict.Mort1Dsmooth: no visible binding for global variable ‘poisson’
predict.Mort2Dsmooth: no visible global function definition for ‘glm’
predict.Mort2Dsmooth: no visible binding for global variable ‘poisson’
print.summary.Mort1Dsmooth: no visible global function definition for
  ‘quantile’
print.summary.Mort2Dsmooth: no visible global function definition for
  ‘quantile’
Undefined global functions or variables:
  glm matplot median plot poisson quantile time
Consider adding
  importFrom("graphics", "matplot", "plot")
  importFrom("stats", "glm", "median", "poisson", "quantile", "time")
to your NAMESPACE file.
getmouseDV: no visible global function definition for ‘tail’
interpltraj: no visible global function definition for ‘approx’
trim1: no visible global function definition for ‘tail’
Undefined global functions or variables:
  approx tail
Consider adding
  importFrom("stats", "approx")
  importFrom("utils", "tail")
to your NAMESPACE file.
File ‘moveWindSpeed/libs/moveWindSpeed.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘corpus.useR.2008.abstracts’
Non-standard file/directory found at top level:
  ‘mpa-Ex.R’
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘mpa/R/zzz.R’:
  .First.lib calls:
    cat("\n mpa: CoWords Method")
    cat("\n ")
    cat("\n Universidad Nacional de Colombia")
    cat("\n ")
    cat("\n Elaborado por: Daniel Rodriguez <dhrodriguezt@unal.edu.co>")
    cat("\n                Campo Elias Pardo <cepardot@unal.edu.co>")
    cat("\n For help: ?mpa   \n\n")

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

diagram.mpa: no visible global function definition for ‘plot’
diagram.mpa: no visible global function definition for ‘abline’
diagram.mpa: no visible global function definition for ‘text’
plotmpa: no visible global function definition for ‘plot’
Undefined global functions or variables:
  abline plot text
Consider adding
  importFrom("graphics", "abline", "plot", "text")
to your NAMESPACE file.
File ‘mpbart/libs/mpbart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
mpcv: no visible binding for global variable ‘median’
mpcv: no visible global function definition for ‘cov’
mpcv: no visible global function definition for ‘dist’
plot.mpcv: no visible binding for global variable ‘median’
plot.mpcv: no visible global function definition for ‘par’
plot.mpcv: no visible global function definition for ‘plot’
plot.mpcv: no visible global function definition for ‘rect’
plot.mpcv: no visible global function definition for ‘lines’
plot.mpcv: no visible global function definition for ‘points’
plot.mpcv: no visible global function definition for ‘legend’
Undefined global functions or variables:
  cov dist legend lines median par plot points rect
Consider adding
  importFrom("graphics", "legend", "lines", "par", "plot", "points",
             "rect")
  importFrom("stats", "cov", "dist", "median")
to your NAMESPACE file.
GetExampleData: no visible binding for global variable ‘MPINetData’
Getenvir: no visible binding for global variable ‘MPINetData’
getPSS: no visible global function definition for ‘lines’
performpcls: no visible global function definition for ‘binomial’
Undefined global functions or variables:
  MPINetData binomial lines
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "binomial")
to your NAMESPACE file.
File ‘mpmi/libs/mpmi.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘MASS’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘KernSmooth’ ‘MASS’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
export.summary.mpm: warning in complex(real = x$Rows[, FdimsR[1]], imag
  = x$Rows[, FdimsR[2]]): partial argument match of ‘imag’ to
  ‘imaginary’
export.summary.mpm: warning in complex(real = x$Columns[, FdimsC[1]],
  imag = x$Columns[, FdimsC[2]]): partial argument match of ‘imag’ to
  ‘imaginary’
.onAttach: no visible global function definition for
  ‘packageDescription’
export.summary.mpm: no visible global function definition for
  ‘write.table’
mpm: no visible binding for global variable ‘median’
plot.mpm: no visible global function definition for ‘rainbow’
plot.mpm: no visible global function definition for ‘quantile’
plot.mpm: no visible global function definition for ‘par’
plot.mpm: no visible global function definition for ‘points’
plot.mpm: no visible global function definition for ‘smoothScatter’
plot.mpm: no visible global function definition for ‘colorRampPalette’
plot.mpm: no visible global function definition for ‘symbols’
plot.mpm: no visible global function definition for ‘text’
plot.mpm: no visible global function definition for ‘lines’
plot.mpm: no visible global function definition for ‘box’
Undefined global functions or variables:
  box colorRampPalette lines median packageDescription par points
  quantile rainbow smoothScatter symbols text write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
  importFrom("graphics", "box", "lines", "par", "points",
             "smoothScatter", "symbols", "text")
  importFrom("stats", "median", "quantile")
  importFrom("utils", "packageDescription", "write.table")
to your NAMESPACE file.
place: no visible global function definition for ‘points’
plot,mproc: no visible binding for global variable ‘rainbow’
plot,mproc: no visible global function definition for ‘plot.default’
plot,mproc: no visible global function definition for ‘axis’
plot,mproc: no visible global function definition for ‘points’
Undefined global functions or variables:
  axis plot.default points rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "plot.default", "points")
to your NAMESPACE file.
File ‘mp/libs/mp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
densityfn: no visible global function definition for ‘dnbinom’
densityfn: no visible global function definition for ‘dpois’
densityfn: no visible global function definition for ‘dgeom’
form.add: no visible global function definition for ‘formula’
mreg: no visible global function definition for ‘model.frame’
mreg: no visible global function definition for ‘model.response’
mreg: no visible global function definition for ‘model.matrix’
mreg: no visible global function definition for ‘model.offset’
mreg: no visible global function definition for ‘nlm’
paper: no visible global function definition for ‘model.matrix’
randfn: no visible global function definition for ‘rnbinom’
randfn: no visible global function definition for ‘rpois’
randfn: no visible global function definition for ‘rgeom’
randfn: no visible global function definition for ‘rbinom’
summary.mreg: no visible global function definition for ‘pnorm’
summary.mreg: no visible global function definition for ‘printCoefmat’
Undefined global functions or variables:
  dgeom dnbinom dpois formula model.frame model.matrix model.offset
  model.response nlm pnorm printCoefmat rbinom rgeom rnbinom rpois
Consider adding
  importFrom("stats", "dgeom", "dnbinom", "dpois", "formula",
             "model.frame", "model.matrix", "model.offset",
             "model.response", "nlm", "pnorm", "printCoefmat", "rbinom",
             "rgeom", "rnbinom", "rpois")
to your NAMESPACE file.
File ‘MRH/libs/MRH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mRm/libs/mRm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.MRSP
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘MRSP/libs/MRSP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
MRsurvival: no visible global function definition for ‘rmvnorm’
MRsurvival: no visible global function definition for ‘optim’
MRsurvival : <anonymous>: no visible global function definition for
  ‘quantile’
Undefined global functions or variables:
  optim quantile rmvnorm
Consider adding
  importFrom("stats", "optim", "quantile")
to your NAMESPACE file.
MRwarp: no visible global function definition for ‘dev.new’
MRwarp: no visible global function definition for ‘plot’
MRwarp: no visible global function definition for ‘lines’
MRwarp: no visible global function definition for ‘points’
MRwarp: no visible global function definition for ‘hist’
Undefined global functions or variables:
  dev.new hist lines plot points
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "hist", "lines", "plot", "points")
to your NAMESPACE file.
File ‘MRwarping/libs/MRwarping.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘interfaceRC_warp.o’
File ‘MRwarping/libs/MRwarping.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 use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
msap: no visible global function definition for ‘packageVersion’
msap: no visible global function definition for ‘read.csv’
msap: no visible global function definition for ‘write.csv’
msap: no visible global function definition for ‘sd’
msap: no visible global function definition for ‘wilcox.test’
msap: no visible global function definition for ‘dist’
msap: no visible global function definition for ‘rainbow’
msap: no visible global function definition for ‘png’
msap: no visible global function definition for ‘legend’
msap: no visible global function definition for ‘dev.off’
pcoa: no visible global function definition for ‘cmdscale’
pcoa: no visible global function definition for ‘png’
pcoa: no visible global function definition for ‘par’
pcoa: no visible global function definition for ‘plot’
pcoa: no visible global function definition for ‘rainbow’
pcoa: no visible global function definition for ‘points’
pcoa: no visible global function definition for ‘dev.off’
pcoa: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  cmdscale dev.off dist legend packageVersion par plot png points
  rainbow read.csv sd wilcox.test write.csv
Consider adding
  importFrom("grDevices", "dev.off", "png", "rainbow")
  importFrom("graphics", "legend", "par", "plot", "points")
  importFrom("stats", "cmdscale", "dist", "sd", "wilcox.test")
  importFrom("utils", "packageVersion", "read.csv", "write.csv")
to your NAMESPACE file.
cv.msda: no visible global function definition for ‘predict’
formatoutput: no visible global function definition for ‘new’
msda.prep: no visible global function definition for ‘cov’
plot.msda: no visible global function definition for ‘par’
plot.msda: no visible global function definition for ‘matplot’
plot.msda: no visible global function definition for ‘rainbow’
plot.msda: no visible global function definition for ‘approx’
plot.msda: no visible global function definition for ‘axis’
predict.msda: no visible binding for global variable ‘sd’
predict.msda: no visible global function definition for ‘predict’
zeromat: no visible global function definition for ‘new’
Undefined global functions or variables:
  approx axis cov matplot new par predict rainbow sd
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "matplot", "par")
  importFrom("methods", "new")
  importFrom("stats", "approx", "cov", "predict", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘msda/libs/msda.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘sample’
csv2list: no visible global function definition for ‘read.csv’
kgml_i: no visible global function definition for ‘xmlTreeParse’
kgml_i: no visible global function definition for ‘xmlRoot’
kgml_i: no visible global function definition for ‘xmlAttrs’
list2xml: no visible global function definition for ‘xmlNode’
list2xml: no visible global function definition for ‘append.xmlNode’
msea_ora: no visible global function definition for ‘fisher.test’
msea_ora: no visible global function definition for ‘p.adjust’
msea_sub: no visible global function definition for ‘sd’
msea_sub: no visible global function definition for ‘cor.test’
pathway_class: no visible global function definition for ‘untar’
pca_scaled: no visible binding for global variable ‘sd’
pca_scaled: no visible global function definition for ‘cor.test’
pca_scaled: no visible global function definition for ‘p.adjust’
pca_scaled: no visible binding for global variable ‘var’
read_pathway: no visible global function definition for ‘xmlTreeParse’
read_pathway: no visible global function definition for ‘xmlRoot’
read_pathway: no visible global function definition for ‘xmlToList’
read_pathway: no visible global function definition for ‘xmlAttrs’
Undefined global functions or variables:
  append.xmlNode cor.test fisher.test p.adjust read.csv sd untar var
  xmlAttrs xmlNode xmlRoot xmlToList xmlTreeParse
Consider adding
  importFrom("stats", "cor.test", "fisher.test", "p.adjust", "sd", "var")
  importFrom("utils", "read.csv", "untar")
to your NAMESPACE file.
Depends: includes the non-default packages:
  ‘amap’ ‘clValid’ ‘cluster’ ‘fpc’ ‘mzR’ ‘xcms’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  ‘amap’ ‘clValid’ ‘cluster’ ‘fpc’ ‘xcms’
  Please remove these calls from your code.
'library' or 'require' call to ‘tcltk’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘mzR’ ‘xcms’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls to packages already attached by Depends:
  ‘MSeasy’ ‘tcltk’
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘grDevices’ ‘xcms’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
File ‘MSGLasso/libs/MSGLasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.step.dfgps
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
bic.dfgps: no visible global function definition for ‘var’
coef.dfgps: no visible binding for global variable ‘var’
coef.step.dfgps: no visible binding for global variable ‘var’
coefmat.dfgps: no visible binding for global variable ‘var’
cp.dfgps: no visible global function definition for ‘var’
dfgps: no visible global function definition for ‘complete.cases’
msgps: no visible global function definition for ‘complete.cases’
msgps: no visible global function definition for ‘var’
plot.df: no visible global function definition for ‘plot’
plot.df: no visible global function definition for ‘par’
plot.msgps: no visible global function definition for ‘plot’
plot.msgps: no visible global function definition for ‘par’
plot.msgps: no visible global function definition for ‘abline’
predict.msgps: no visible global function definition for
  ‘complete.cases’
Undefined global functions or variables:
  abline complete.cases par plot var
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "complete.cases", "var")
to your NAMESPACE file.
File ‘msgps/libs/msgps.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
MSIseq.classify: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
BS.var: no visible binding for global variable ‘var’
BS.var: no visible global function definition for ‘cov’
Dist.CIs: no visible global function definition for ‘qnorm’
MSM.CIs: no visible global function definition for ‘qnorm’
plot,msSurv-missing: no visible global function definition for ‘update’
summary,msSurv: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  cov qnorm quantile update var
Consider adding
  importFrom("stats", "cov", "qnorm", "quantile", "update", "var")
to your NAMESPACE file.
'library' or 'require' call to ‘MASS’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Designer.sobol: no visible global function definition for ‘runif’
basicMonteCarlo: no visible global function definition for ‘runif’
lhs003: no visible global function definition for ‘runif’
plmm.mtk : GenereXplmm: no visible binding for global variable ‘poly’
plmm.mtk : calc.plm: no visible global function definition for ‘lm.fit’
plmm.mtk: no visible global function definition for ‘var’
plmm.mtk: no visible global function definition for ‘lm’
plmm.mtk: no visible global function definition for ‘formula’
plmm.mtk: no visible global function definition for ‘update’
plmm.mtk: no visible global function definition for ‘stepAIC’
plot.plmm: no visible global function definition for ‘par’
plot.plmm: no visible global function definition for ‘barplot’
plot.plmm: no visible global function definition for ‘segments’
plot.plmm: no visible global function definition for ‘abline’
plot.plmm: no visible global function definition for ‘title’
plot.plmm: no visible global function definition for ‘legend’
plot.regressionSI: no visible global function definition for ‘par’
plot.regressionSI: no visible global function definition for ‘title’
plot.regressionSI: no visible global function definition for ‘abline’
plot,mtkProcess: no visible global function definition for ‘dev.new’
Undefined global functions or variables:
  abline barplot dev.new formula legend lm lm.fit par poly runif
  segments stepAIC title update var
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "barplot", "legend", "par",
             "segments", "title")
  importFrom("stats", "formula", "lm", "lm.fit", "poly", "runif",
             "update", "var")
to your NAMESPACE file.
File ‘MTS/libs/MTS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.
Packages in Depends field not imported from:
  ‘NightDay’ ‘RSQLite’ ‘XML’ ‘geosphere’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
drawMap: no visible global function definition for ‘plot’
drawMap: no visible global function definition for ‘box’
drawMap: no visible global function definition for ‘points’
getFlights: no visible binding for global variable ‘htmlTreeParse’
getFlights: no visible binding for global variable ‘xpathSApply’
getFlights: no visible binding for global variable ‘xmlAttrs’
getFlights: no visible binding for global variable ‘free’
movie.routes: no visible global function definition for
  ‘txtProgressBar’
movie.routes: no visible global function definition for ‘jpeg’
movie.routes: no visible global function definition for ‘plot’
movie.routes: no visible global function definition for
  ‘setTxtProgressBar’
movie.routes: no visible global function definition for ‘dev.off’
plot.routes: no visible global function definition for ‘plot’
plot.routes: no visible global function definition for ‘points’
plot.routes: no visible global function definition for ‘mtext’
plot.routes : a: no visible global function definition for ‘points’
plot.routes : a: no visible global function definition for ‘text’
plot.routes : a: no visible global function definition for
  ‘gcIntermediate’
plot.routes : a: no visible global function definition for ‘lines’
routes: no visible global function definition for ‘data’
routes: no visible global function definition for ‘distHaversine’
routes: no visible global function definition for ‘gcIntermediate’
Undefined global functions or variables:
  box data dev.off distHaversine free gcIntermediate htmlTreeParse jpeg
  lines mtext plot points setTxtProgressBar text txtProgressBar
  xmlAttrs xpathSApply
Consider adding
  importFrom("grDevices", "dev.off", "jpeg")
  importFrom("graphics", "box", "lines", "mtext", "plot", "points",
             "text")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Rd file 'flights.Rd':
  \usage lines wider than 90 characters:
     flights(from = NULL, to = NULL, path = system.file("MUCflights.RData", package = "MUCflights"))

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

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

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

These lines will be truncated in the PDF manual.
Found the following apparent S3 methods exported but not registered:
  print.pehaz summary.muhaz
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
kphaz.plot: no visible global function definition for ‘stepfun’
muhaz: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx stepfun
Consider adding
  importFrom("stats", "approx", "stepfun")
to your NAMESPACE file.
File ‘muhaz/libs/muhaz.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
multeq.diff: no visible global function definition for ‘cov’
multeq.diff: no visible global function definition for ‘pt’
multeq.diff: no visible global function definition for ‘qt’
multeq.rat: no visible global function definition for ‘cov’
multeq.rat: no visible global function definition for ‘pt’
multeq.rat: no visible global function definition for ‘qt’
Undefined global functions or variables:
  cov pt qt
Consider adding
  importFrom("stats", "cov", "pt", "qt")
to your NAMESPACE file.
plotOptionValues: no visible global function definition for ‘plot’
plotOptionValues: no visible global function definition for ‘persp’
Undefined global functions or variables:
  persp plot
Consider adding
  importFrom("graphics", "persp", "plot")
to your NAMESPACE file.
synthetic_multiband: no visible global function definition for ‘runif’
synthetic_multiband: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
File ‘MultiBD/libs/MultiBD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
betas_plot: no visible global function definition for ‘cov2cor’
betas_plot: no visible global function definition for
  ‘colorRampPalette’
betas_plot: no visible global function definition for ‘pdf’
betas_plot: no visible global function definition for ‘dev.off’
mhplot: no visible global function definition for ‘read.table’
mhplot: no visible global function definition for ‘pdf’
mhplot: no visible global function definition for ‘plot’
mhplot: no visible global function definition for ‘points’
mhplot: no visible global function definition for ‘abline’
mhplot: no visible global function definition for ‘axis’
mhplot: no visible global function definition for ‘dev.off’
multi_meta: no visible global function definition for ‘write.table’
multi_meta: no visible global function definition for ‘read.table’
multi_meta: no visible global function definition for ‘pchisq’
qqplotter: no visible global function definition for ‘read.table’
qqplotter: no visible global function definition for ‘qchisq’
qqplotter: no visible global function definition for ‘ppoints’
qqplotter: no visible global function definition for ‘median’
qqplotter: no visible global function definition for ‘pchisq’
qqplotter: no visible global function definition for ‘pdf’
qqplotter: no visible global function definition for ‘plot’
qqplotter: no visible global function definition for ‘abline’
qqplotter: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  abline axis colorRampPalette cov2cor dev.off median pchisq pdf plot
  points ppoints qchisq read.table write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf")
  importFrom("graphics", "abline", "axis", "plot", "points")
  importFrom("stats", "cov2cor", "median", "pchisq", "ppoints", "qchisq")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
multinb.fit: no visible global function definition for ‘nlminb’
multinbmod: no visible global function definition for ‘is.empty.model’
multinbmod: no visible global function definition for ‘model.matrix’
multinbmod: no visible binding for global variable ‘contrasts’
multinbmod: no visible global function definition for ‘model.response’
multinbmod: no visible global function definition for ‘model.offset’
Undefined global functions or variables:
  contrasts is.empty.model model.matrix model.offset model.response
  nlminb
Consider adding
  importFrom("stats", "contrasts", "is.empty.model", "model.matrix",
             "model.offset", "model.response", "nlminb")
to your NAMESPACE file.
.moments: no visible global function definition for ‘ppois’
.truncpoi: no visible global function definition for ‘ppois’
Undefined global functions or variables:
  ppois
Consider adding
  importFrom("stats", "ppois")
to your NAMESPACE file.
Package in Depends field not imported from: ‘rgenoud’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.onAttach: no visible global function definition for
  ‘packageDescription’
genoudRob: no visible global function definition for ‘genoud’
get.XYdata: no visible global function definition for ‘terms’
get.xdata: no visible global function definition for ‘terms’
get.xdata: no visible global function definition for ‘model.matrix’
get.xy: no visible global function definition for ‘terms’
get.xynames: no visible global function definition for ‘terms’
get.ydata: no visible global function definition for ‘terms’
get.ydata: no visible global function definition for ‘model.response’
get.ydata: no visible global function definition for ‘model.frame’
mt.dev: no visible global function definition for ‘pt’
mt.dev.grad: no visible global function definition for ‘pt’
mt.dev.grad: no visible global function definition for ‘dt’
mt.mle: no visible global function definition for ‘optim’
multinomRob: no visible global function definition for ‘var’
plot.multinomRob: no visible global function definition for ‘par’
plot.multinomRob: no visible global function definition for ‘plot’
plot.multinomRob: no visible global function definition for ‘title’
rdirich: no visible global function definition for ‘rgamma’
residual.generator: no visible global function definition for ‘median’
rmultinomial: no visible global function definition for ‘runif’
rmultinomial: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  dt genoud median model.frame model.matrix model.response optim
  packageDescription par plot pt rbinom rgamma runif terms title var
Consider adding
  importFrom("graphics", "par", "plot", "title")
  importFrom("stats", "dt", "median", "model.frame", "model.matrix",
             "model.response", "optim", "pt", "rbinom", "rgamma",
             "runif", "terms", "var")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
File ‘multinomRob/libs/multinomRob.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
multiPIM : expand.factors: no visible global function definition for
  ‘formula’
multiPIM : expand.factors: no visible global function definition for
  ‘model.matrix’
multiPIM : <anonymous>: no visible global function definition for ‘glm’
multiPIM : <anonymous>: no visible binding for global variable
  ‘binomial’
multiPIM : <anonymous>: no visible global function definition for
  ‘qlogis’
multiPIM : <anonymous>: no visible global function definition for
  ‘as.formula’
multiPIM : <anonymous>: no visible global function definition for ‘lm’
multiPIM: no visible global function definition for ‘glm’
multiPIM: no visible global function definition for ‘qlogis’
multiPIM: no visible binding for global variable ‘binomial’
multiPIM: no visible global function definition for ‘plogis’
multiPIM: no visible global function definition for ‘sd’
multiPIM: no visible global function definition for ‘lm’
summary.multiPIM: no visible binding for global variable ‘sd’
summary.multiPIM: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as.formula binomial formula glm lm model.matrix plogis pnorm qlogis
  sd
Consider adding
  importFrom("stats", "as.formula", "binomial", "formula", "glm", "lm",
             "model.matrix", "plogis", "pnorm", "qlogis", "sd")
to your NAMESPACE file.
CCM_boot : <anonymous>: no visible global function definition for ‘sd’
SSR_check_signal: no visible global function definition for ‘cor’
SSR_check_signal: no visible global function definition for ‘cor.test’
SSR_check_signal: no visible global function definition for ‘lm’
SSR_pred_boot: no visible global function definition for ‘cor’
make_ccm_data: no visible global function definition for ‘rnorm’
make_ccm_data: no visible global function definition for ‘runif’
make_ccm_data: no visible global function definition for ‘rlnorm’
Undefined global functions or variables:
  cor cor.test lm rlnorm rnorm runif sd
Consider adding
  importFrom("stats", "cor", "cor.test", "lm", "rlnorm", "rnorm",
             "runif", "sd")
to your NAMESPACE file.
File ‘multispatialCCM/libs/multispatialCCM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
PrbMlt.default: no visible binding for global variable ‘na.omit’
PrbMlt.default: no visible global function definition for ‘anova’
Undefined global functions or variables:
  anova na.omit
Consider adding
  importFrom("stats", "anova", "na.omit")
to your NAMESPACE file.
File ‘multxpert/R/zzz.R’:
  .onLoad calls:
    cat("multxpert: Implementation of commonly used p-value based and parametric\n",     "multiple testing procedures and parallel gatekeeping procedures.\n",     "For more information visit http://multxpert.com/wiki/MultXpert_package\n",     sep = "")

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

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

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

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

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

These lines will be truncated in the PDF manual.
plotFID: no visible global function definition for ‘plot’
plotFID: no visible global function definition for ‘points’
Undefined global functions or variables:
  plot points
Consider adding
  importFrom("graphics", "plot", "points")
to your NAMESPACE file.
prentice.test: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
mvb.simu: no visible global function definition for ‘runif’
plot.lps: no visible global function definition for ‘matplot’
unifit: no visible global function definition for ‘model.frame’
unifit: no visible global function definition for ‘model.matrix’
unifit: no visible global function definition for ‘model.response’
unilps: no visible global function definition for ‘model.frame’
unilps: no visible global function definition for ‘model.matrix’
unilps: no visible global function definition for ‘model.response’
Undefined global functions or variables:
  matplot model.frame model.matrix model.response runif
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "runif")
to your NAMESPACE file.
File ‘MVB/libs/MVB.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 which should be '::':
  ‘base:::call’ ‘base:::importIntoEnv’ ‘base:::lockEnvironment’
  ‘base:::match.call’ ‘base:::print.default’ ‘base:::print.function’
  ‘tools:::Rd2txt’ ‘utils:::?’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘tools:::.Rd_get_metadata’ ‘tools:::.get_package_metadata’
  ‘tools:::.install_package_Rd_indices’
  ‘tools:::.install_package_Rd_objects’
  ‘tools:::.install_package_description’
  ‘tools:::.install_package_namespace_info’ ‘tools:::.read_description’
  ‘tools:::.writePkgIndices’ ‘tools:::.writeVignetteHtmlIndex’
  ‘tools:::RdTags’ ‘tools:::fetchRdDB’ ‘tools:::makeLazyLoadDB’
  ‘tools:::prepare_Rd’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘Save’ ‘body.print.function’ ‘cd’ ‘rbind.data.frame’
  ‘search.task.trees’ ‘untetherBalloon’
Found the following apparent S3 methods exported but not registered:
  plot.cdtree plot.foodweb
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘mvcluster/libs/mvcluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
conceptIndicesSkm: no visible global function definition for
  ‘txtProgressBar’
conceptIndicesSkm: no visible global function definition for
  ‘setTxtProgressBar’
conceptVectorsSkm: no visible global function definition for
  ‘txtProgressBar’
conceptVectorsSkm: no visible global function definition for
  ‘setTxtProgressBar’
mvcmb: no visible global function definition for ‘runif’
mvcmb: no visible global function definition for ‘str’
mvcsph: no visible global function definition for ‘pdf’
mvcsph: no visible global function definition for ‘heatmap’
mvcsph: no visible global function definition for ‘dev.off’
mvcsph: no visible global function definition for ‘hclust’
mvcsph: no visible global function definition for ‘dist’
mvcsph: no visible global function definition for ‘str’
Undefined global functions or variables:
  dev.off dist hclust heatmap pdf runif setTxtProgressBar str
  txtProgressBar
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("stats", "dist", "hclust", "heatmap", "runif")
  importFrom("utils", "setTxtProgressBar", "str", "txtProgressBar")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  contour.mvcwt image.mvcwt plot.mvcwt
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
contour.mvcwt: no visible global function definition for ‘par’
get.min.scale: no visible global function definition for ‘median’
image.mvcwt: no visible global function definition for ‘par’
plot.mvcwt: no visible global function definition for ‘par’
print.mvcwt: no visible global function definition for ‘str’
Undefined global functions or variables:
  median par str
Consider adding
  importFrom("graphics", "par")
  importFrom("stats", "median")
  importFrom("utils", "str")
to your NAMESPACE file.
File ‘mvnmle/libs/mvnmle.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
mvnpermute: no visible global function definition for ‘lm’
mvnpermute: no visible global function definition for ‘coef’
mvnpermute: no visible global function definition for ‘resid’
Undefined global functions or variables:
  coef lm resid
Consider adding
  importFrom("stats", "coef", "lm", "resid")
to your NAMESPACE file.
mvorpb: no visible global function definition for ‘pnorm’
mvorpb: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm pnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm")
to your NAMESPACE file.
rtn: no visible global function definition for ‘runif’
rtn: no visible global function definition for ‘qnorm’
rtn: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm runif
Consider adding
  importFrom("stats", "pnorm", "qnorm", "runif")
to your NAMESPACE file.
File ‘mvrtn/libs/mvrtn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: mvsf.Rd:16-17: Dropping empty section \details
mvtmeta_fe: no visible global function definition for ‘combinations’
Undefined global functions or variables:
  combinations
'library' or 'require' call to ‘RColorBrewer’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘RColorBrewer’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plot.matchedwake: no visible global function definition for
  ‘filled.contour’
plot.matchedwake: no visible binding for global variable ‘gray.colors’
plot.matchedwake: no visible global function definition for ‘axis’
plot.matchedwake: no visible global function definition for ‘rect’
slideWakeMatch: no visible binding for global variable ‘lm’
slideWakeMatch: no visible global function definition for ‘as.formula’
slideWakeMatch: no visible global function definition for ‘summary.glm’
Undefined global functions or variables:
  as.formula axis filled.contour gray.colors lm rect summary.glm
Consider adding
  importFrom("grDevices", "gray.colors")
  importFrom("graphics", "axis", "filled.contour", "rect")
  importFrom("stats", "as.formula", "lm", "summary.glm")
to your NAMESPACE file.
mxkssd: no visible global function definition for ‘txtProgressBar’
mxkssd: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
abcpred_nmer: no visible global function definition for ‘write.table’
algpred: no visible global function definition for ‘read.table’
algpred: no visible global function definition for ‘write.table’
allermatch: no visible global function definition for ‘read.table’
allermatch: no visible global function definition for ‘write.table’
bcepred_nmer: no visible global function definition for ‘write.table’
bimas_nmer: no visible global function definition for ‘write.table’
filter.firstlayer: no visible global function definition for
  ‘read.table’
filter.firstlayer: no visible global function definition for
  ‘write.table’
iedb_arb_mhci_nmer: no visible global function definition for
  ‘write.table’
iedb_arb_mhcii_nmer: no visible global function definition for
  ‘write.table’
iedb_consensus_mhci_nmer: no visible global function definition for
  ‘write.table’
iedb_consensus_mhcii_nmer: no visible global function definition for
  ‘write.table’
netmhcNN_nmer: no visible global function definition for ‘write.table’
netmhcWT_nmer: no visible global function definition for ‘write.table’
propred_nmer: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
update_episode: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
Rd file 'myepisodes_feed_url.Rd':
  \examples lines wider than 100 characters:
     ## Not run: myepisodes_feed_url("foouser", "321654321654321", feed = "mylist", onlyunacquired = TRUE, showignored = FALSE)

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

These lines will be truncated in the PDF manual.
abs_dif: no visible global function definition for ‘as.formula’
env_dif: no visible global function definition for ‘lm’
env_dif: no visible global function definition for ‘as.formula’
env_dif_logistic: no visible global function definition for
  ‘as.formula’
fam_env: no visible global function definition for ‘as.formula’
log_dif: no visible global function definition for ‘as.formula’
Undefined global functions or variables:
  as.formula lm
Consider adding
  importFrom("stats", "as.formula", "lm")
to your NAMESPACE file.
File ‘namespace/libs/namespace.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  Functions.cpp:702:39: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  Functions.cpp:702:66: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/NAM.Rcheck/00install.out’ for details.
File ‘nanop/libs/nanop.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
NAPPA: no visible binding for global variable ‘sd’
NAPPA: no visible global function definition for ‘sd’
calibrate.sigmoid.curve : <anonymous> : <anonymous>: no visible global
  function definition for ‘coef’
calibrate.sigmoid.curve : <anonymous> : <anonymous>: no visible global
  function definition for ‘lm’
calibrate.sigmoid.curve: no visible global function definition for
  ‘nls’
calibrate.sigmoid.curve: no visible binding for global variable
  ‘weights’
calibrate.sigmoid.curve: no visible global function definition for
  ‘coef’
calibrate.sigmoid.curve: no visible global function definition for
  ‘plot’
calibrate.sigmoid.curve: no visible global function definition for
  ‘rgb’
calibrate.sigmoid.curve: no visible global function definition for
  ‘box’
calibrate.sigmoid.curve: no visible global function definition for
  ‘axis’
calibrate.sigmoid.curve: no visible global function definition for
  ‘abline’
calibrate.sigmoid.curve: no visible global function definition for
  ‘lines’
calibrate.sigmoid.curve: no visible global function definition for
  ‘predict’
calibrate.sigmoid.curve: no visible global function definition for
  ‘smooth.spline’
calibrate.sigmoid.curve : <anonymous>: no visible global function
  definition for ‘nls’
calibrate.sigmoid.curve : <anonymous>: no visible binding for global
  variable ‘weights’
calibrate.sigmoid.curve: no visible binding for global variable ‘coef’
calibrate.sigmoid.curve: no visible global function definition for ‘pf’
calibrate.sigmoid.curve: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  abline axis box coef legend lines lm nls pf plot predict rgb sd
  smooth.spline weights
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "abline", "axis", "box", "legend", "lines",
             "plot")
  importFrom("stats", "coef", "lm", "nls", "pf", "predict", "sd",
             "smooth.spline", "weights")
to your NAMESPACE file.
File ‘nbpMatching/libs/nbpMatching.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
NB.estimator: no visible global function definition for ‘optimize’
NB.estimator: no visible global function definition for ‘uniroot’
NB.example.dataset: no visible global function definition for
  ‘write.table’
NB.plot.likelihood: no visible global function definition for ‘plot’
Undefined global functions or variables:
  optimize plot uniroot write.table
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "optimize", "uniroot")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following significant warnings:

  Warning: '%+%' is deprecated.
  Warning: '%+%' is deprecated.
  Warning: '%+%' is deprecated.
  Warning: '%+%' is deprecated.
  Warning: '%+%' is deprecated.
  Warning: '%+%' is deprecated.
  Warning: '%+%' is deprecated.
  Warning: '%+%' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
ncbit : FUN: no visible global function definition for ‘read.table’
ncbit : FUN: no visible global function definition for ‘head’
Undefined global functions or variables:
  head read.table
Consider adding
  importFrom("utils", "head", "read.table")
to your NAMESPACE file.
get.split.filename.cmip5: no visible global function definition for
  ‘tail’
nc.conform.data : <anonymous>: no visible global function definition
  for ‘na.omit’
nc.get.subset.recursive: no visible global function definition for
  ‘head’
nc.get.subset.recursive: no visible global function definition for
  ‘tail’
nc.put.subset.recursive: no visible global function definition for
  ‘head’
nc.put.subset.recursive: no visible global function definition for
  ‘tail’
Undefined global functions or variables:
  head na.omit tail
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
infoNcdfVars: no visible global function definition for ‘na.omit’
modifyNcdfDefAtts: no visible global function definition for ‘na.omit’
plotDatacube: no visible global function definition for ‘runif’
plotDatacube: no visible global function definition for
  ‘colorRampPalette’
plotDatacube: no visible global function definition for ‘dev.cur’
plotDatacube: no visible global function definition for ‘dev.new’
plotDatacube: no visible global function definition for ‘layout’
plotDatacube: no visible global function definition for ‘par’
plotDatacube: no visible global function definition for ‘points’
plotDatacube: no visible global function definition for ‘text’
plotDatacube: no visible global function definition for ‘plot.new’
plotDatacube: no visible global function definition for ‘mtext’
plotDatacube: no visible global function definition for ‘rgb’
plotDatacube: no visible global function definition for ‘legend’
transNcdfRotate: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  colorRampPalette dev.cur dev.new layout legend mtext na.omit par
  plot.new points rgb runif text
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.cur", "dev.new",
             "rgb")
  importFrom("graphics", "layout", "legend", "mtext", "par", "plot.new",
             "points", "text")
  importFrom("stats", "na.omit", "runif")
to your NAMESPACE file.
d0: no visible global function definition for ‘qnorm’
dncgamma: no visible global function definition for ‘dpois’
indncgamma: no visible global function definition for ‘pgamma’
indncgamma: no visible global function definition for ‘dpois’
inxncgamma: no visible global function definition for ‘qnorm’
inxncgamma: no visible global function definition for ‘pgamma’
inxncgamma: no visible global function definition for ‘dpois’
pncgamma: no visible global function definition for ‘pgamma’
pncgamma: no visible global function definition for ‘dpois’
Undefined global functions or variables:
  dpois pgamma qnorm
Consider adding
  importFrom("stats", "dpois", "pgamma", "qnorm")
to your NAMESPACE file.
File ‘ndl/libs/ndl.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘neariso/libs/neariso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.reduction: no visible global function definition for ‘prcomp’
data.reduction: no visible global function definition for ‘hclust’
data.reduction: no visible global function definition for ‘as.dist’
data.reduction: no visible global function definition for ‘cor’
data.reduction: no visible global function definition for ‘dist’
heatmap1: no visible global function definition for ‘sd’
lineplot: no visible global function definition for ‘sd’
normalize: no visible global function definition for ‘sd’
profileplot3d : ColorFunction: no visible global function definition
  for ‘rgb’
profileplot3d : ColorFunction: no visible global function definition
  for ‘colorRamp’
profileplot3d: no visible global function definition for ‘sd’
profileplot3d: no visible global function definition for ‘gray’
Undefined global functions or variables:
  as.dist colorRamp cor dist gray hclust prcomp rgb sd
Consider adding
  importFrom("grDevices", "colorRamp", "gray", "rgb")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "prcomp", "sd")
to your NAMESPACE file.
File ‘NeatMap/libs/NeatMap.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘nMDS_R.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘nMDS_R.o’
File ‘NeatMap/libs/NeatMap.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 use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
population: no visible global function definition for ‘weighted.mean’
population: no visible global function definition for ‘rpois’
population: no visible global function definition for ‘lm’
population: no visible global function definition for ‘coefficients’
population: no visible global function definition for ‘sd’
population: no visible global function definition for ‘par’
population: no visible global function definition for ‘plot’
population: no visible global function definition for ‘lines’
Undefined global functions or variables:
  coefficients lines lm par plot rpois sd weighted.mean
Consider adding
  importFrom("graphics", "lines", "par", "plot")
  importFrom("stats", "coefficients", "lm", "rpois", "sd",
             "weighted.mean")
to your NAMESPACE file.
The following files look like leftovers/mistakes:
  ‘Rplots.pdf’, ‘Rplots.ps’
Please remove them from your package.
nestedRanksTest.default: no visible global function definition for
  ‘setNames’
nestedRanksTest.default: no visible global function definition for
  ‘quantile’
nestedRanksTest.formula: no visible global function definition for
  ‘terms’
plot.htest_boot: no visible global function definition for ‘hist’
plot.htest_boot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline hist quantile setNames terms
Consider adding
  importFrom("graphics", "abline", "hist")
  importFrom("stats", "quantile", "setNames", "terms")
to your NAMESPACE file.
clustConfigurations: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
File ‘netcoh/libs/netcoh.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
netVal: no visible global function definition for ‘cutree’
netVal: no visible global function definition for ‘hclust’
netVal: no visible global function definition for ‘as.dist’
Undefined global functions or variables:
  as.dist cutree hclust
Consider adding
  importFrom("stats", "as.dist", "cutree", "hclust")
to your NAMESPACE file.
File ‘NetComp/libs/NetComp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘buildcmds’
EnvInd: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: ‘fastshp’
File ‘NetPreProc/libs/NetPreProc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
balloon: no visible global function definition for ‘convolve’
physnoise: no visible global function definition for ‘sd’
physnoise: no visible global function definition for ‘rnorm’
rrice: no visible global function definition for ‘rnorm’
simTSrestingstate: no visible global function definition for ‘runif’
simTSrestingstate: no visible global function definition for ‘fft’
spatialnoise: no visible global function definition for ‘rnorm’
spatialnoise: no visible global function definition for ‘qgamma’
spatialnoise: no visible global function definition for ‘pnorm’
specifydesign: no visible global function definition for ‘convolve’
systemnoise: no visible global function definition for ‘rnorm’
tasknoise: no visible global function definition for ‘rnorm’
tasknoise: no visible global function definition for ‘sd’
temporalnoise: no visible global function definition for ‘arima.sim’
Undefined global functions or variables:
  arima.sim convolve fft pnorm qgamma rnorm runif sd
Consider adding
  importFrom("stats", "arima.sim", "convolve", "fft", "pnorm", "qgamma",
             "rnorm", "runif", "sd")
to your NAMESPACE file.
File ‘neuRosim/libs/neuRosim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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’ ‘boot’ ‘lattice’ ‘psych’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
nfca : nFCAmain: no visible global function definition for ‘hist’
nfca : nFCAmain: no visible global function definition for
  ‘flush.console’
nfca : nFCAmain: no visible global function definition for ‘qnorm’
nfca : nFCAmain: no visible global function definition for ‘read.csv’
nfca : nFCAmain: no visible global function definition for ‘cor’
nfca : nFCAmain: no visible global function definition for ‘as.dist’
nfca : nFCAmain: no visible global function definition for ‘cophenetic’
nfca : nFCAmain: no visible global function definition for ‘hclust’
nfca : thresholdTEST: no visible global function definition for
  ‘read.csv’
nfca : gScript: no visible global function definition for ‘read.csv’
nfca : gScript0: no visible global function definition for ‘read.csv’
nfca : gMatrix: no visible global function definition for ‘read.csv’
nfca: no visible global function definition for ‘cor’
Undefined global functions or variables:
  as.dist cophenetic cor flush.console hclust hist qnorm read.csv
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "as.dist", "cophenetic", "cor", "hclust", "qnorm")
  importFrom("utils", "flush.console", "read.csv")
to your NAMESPACE file.
Package suggested but not available for checking: ‘NFPdata’
compare.CDF: no visible global function definition for ‘quantile’
download.single.game: no visible global function definition for
  ‘download.file’
fit.shot.probs.simple: no visible global function definition for
  ‘predict’
integrate.old.pieces: no visible global function definition for
  ‘na.omit’
prob.score.simple.objects: no visible global function definition for
  ‘binomial’
prob.score.simple.objects: no visible binding for global variable
  ‘logit’
prob.score.simple.objects: no visible global function definition for
  ‘predict’
process.pl.new: no visible global function definition for ‘na.omit’
read.gif: no visible global function definition for ‘download.file’
read.gif: no visible global function definition for ‘rgb’
solver.with.nlm: no visible global function definition for ‘nlm’
team.table : thisplot: no visible global function definition for ‘par’
team.table : thisplot: no visible global function definition for ‘plot’
team.table : thisplot: no visible global function definition for ‘text’
team.table : thisplot: no visible global function definition for
  ‘abline’
Undefined global functions or variables:
  abline binomial download.file logit na.omit nlm par plot predict
  quantile rgb text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "abline", "par", "plot", "text")
  importFrom("stats", "binomial", "na.omit", "nlm", "predict",
             "quantile")
  importFrom("utils", "download.file")
to your NAMESPACE file.
File ‘nhlscrapr/libs/nhlscrapr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
nlmeODE: no visible global function definition for ‘deriv’
Undefined global functions or variables:
  deriv
Consider adding
  importFrom("stats", "deriv")
to your NAMESPACE file.
Pwr.lme: no visible global function definition for ‘anova’
Pwr.lme: no visible global function definition for ‘qf’
Pwr.lme: no visible global function definition for ‘pf’
logLik1.lme: no visible global function definition for ‘coef’
logLik1.lme: no visible global function definition for ‘model.matrix’
logLik1.lme: no visible global function definition for ‘predict’
logLik1.lme: no visible global function definition for ‘formula’
runScript: no visible binding for global variable ‘example’
sigmaTolme: no visible global function definition for ‘vcov’
simulateY.lme: no visible global function definition for ‘runif’
simulateY.lme: no visible global function definition for ‘fitted’
simulateY.lme: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  anova coef example fitted formula model.matrix pf predict qf rnorm
  runif vcov
Consider adding
  importFrom("stats", "anova", "coef", "fitted", "formula",
             "model.matrix", "pf", "predict", "qf", "rnorm", "runif",
             "vcov")
  importFrom("utils", "example")
to your NAMESPACE file.
File ‘nloptr/libs/nloptr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  all.profiles.nlreg fitted.values.nlreg
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Package in Depends field not imported from: ‘proto’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘stats:::nlsModel’ ‘stats:::nlsModel.plinear’
  See the note in ?`:::` about the use of this operator.
nls2: no visible global function definition for ‘nls.control’
nls2: no visible global function definition for ‘as.formula’
nls2: no visible global function definition for ‘coef’
nls2: no visible global function definition for ‘runif’
nls2 : <anonymous>: no visible global function definition for
  ‘deviance’
Undefined global functions or variables:
  as.formula coef deviance nls.control runif
Consider adding
  importFrom("stats", "as.formula", "coef", "deviance", "nls.control",
             "runif")
to your NAMESPACE file.
Rd file 'smsn.nl.Rd':
  \usage lines wider than 90 characters:
             nu = NULL, nlf = NULL, rho.func = 1, reg.type = "Homoscedastic", criteria = FALSE, 

These lines will be truncated in the PDF manual.
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(nlstimedist)
  > 
  > test_check("nlstimedist")
  ── 1. Failure: Ensure the glance method is returning expected values (@test-glan
  `out` not equal to `expect`.
  Rows in x but not y: 1. Rows in y but not x: 1. 
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 6 SKIPPED: 0 FAILED: 1
  1. Failure: Ensure the glance method is returning expected values (@test-glance.timedist.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘nmfgpu4R/libs/nmfgpu4R.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
makeRules: no visible global function definition for ‘sd’
makeRules: no visible global function definition for ‘rnorm’
nodeHarvest: no visible global function definition for ‘capture.output’
nodeHarvest: no visible global function definition for ‘lm’
nodeHarvest: no visible global function definition for ‘coef’
plot.nodeHarvest: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  capture.output coef lm rgb rnorm sd
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "coef", "lm", "rnorm", "sd")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Running examples in ‘nomine-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_ethnicities
> ### Title: Classifies names based on 6 U.S. ethnicities
> ### Aliases: get_ethnicities
> 
> ### ** Examples
> 
> x <- c("Charles Crabtree", "Volha Chykina")
> y <- get_ethnicities(x)

  |                                                                            
  |                                                                      |   0%Error in r[[5]] : subscript out of bounds
Calls: get_ethnicities
Execution halted
File ‘noncompliance/libs/noncompliance.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 not declared from:
  ‘AER’ ‘MASS’ ‘faraway’ ‘mlogit’ ‘ordinal’ ‘pscl’
'data(package=)' calls not declared from:
  ‘AER’ ‘MASS’ ‘mlogit’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
This is lavaan 0.6-2
lavaan is BETA software! Please report any bugs.
This is nonnest2 0.5-1.
nonnest2 has not been tested with all combinations of model classes.
Quitting from lines 64-65 (nonnest2.Rmd) 
Error: processing vignette ‘nonnest2.Rmd’ failed with diagnostics:
no applicable method for ‘estfun’ applied to an object of class "lavaan"
Execution halted
Depends: includes the non-default packages:
  ‘lpSolve’ ‘gdata’ ‘Hmisc’ ‘rms’ ‘geometry’ ‘psych’ ‘pwt’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  ‘Hmisc’ ‘gdata’ ‘geometry’ ‘lpSolve’ ‘psych’ ‘rms’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Hmisc’ ‘gdata’ ‘geometry’ ‘lpSolve’ ‘psych’ ‘pwt’ ‘rms’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
additive: no visible global function definition for ‘lp’
ar.dual.dea: no visible global function definition for ‘lp’
cost.dea: no visible global function definition for ‘lp’
ddf: no visible global function definition for ‘lp’
dea: no visible global function definition for ‘lp’
direc.dea: no visible global function definition for ‘lp’
dual.dea: no visible global function definition for ‘lp’
effdea.b.f: no visible global function definition for ‘convhulln’
effdea.b.f: no visible global function definition for ‘lp’
faremalm2: no visible binding for global variable ‘Lag’
faremalm2: no visible global function definition for ‘na.omit’
int.dea: no visible global function definition for ‘lp’
lp2: no visible global function definition for ‘lp’
revenue.dea: no visible global function definition for ‘lp’
sbm.tone: no visible global function definition for ‘lp’
sbm.vrs: no visible global function definition for ‘lp’
Undefined global functions or variables:
  Lag convhulln lp na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
'library' or 'require' call to ‘colorspace’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  plot.pscore plot.stdf
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘nontarget/libs/nontarget.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘histogram’ ‘optimx’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dnormgam: no visible global function definition for ‘qgamma’
dnormgam: no visible global function definition for ‘fft’
dnormgam: no visible global function definition for ‘dgamma’
dnormgam: no visible global function definition for ‘approx’
normgam.fit : mkdfftNormalGammaOptim : <anonymous>: no visible global
  function definition for ‘dnorm’
normgam.fit : estimation_param_normexp_RMA : max.density: no visible
  global function definition for ‘density’
normgam.fit: no visible global function definition for ‘sd’
normgam.fit: no visible global function definition for ‘median’
normgam.fit: no visible global function definition for ‘IQR’
normgam.fit: no visible global function definition for ‘optimx’
normgam.fit: no visible global function definition for ‘coef’
normgam.signal: no visible global function definition for ‘approx’
normgam.signal: no visible global function definition for ‘hist’
Undefined global functions or variables:
  IQR approx coef density dgamma dnorm fft hist median optimx qgamma sd
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "IQR", "approx", "coef", "density", "dgamma",
             "dnorm", "fft", "median", "qgamma", "sd")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  lmp.default paramp.default plot.lmp plot.simul.lmp plot.simul.mp
  print.paramp print.simul.mp print.summary.lmp print.summary.simul.lmp
  qqnormp.default summary.lmp summary.simul.lmp
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Running examples in ‘normalp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lmp
> ### Title: Fitted linear model with exponential power distribution errors
> ### Aliases: lmp lmp.default
> ### Keywords: regression
> 
> ### ** Examples
> 
> e<-rnormp(n=100,mu=0,sigmap=4,p=3,method="d")
> x<-runif(100)
> y<-0.5+2*x+e
> lmp(y~x)
Error in UseMethod("lmp") : 
  no applicable method for 'lmp' applied to an object of class "formula"
Calls: lmp
Execution halted
File ‘norm/libs/norm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘NORMT3/libs/NORMT3.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
ajb.norm.test: no visible global function definition for ‘rnorm’
frosini.norm.test: no visible global function definition for ‘var’
frosini.norm.test: no visible global function definition for ‘pnorm’
frosini.norm.test: no visible global function definition for ‘rnorm’
geary.norm.test: no visible global function definition for ‘rnorm’
hegazy1.norm.test: no visible global function definition for ‘var’
hegazy1.norm.test: no visible global function definition for ‘qnorm’
hegazy1.norm.test: no visible global function definition for ‘rnorm’
hegazy2.norm.test: no visible global function definition for ‘var’
hegazy2.norm.test: no visible global function definition for ‘qnorm’
hegazy2.norm.test: no visible global function definition for ‘rnorm’
jb.norm.test: no visible global function definition for ‘rnorm’
kurtosis.norm.test: no visible global function definition for ‘rnorm’
skewness.norm.test: no visible global function definition for ‘rnorm’
spiegelhalter.norm.test: no visible global function definition for
  ‘rnorm’
wb.norm.test: no visible global function definition for ‘qnorm’
wb.norm.test: no visible global function definition for ‘var’
wb.norm.test: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  pnorm qnorm rnorm var
Consider adding
  importFrom("stats", "pnorm", "qnorm", "rnorm", "var")
to your NAMESPACE file.
normality.test1: no visible global function definition for ‘cov.wt’
normality.test1: no visible global function definition for ‘cor’
normality.test1: no visible global function definition for ‘pnorm’
normality.test1: no visible global function definition for ‘pchisq’
normality.test2: no visible global function definition for ‘cov.wt’
normality.test2: no visible global function definition for ‘cor’
normality.test2: no visible global function definition for ‘acf’
normality.test2: no visible global function definition for ‘pnorm’
normality.test2: no visible global function definition for ‘pchisq’
whitenoise.test: no visible global function definition for ‘acf’
whitenoise.test: no visible global function definition for ‘spec.pgram’
whitenoise.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  acf cor cov.wt pchisq pnorm spec.pgram
Consider adding
  importFrom("stats", "acf", "cor", "cov.wt", "pchisq", "pnorm",
             "spec.pgram")
to your NAMESPACE file.
CIPW: no visible global function definition for ‘data’
CIPW: no visible binding for global variable ‘AtomWeight’
CIPW: no visible binding for global variable ‘MinWeight’
CIPW: no visible binding for global variable ‘OxiWeight’
CIPW.trace: no visible global function definition for ‘data’
CIPW.trace: no visible binding for global variable ‘AtomWeight’
CIPW.trace: no visible binding for global variable ‘MinWeight’
CIPW.trace: no visible binding for global variable ‘OxiWeight’
Undefined global functions or variables:
  AtomWeight MinWeight OxiWeight data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
BoundingRA: no visible global function definition for ‘rnorm’
check_y_estimator: no visible global function definition for ‘rnorm’
genNORTARA: no visible global function definition for ‘rnorm’
genNORTARA: no visible global function definition for ‘pnorm’
valid_input_cormat: no visible global function definition for ‘rnorm’
valid_input_cormat: no visible global function definition for ‘pnorm’
valid_input_cormat: no visible global function definition for ‘cor’
y_control_estimator: no visible global function definition for ‘pnorm’
y_control_estimator: no visible global function definition for ‘cor’
y_control_estimator : <anonymous>: no visible global function
  definition for ‘cor’
y_control_estimator: no visible global function definition for ‘cov’
y_control_estimator: no visible global function definition for ‘var’
y_crude_estimator: no visible global function definition for ‘pnorm’
y_crude_estimator: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor cov pnorm rnorm var
Consider adding
  importFrom("stats", "cor", "cov", "pnorm", "rnorm", "var")
to your NAMESPACE file.
Rd file 'notifyR-package.Rd':
  \examples lines wider than 100 characters:
     send_push(userkey,message="finished.",title="World Simulation",url="http://www.myRresults.com/",url_title="View Results online.",priori ... [TRUNCATED]

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

These lines will be truncated in the PDF manual.
File ‘not/libs/not.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

These lines will be truncated in the PDF manual.
File ‘NPsimex/libs/NPsimex.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.fkk.test print.hogg.test print.rank.test
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘npsp/libs/npsp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

These lines will be truncated in the PDF manual.
File ‘nse/libs/nse.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘mco’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
boundedPolyMutation: no visible global function definition for ‘runif’
boundedSBXover: no visible global function definition for ‘runif’
nsga2R : <anonymous>: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
.mcmc.bar: no visible global function definition for ‘rnorm’
.mcmc.bar: no visible global function definition for ‘runif’
.mcmc.comb: no visible global function definition for ‘rnorm’
.mcmc.comb: no visible global function definition for ‘runif’
.mcmc.rd: no visible global function definition for ‘rnorm’
.mcmc.rd: no visible global function definition for ‘runif’
.mcmc.trans: no visible global function definition for ‘rnorm’
.mcmc.trans: no visible global function definition for ‘runif’
.simulate.bar: no visible global function definition for ‘rlnorm’
.simulate.bar: no visible global function definition for ‘rbeta’
.simulate.bar: no visible global function definition for ‘rbinom’
.simulate.comb: no visible global function definition for ‘rlnorm’
.simulate.comb: no visible global function definition for ‘rbeta’
.simulate.comb: no visible global function definition for ‘rbinom’
.simulate.rd: no visible global function definition for ‘rlnorm’
.simulate.rd: no visible global function definition for ‘rbinom’
.simulate.trans: no visible global function definition for ‘rlnorm’
.simulate.trans: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  rbeta rbinom rlnorm rnorm runif
Consider adding
  importFrom("stats", "rbeta", "rbinom", "rlnorm", "rnorm", "runif")
to your NAMESPACE file.
box_dist: no visible global function definition for ‘quantile’
calc_mean_dist: no visible global function definition for ‘filter’
n: no visible global function definition for ‘resid’
null_dist : <anonymous>: no visible global function definition for
  ‘coef’
null_lm : <anonymous>: no visible global function definition for
  ‘predict’
reg_dist: no visible global function definition for ‘coef’
reg_dist: no visible global function definition for ‘lm’
resid_boot: no visible global function definition for ‘resid’
resid_pboot: no visible global function definition for ‘rnorm’
resid_rotate: no visible global function definition for ‘rnorm’
resid_rotate: no visible global function definition for ‘update’
resid_rotate: no visible global function definition for ‘resid’
resid_sigma: no visible global function definition for ‘rnorm’
rorschach: no visible global function definition for ‘rbinom’
rss: no visible global function definition for ‘resid’
sep_dist: no visible global function definition for ‘dist’
sep_dist: no visible global function definition for ‘cutree’
sep_dist: no visible global function definition for ‘hclust’
uni_dist: no visible global function definition for ‘sd’
Undefined global functions or variables:
  coef cutree dist filter hclust lm predict quantile rbinom resid rnorm
  sd update
Consider adding
  importFrom("stats", "coef", "cutree", "dist", "filter", "hclust", "lm",
             "predict", "quantile", "rbinom", "resid", "rnorm", "sd",
             "update")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Deprecated license: CC BY-NC-SA 3.0
Malformed Description field: should contain one or more complete sentences.
Deprecated license: CC BY-NC-ND 3.0 US
Packages in Depends field not imported from:
  ‘nutshell.audioscrobbler’ ‘nutshell.bbdb’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘nws/R/zzz.R’:
  .onLoad calls:
    require(methods)

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

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

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

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

These lines will be truncated in the PDF manual.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
Signal.gen: no visible global function definition for ‘new’
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
obliclus: no visible global function definition for ‘rnorm’
obliclus: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  kmeans rnorm
Consider adding
  importFrom("stats", "kmeans", "rnorm")
to your NAMESPACE file.
File ‘obliclus/libs/obliclus.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘random_cluster_C.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘random_cluster_C.o’
File ‘obliclus/libs/obliclus.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 use Fortran I/O
nor system RNGs.
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:
  ‘ROCR’ ‘e1071’ ‘mda’ ‘pls’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
log_wrapper: no visible global function definition for ‘glm’
log_wrapper: no visible global function definition for ‘binomial’
log_wrapper: no visible global function definition for ‘coef’
log_wrapper: no visible global function definition for ‘anova’
obliqueRF.default: no visible binding for global variable ‘predict’
obliqueRF.default: no visible global function definition for
  ‘prediction’
obliqueRF.default: no visible global function definition for
  ‘performance’
pls_wrapper: no visible global function definition for ‘kernelpls.fit’
pls_wrapper: no visible global function definition for ‘coef’
ridge_slow_wrapper: no visible global function definition for
  ‘gen.ridge’
ridge_slow_wrapper: no visible global function definition for ‘predict’
ridge_svd_wrapper: no visible global function definition for
  ‘gen.ridge’
rnd_wrapper: no visible global function definition for ‘rnorm’
svm_wrapper: no visible global function definition for ‘svm’
svm_wrapper: no visible global function definition for ‘predict’
Undefined global functions or variables:
  anova binomial coef gen.ridge glm kernelpls.fit performance predict
  prediction rnorm svm
Consider adding
  importFrom("stats", "anova", "binomial", "coef", "glm", "predict",
             "rnorm")
to your NAMESPACE file.
IBMD: no visible global function definition for ‘runif’
IBMD: no visible global function definition for ‘quantile’
RAI: no visible global function definition for ‘runif’
RAI: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile runif
Consider adding
  importFrom("stats", "quantile", "runif")
to your NAMESPACE file.
obsSensCCC: no visible global function definition for ‘coef’
obsSensCCC: no visible global function definition for ‘confint’
obsSensCCN: no visible global function definition for ‘coef’
obsSensCCN: no visible global function definition for ‘confint’
obsSensCNN: no visible global function definition for ‘coef’
obsSensCNN: no visible global function definition for ‘confint’
obsSensCNN: no visible global function definition for ‘sd’
obsSensCNN: no visible global function definition for ‘model.matrix’
obsSensNNN: no visible global function definition for ‘coef’
obsSensNNN: no visible global function definition for ‘confint’
obsSensNNN: no visible global function definition for ‘sd’
obsSensNNN: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  coef confint model.matrix sd
Consider adding
  importFrom("stats", "coef", "confint", "model.matrix", "sd")
to your NAMESPACE file.
Rd file 'obsSensCCC.Rd':
  \usage lines wider than 90 characters:
     obsSensCCC(model, which = 2, g0 = c(2, 6, 10), g1, p0 = seq(0, 1, 0.2), p1 = p0, logOdds = FALSE, method = c("approx", "sim"))
     obsSensCCN(model, which = 2, gamma = round(seq(0, 2 * bstar, length = 6), 4), delta = seq(0, 3, 0.5), logOdds = FALSE, method = c("appr ... [TRUNCATED]
     obsSensCNN(model, which = 2, gamma = round(seq(0, 2 * bstar, length = 6), 4), rho = c(0, 0.5, 0.75, 0.85, 0.9, 0.95, 0.98, 0.99), sdx,  ... [TRUNCATED]
     obsSensNCC(model, which = 2, g0 = c(2, 6, 10), g1, p0 = seq(0, 1, 0.2), p1 = p0, log = TRUE, method = c("approx", "sim"))
     obsSensNCN(model, which = 2, gamma = round(seq(0, 3, length = 6), 4), delta = seq(0, 3, 0.5), log = TRUE, method = c("approx", "sim"))
     6), 4), rho = c(0, 0.5, 0.75, 0.85, 0.9, 0.95, 0.98, 0.99), sdx, log = TRUE, method = c("approx", "sim"))
     obsSensSCC(model, which = 2, g0 = c(2, 6, 10), g1, p0 = seq(0, 1, 0.2), p1 = p0, logHaz = FALSE, method = c("approx", "sim"))
     obsSensSCN(model, which = 2, gamma = round(seq(0, 3, length = 6), 4), delta = seq(0, 3, 0.5), logHaz = FALSE, method = c("approx", "sim ... [TRUNCATED]
     obsSensSNN(model, which = 2, gamma = round(seq(0, 3, length = 6), 4), rho = c(0, 0.5, 0.75, 0.85, 0.9, 0.95, 0.98, 0.99), sdx, logHaz = ... [TRUNCATED]

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

Found the following calls to data() loading into the global environment:
File ‘OIdata/R/mapvar.R’:
  data(state.fips)
See section ‘Good practice’ in ‘?data’.
Package in Depends field not imported from: ‘KMsurv’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
avgokmts: no visible global function definition for ‘aggregate’
downloadstn: no visible global function definition for ‘read.csv’
nearstn: no visible binding for global variable ‘okstations’
nearstn: no visible binding for global variable ‘Commissioned’
nearstn: no visible binding for global variable ‘Decommissioned’
okcurobs: no visible global function definition for ‘read.csv’
okmts: no visible binding for global variable ‘okstations’
okmts: no visible binding for global variable ‘TIME’
retrievemts: no visible global function definition for ‘read.csv’
totalprecip: no visible binding for global variable ‘TIME’
totalprecip: no visible global function definition for ‘aggregate’
vincenty: no visible global function definition for ‘runif’
Undefined global functions or variables:
  Commissioned Decommissioned TIME aggregate okstations read.csv runif
Consider adding
  importFrom("stats", "aggregate", "runif")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
File ‘olctools/libs/olctools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
OLScurve: no visible global function definition for ‘as.formula’
OLScurve: no visible global function definition for ‘na.omit’
OLScurve: no visible global function definition for ‘lm’
OLScurve: no visible global function definition for ‘predict’
OLScurve: no visible global function definition for ‘residuals’
OLScurve: no visible global function definition for ‘model.frame’
OLScurve: no visible global function definition for ‘model.matrix’
plot.OLScurve : plotOLScurve: no visible global function definition for
  ‘reshape’
print.OLScurve: no visible global function definition for ‘na.omit’
print.OLScurve: no visible global function definition for ‘model.frame’
print.OLScurve: no visible global function definition for
  ‘model.matrix’
print.OLScurve: no visible global function definition for ‘cov’
print.OLScurve: no visible global function definition for ‘cor’
print.OLScurve: no visible global function definition for ‘sd’
subjplot.OLScurve : plotOLScurve: no visible global function definition
  for ‘devAskNewPage’
subjplot.OLScurve : plotOLScurve: no visible global function definition
  for ‘reshape’
subjplot.OLScurve : plotOLScurve : mypanel: no visible global function
  definition for ‘gray’
subjplot.OLScurve: no visible global function definition for
  ‘devAskNewPage’
Undefined global functions or variables:
  as.formula cor cov devAskNewPage gray lm model.frame model.matrix
  na.omit predict reshape residuals sd
Consider adding
  importFrom("grDevices", "devAskNewPage", "gray")
  importFrom("stats", "as.formula", "cor", "cov", "lm", "model.frame",
             "model.matrix", "na.omit", "predict", "reshape",
             "residuals", "sd")
to your NAMESPACE file.
fhcor: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor
Consider adding
  importFrom("stats", "cor")
to your NAMESPACE file.
Found an obsolete/platform-specific call in the following function:
  ‘comp.freq’
Found the platform-specific device:
  ‘x11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
MLparameters: no visible global function definition for ‘optim’
comp.freq: no visible global function definition for ‘x11’
comp.freq: no visible global function definition for ‘par’
comp.freq: no visible global function definition for ‘plot’
Undefined global functions or variables:
  optim par plot x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par", "plot")
  importFrom("stats", "optim")
to your NAMESPACE file.
Rd file 'oncomodel-package.Rd':
  \examples lines wider than 100 characters:
       #plot.phylog(y.phyl, cnodes =1,  clabel.n=0.6, f=0.75, sub="Oncogenetic tree of given aberrations")

These lines will be truncated in the PDF manual.
generate.data: no visible global function definition for ‘rbinom’
least.common.ancestor: no visible global function definition for
  ‘na.omit’
oncotree.fit : estimate.error.rates: no visible global function
  definition for ‘optim’
plot.boottree: no visible global function definition for ‘par’
plot.boottree: no visible global function definition for
  ‘dev.interactive’
plot.boottree: no visible global function definition for ‘mtext’
plot.oncotree: no visible global function definition for ‘par’
plot.oncotree: no visible global function definition for ‘xinch’
plot.oncotree: no visible global function definition for ‘yinch’
plot.oncotree: no visible global function definition for ‘lines’
plot.oncotree: no visible global function definition for ‘rect’
plot.oncotree: no visible global function definition for ‘strwidth’
plot.oncotree: no visible global function definition for ‘strheight’
plot.oncotree: no visible global function definition for ‘text’
Undefined global functions or variables:
  dev.interactive lines mtext na.omit optim par rbinom rect strheight
  strwidth text xinch yinch
Consider adding
  importFrom("grDevices", "dev.interactive")
  importFrom("graphics", "lines", "mtext", "par", "rect", "strheight",
             "strwidth", "text", "xinch", "yinch")
  importFrom("stats", "na.omit", "optim", "rbinom")
to your NAMESPACE file.
File ‘onlinePCA/libs/onlinePCA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
ci.prop: no visible global function definition for ‘qf’
ci.prop: no visible global function definition for ‘qnorm’
ePCP: no visible global function definition for ‘qnorm’
sevennum: no visible global function definition for ‘na.omit’
sevennum: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  na.omit qf qnorm quantile
Consider adding
  importFrom("stats", "na.omit", "qf", "qnorm", "quantile")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  [.clFloat [<-.clFloat as.character.clFloat as.double.clFloat
  as.integer.clFloat length.clFloat length<-.clFloat oclInfo.clDeviceID
  oclInfo.clPlatformID oclInfo.list print.clFloat
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘OpenCL/libs/OpenCL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘openNLPmodels.en’
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


Attaching package: 'lubridate'

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

    date


Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Warning in bind_rows_(x, .id) :
  Unequal factor levels: coercing to character
Warning in bind_rows_(x, .id) :
  binding character and factor vector, coercing into character vector
Warning in bind_rows_(x, .id) :
  binding character and factor vector, coercing into character vector
Warning: Removed 5 rows containing missing values (geom_path).
Don't know how to automatically pick scale for object of type difftime. Defaulting to continuous.
Don't know how to automatically pick scale for object of type difftime. Defaulting to continuous.
Don't know how to automatically pick scale for object of type difftime. Defaulting to continuous.
Loading required package: maps
Loading required package: maptools
Loading required package: sp
Checking rgeos availability: TRUE
Loading required package: rgeos
rgeos version: 0.3-28, (SVN revision 572)
 GEOS runtime version: 3.6.2-CAPI-1.10.2 4d2925d6 
 Linking to sp version: 1.3-1 
 Polygon checking: TRUE 

Quitting from lines 142-143 (osem-intro.Rmd) 
Error: processing vignette ‘osem-intro.Rmd’ failed with diagnostics:
no simple features geometry column present
Execution halted
Df2SpLinesDf: no visible global function definition for ‘slot’
PlotTraj: no visible global function definition for ‘par’
PlotTraj: no visible global function definition for ‘grid’
PlotTraj: no visible global function definition for ‘box’
PlotTrajFreq: no visible global function definition for ‘par’
PlotTrajFreq: no visible global function definition for ‘grid’
PlotTrajFreq: no visible global function definition for
  ‘colorRampPalette’
PlotTrajFreq: no visible global function definition for ‘legend’
PlotTrajFreq: no visible binding for global variable ‘title’
PlotTrajFreq: no visible global function definition for ‘dev.off’
ReadFiles: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  box colorRampPalette dev.off grid legend par read.table slot title
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off")
  importFrom("graphics", "box", "grid", "legend", "par", "title")
  importFrom("methods", "slot")
  importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
prepare_Rd: distance.Rd:21-22: Dropping empty section \details
prepare_Rd: distance.Rd:32-33: Dropping empty section \note
prepare_Rd: filter.Rd:26-27: Dropping empty section \details
prepare_Rd: filter.Rd:28-29: Dropping empty section \value
prepare_Rd: filter.Rd:36-37: Dropping empty section \note
prepare_Rd: findP.Rd:21-22: Dropping empty section \details
prepare_Rd: findP.Rd:34-35: Dropping empty section \note
prepare_Rd: ops-package.Rd:30-31: Dropping empty section \seealso
nlsolve: no visible global function definition for ‘optim’
nlsolve: no visible global function definition for ‘runif’
optAUC: no visible global function definition for ‘var’
Undefined global functions or variables:
  optim runif var
Consider adding
  importFrom("stats", "optim", "runif", "var")
to your NAMESPACE file.
Rd file 'optAUC-package.Rd':
  \examples lines wider than 100 characters:
     Y1Y2<-mvrnorm(n, c(y1.mean,y2.mean), matrix(c(y1.sd^2,rho*y1.sd*y2.sd, rho*y1.sd*y2.sd, y2.sd^2),2,2))
     # two markers in the model, the AUC from GCV is smaller than just first marker in the model, because the second marker is noise
     # the AUC from ACV (apearent estimate by substituting the estimated beta into the model) is larger than previous model, because overfit ... [TRUNCATED]

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

These lines will be truncated in the PDF manual.
avg2Lower: no visible global function definition for ‘optimize’
classificationError.data.frame: no visible binding for global variable
  ‘na.omit’
classificationError.data.frame: no visible global function definition
  for ‘terms’
classificationError.data.frame: no visible binding for global variable
  ‘predict’
classpredict.lda: no visible global function definition for ‘predict’
simData: no visible global function definition for ‘rnorm’
simData: no visible global function definition for ‘runif’
simData: no visible global function definition for ‘var’
tnormAvg: no visible global function definition for ‘dnorm’
tnormAvg: no visible global function definition for ‘pnorm’
yapprox: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx dnorm na.omit optimize pnorm predict rnorm runif terms var
Consider adding
  importFrom("stats", "approx", "dnorm", "na.omit", "optimize", "pnorm",
             "predict", "rnorm", "runif", "terms", "var")
to your NAMESPACE file.
File ‘OptGS/libs/OptGS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
calculate.empirical.AUC: no visible global function definition for
  ‘qnorm’
ci.AgrestiCoull: no visible global function definition for ‘qnorm’
ci.GartNam: no visible global function definition for ‘qnorm’
ci.NotTransformed: no visible global function definition for ‘qnorm’
ci.RubinSchenker: no visible global function definition for ‘qnorm’
ci.RubinSchenker: no visible global function definition for ‘plogis’
ci.RubinSchenker: no visible global function definition for ‘qlogis’
ci.exact: no visible global function definition for ‘qf’
ci.quadratic: no visible global function definition for ‘qnorm’
ci.transformed: no visible global function definition for ‘qnorm’
ci.wald: no visible global function definition for ‘qnorm’
function.MinPvalue: no visible global function definition for
  ‘chisq.test’
function.MinPvalue : PADJMS: no visible global function definition for
  ‘qnorm’
function.MinPvalue : PADJMS: no visible global function definition for
  ‘dnorm’
optimal.cutpoints.default: no visible global function definition for
  ‘na.omit’
optimal.cutpoints.formula: no visible global function definition for
  ‘terms’
plot.optimal.cutpoints: no visible global function definition for ‘par’
plot.optimal.cutpoints: no visible global function definition for
  ‘plot’
plot.optimal.cutpoints: no visible global function definition for
  ‘abline’
plot.optimal.cutpoints: no visible global function definition for
  ‘lines’
plot.optimal.cutpoints: no visible global function definition for
  ‘points’
Undefined global functions or variables:
  abline chisq.test dnorm lines na.omit par plogis plot points qf
  qlogis qnorm terms
Consider adding
  importFrom("graphics", "abline", "lines", "par", "plot", "points")
  importFrom("stats", "chisq.test", "dnorm", "na.omit", "plogis", "qf",
             "qlogis", "qnorm", "terms")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘gurobi’
print.optimbase: no visible global function definition for ‘str’
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
optimx.run: no visible global function definition for ‘optim’
optimx.run: no visible global function definition for ‘nlminb’
optimx.run: no visible global function definition for ‘nlm’
Undefined global functions or variables:
  nlm nlminb optim
Consider adding
  importFrom("stats", "nlm", "nlminb", "optim")
to your NAMESPACE file.
Rd file 'TestStage.Rd':
  \examples lines wider than 100 characters:
     object1 <- OptimDes(B.init,m.init,alpha,beta,param,x,target="EDA",sf="futility",num.arm=1,num.stage=2)
     mda <- ifelse(l>1,B.init[l-1]+(B.init[l]-B.init[l-1])*(n-sum(m.init[1:(l-1)]))/m.init[l],B.init[l]*(n/m.init[l]))

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

These lines will be truncated in the PDF manual.
calc.stress: no visible global function definition for ‘sd’
opscale: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
File ‘optpart/libs/optpart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘Rmosek’
getMinimumArborescence: no visible global function definition for
  ‘capture.output’
getMinimumCutTree: no visible global function definition for
  ‘capture.output’
getMinimumCutTree: no visible global function definition for ‘par’
getMinimumSpanningTree: no visible global function definition for
  ‘capture.output’
getShortestPathTree: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  capture.output par
Consider adding
  importFrom("graphics", "par")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
File ‘orca/libs/orca.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

These lines will be truncated in the PDF manual.
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of ‘nr’ to ‘nrow’
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of ‘nc’ to ‘ncol’
bgmm: no visible global function definition for ‘ecdf’
bgmm : SplineGMM: no visible global function definition for
  ‘constrOptim’
blr: no visible global function definition for ‘ecdf’
blr: no visible global function definition for ‘constrOptim’
blr: no visible global function definition for ‘lm’
parentcdf : combinations: no visible global function definition for
  ‘combn’
parentcdf : solver: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  combn constrOptim ecdf lm uniroot
Consider adding
  importFrom("stats", "constrOptim", "ecdf", "lm", "uniroot")
  importFrom("utils", "combn")
to your NAMESPACE file.
'library' or 'require' call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘grid’ ‘lattice’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  predict.orderedLasso predict.orderedLasso.path predict.timeLagLasso
  predict.timeLagLasso.path
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
error.bars: no visible global function definition for ‘segments’
lambda.interp: no visible global function definition for ‘approx’
orderedLasso: no visible binding for global variable ‘sd’
orderedLasso.cv: no visible binding for global variable ‘var’
plot.orderedLasso.cv: no visible global function definition for ‘par’
plot.orderedLasso.cv: no visible global function definition for ‘plot’
plot.orderedLasso.cv: no visible global function definition for ‘axis’
plot.orderedLasso.cv: no visible global function definition for ‘mtext’
plot.orderedLasso.cv: no visible global function definition for
  ‘points’
plot.orderedLasso.cv: no visible global function definition for
  ‘abline’
plot.timeLagLasso.cv: no visible global function definition for ‘par’
plot.timeLagLasso.cv: no visible global function definition for ‘plot’
plot.timeLagLasso.cv: no visible global function definition for ‘axis’
plot.timeLagLasso.cv: no visible global function definition for ‘mtext’
plot.timeLagLasso.cv: no visible global function definition for
  ‘points’
plot.timeLagLasso.cv: no visible global function definition for
  ‘abline’
timeLagLasso: no visible binding for global variable ‘sd’
timeLagLasso.cv: no visible binding for global variable ‘sd’
timeLagLasso.cv: no visible binding for global variable ‘var’
timeLagLasso.path: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  abline approx axis mtext par plot points sd segments var
Consider adding
  importFrom("graphics", "abline", "axis", "mtext", "par", "plot",
             "points", "segments")
  importFrom("stats", "approx", "sd", "var")
to your NAMESPACE file.
genRidge: no visible global function definition for ‘plogis’
ordGene: no visible global function definition for ‘anova’
ordGene: no visible global function definition for ‘lm’
ordSelect: no visible binding for global variable ‘sd’
ordSmooth: no visible binding for global variable ‘sd’
plot.ordPen: no visible global function definition for ‘grey’
plot.ordPen: no visible global function definition for ‘devAskNewPage’
plot.ordPen: no visible global function definition for ‘plot’
plot.ordPen: no visible global function definition for ‘lines’
predict.ordPen: no visible global function definition for ‘plogis’
Undefined global functions or variables:
  anova devAskNewPage grey lines lm plogis plot sd
Consider adding
  importFrom("grDevices", "devAskNewPage", "grey")
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "anova", "lm", "plogis", "sd")
to your NAMESPACE file.
ORICC1: no visible binding for global variable ‘sd’
ORICC1: no visible global function definition for ‘write.table’
ORICC1: no visible global function definition for ‘postscript’
ORICC1: no visible global function definition for ‘jpeg’
ORICC1: no visible global function definition for ‘plot’
ORICC1: no visible global function definition for ‘points’
ORICC1: no visible global function definition for ‘dev.off’
ORICC1: no visible global function definition for ‘par’
ORICC2: no visible binding for global variable ‘sd’
ORICC2: no visible global function definition for ‘write.table’
ORICC2: no visible global function definition for ‘postscript’
ORICC2: no visible global function definition for ‘jpeg’
ORICC2: no visible global function definition for ‘plot’
ORICC2: no visible global function definition for ‘points’
ORICC2: no visible global function definition for ‘dev.off’
ORICC2: no visible global function definition for ‘par’
Undefined global functions or variables:
  dev.off jpeg par plot points postscript sd write.table
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "postscript")
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
boat3d: no visible global function definition for ‘rgl.cur’
boat3d: no visible global function definition for ‘open3d’
boat3d: no visible global function definition for ‘clear3d’
boat3d: no visible global function definition for ‘bg3d’
boat3d: no visible global function definition for ‘rgl.set’
boat3d: no visible global function definition for ‘triangles3d’
boat3d: no visible global function definition for ‘quads3d’
boat3d: no visible global function definition for ‘decorate3d’
boat3d: no visible global function definition for ‘scatterplot3d’
orientlm: no visible global function definition for ‘model.matrix’
orientlm: no visible global function definition for ‘lm’
Undefined global functions or variables:
  bg3d clear3d decorate3d lm model.matrix open3d quads3d rgl.cur
  rgl.set scatterplot3d triangles3d
Consider adding
  importFrom("stats", "lm", "model.matrix")
to your NAMESPACE file.
File ‘OriGen/libs/OriGen.so’:
  Found ‘_gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘_gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘_gfortran_st_read’, possibly from ‘read’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘_gfortran_st_rewind’, possibly from ‘rewind’ (Fortran)
    Object: ‘OriGen.o’
File ‘OriGen/libs/OriGen.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 use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
dicomTable: no visible global function definition for ‘txtProgressBar’
dicomTable: no visible global function definition for
  ‘setTxtProgressBar’
readDICOM: no visible global function definition for ‘txtProgressBar’
readDICOM: no visible global function definition for
  ‘setTxtProgressBar’
writeHeader: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar write.table
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar",
             "write.table")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘genefilter’ ‘gtools’ ‘nlme’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
est.lme : <anonymous>: warning in rank(iru, ties = "min"): partial
  argument match of ‘ties’ to ‘ties.method’
est.lme : <anonymous>: no visible global function definition for ‘lme’
est.lme : <anonymous>: no visible global function definition for
  ‘VarCorr’
guo: no visible global function definition for ‘p.adjust’
guo: no visible global function definition for ‘na.omit’
pttest : ptest: no visible global function definition for ‘na.omit’
srt : <anonymous>: no visible global function definition for
  ‘rowttests’
Undefined global functions or variables:
  VarCorr lme na.omit p.adjust rowttests
Consider adding
  importFrom("stats", "na.omit", "p.adjust")
to your NAMESPACE file.
File ‘orQA/libs/orQA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.SplineBasis: no visible global function definition for ‘matplot’
plot,SplineBasis-matrix: no visible global function definition for
  ‘matplot’
plot,SplineBasis-missing: no visible global function definition for
  ‘matplot’
Undefined global functions or variables:
  matplot
Consider adding
  importFrom("graphics", "matplot")
to your NAMESPACE file.
'library' or 'require' call to ‘polynom’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘polynom’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
chebyshev.c.polynomials: no visible global function definition for
  ‘polynomial’
chebyshev.s.polynomials: no visible global function definition for
  ‘polynomial’
chebyshev.t.polynomials: no visible global function definition for
  ‘polynomial’
chebyshev.u.polynomials: no visible global function definition for
  ‘polynomial’
gegenbauer.polynomials: no visible global function definition for
  ‘polynomial’
ghermite.h.polynomials: no visible global function definition for
  ‘polynomial’
glaguerre.polynomials: no visible global function definition for
  ‘polynomial’
hermite.h.polynomials: no visible global function definition for
  ‘polynomial’
hermite.he.polynomials: no visible global function definition for
  ‘polynomial’
jacobi.g.polynomials: no visible global function definition for
  ‘polynomial’
jacobi.p.polynomials: no visible global function definition for
  ‘polynomial’
legendre.polynomials: no visible global function definition for
  ‘polynomial’
monic.polynomials: no visible global function definition for
  ‘polynomial’
orthogonal.polynomials: no visible global function definition for
  ‘polynomial’
orthonormal.polynomials: no visible global function definition for
  ‘polynomial’
polynomial.derivatives: no visible global function definition for
  ‘deriv’
polynomial.integrals: no visible global function definition for
  ‘integral’
polynomial.values: no visible global function definition for ‘predict’
schebyshev.t.polynomials: no visible global function definition for
  ‘polynomial’
schebyshev.u.polynomials: no visible global function definition for
  ‘polynomial’
slegendre.polynomials: no visible global function definition for
  ‘polynomial’
Undefined global functions or variables:
  deriv integral polynomial predict
Consider adding
  importFrom("stats", "deriv", "predict")
to your NAMESPACE file.
Found the following significant warnings:
  ccaRevolution.c:31:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:44:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:97:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:98:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:110:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:111:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/osc.Rcheck/00install.out’ for details.
File ‘osc/libs/osc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘osDesign/libs/osDesign.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘igraph’ ‘sp’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
as_igraph : <anonymous>: no visible global function definition for
  ‘distHaversine’
as_igraph: no visible global function definition for ‘graph.edgelist’
as_igraph: no visible global function definition for ‘E’
as_igraph: no visible global function definition for ‘E<-’
as_sp_lines: no visible global function definition for ‘Lines’
as_sp_points: no visible global function definition for
  ‘SpatialPointsDataFrame’
as_sp_polygons: no visible global function definition for ‘Polygons’
as_sp_polygons: no visible global function definition for
  ‘SpatialPolygons’
as_sp_polygons: no visible global function definition for
  ‘SpatialPolygonsDataFrame’
make_SLDF: no visible global function definition for ‘SpatialLines’
make_SLDF: no visible global function definition for
  ‘SpatialLinesDataFrame’
osm_crs: no visible global function definition for ‘CRS’
plot.osmar: no visible global function definition for ‘gray’
plot_nodes: no visible global function definition for ‘points’
plot_nodes: no visible global function definition for ‘plot’
plot_ways: no visible global function definition for ‘plot’
plot_ways: no visible global function definition for ‘lines’
ways_nodes2Line: no visible global function definition for ‘Line’
ways_nodes2Polygon: no visible global function definition for ‘Polygon’
Undefined global functions or variables:
  CRS E E<- Line Lines Polygon Polygons SpatialLines
  SpatialLinesDataFrame SpatialPointsDataFrame SpatialPolygons
  SpatialPolygonsDataFrame distHaversine graph.edgelist gray lines plot
  points
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
odm: no visible binding for global variable ‘sd’
odm : <anonymous>: no visible global function definition for ‘sd’
odm : <anonymous>: no visible global function definition for ‘quantile’
odm: no visible global function definition for ‘prcomp’
quant.const: no visible global function definition for ‘quantile’
quant.const.D: no visible global function definition for ‘reshape’
quant.const.D: no visible global function definition for ‘quantile’
quant.linear.D: no visible global function definition for ‘reshape’
quant.nonlin : FrankModel: no visible global function definition for
  ‘qt’
quant.nonlin : FrankModel: no visible global function definition for
  ‘pt’
quant.nonlin: no visible global function definition for ‘predict’
quant.nonlin.D: no visible global function definition for ‘reshape’
quant.nonlin.D: no visible global function definition for ‘predict’
quant.nonpar.D: no visible global function definition for ‘reshape’
rgrubbs.test: no visible global function definition for ‘sd’
plot,OutlierDM-missing: no visible binding for global variable ‘pch’
summary,OutlierDM: no visible global function definition for ‘head’
Undefined global functions or variables:
  head pch prcomp predict pt qt quantile reshape sd
Consider adding
  importFrom("stats", "prcomp", "predict", "pt", "qt", "quantile",
             "reshape", "sd")
  importFrom("utils", "head")
to your NAMESPACE file.
Electre3_AlphaBetaThresholds: no visible global function definition for
  ‘plot’
Electre3_SimpleThresholds: no visible global function definition for
  ‘plot’
Electre_1: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Packages suggested but not available for checking:
  ‘genealogicalSorting’ ‘phybase’
ms.exec: no visible global function definition for ‘tail’
p2c2m.readstarb: no visible global function definition for ‘head’
p2c2m.readstarb: no visible binding for global variable ‘head’
rmOutlrs: no visible global function definition for ‘boxplot.stats’
rmext: no visible global function definition for ‘tail’
rowMedians: no visible binding for global variable ‘median’
stats.acrGenes: no visible binding for global variable ‘sd’
stats.perGene: no visible binding for global variable ‘sd’
statshelpers.cv: no visible binding for global variable ‘sd’
statshelpers.qntls: no visible binding for global variable ‘quantile’
Undefined global functions or variables:
  boxplot.stats head median quantile sd tail
Consider adding
  importFrom("grDevices", "boxplot.stats")
  importFrom("stats", "median", "quantile", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
loadCSVtoP2distance: no visible global function definition for
  ‘read.table’
p2distance : calcularDistancia: no visible binding for global variable
  ‘sd’
p2distance : ordenarVariables: no visible global function definition
  for ‘cor’
p2distance : calculoFactoresPonderacion: no visible global function
  definition for ‘lm’
p2distance: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor lm read.table sd
Consider adding
  importFrom("stats", "cor", "lm", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'library' or 'require' call to ‘survival’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
p3state: no visible global function definition for ‘survfit’
p3state: no visible global function definition for ‘terms’
p3state: no visible global function definition for ‘as.formula’
p3state: no visible global function definition for ‘coxph’
p3state: no visible binding for global variable ‘na.exclude’
plot.p3state: no visible global function definition for ‘matplot’
plot.p3state: no visible global function definition for ‘devAskNewPage’
plot.p3state: no visible global function definition for ‘persp’
plot.p3state: no visible global function definition for ‘colours’
plot.p3state: no visible global function definition for
  ‘filled.contour’
Undefined global functions or variables:
  as.formula colours coxph devAskNewPage filled.contour matplot
  na.exclude persp survfit terms
Consider adding
  importFrom("grDevices", "colours", "devAskNewPage")
  importFrom("graphics", "filled.contour", "matplot", "persp")
  importFrom("stats", "as.formula", "na.exclude", "terms")
to your NAMESPACE file.
pacbpred : thetaFunc: no visible global function definition for ‘lsfit’
pacbpred : thetaFunc: no visible global function definition for ‘rnorm’
pacbpred: no visible global function definition for ‘var’
pacbpred: no visible global function definition for ‘runif’
pacbpred: no visible global function definition for ‘rnorm’
pacbpred: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  lsfit rbinom rnorm runif var
Consider adding
  importFrom("stats", "lsfit", "rbinom", "rnorm", "runif", "var")
to your NAMESPACE file.
Non-standard files/directories found at top level:
  ‘DESCRIPTION_EX’ ‘divers’ ‘main.R’ ‘testsDev’
[,ClassW: warning in switch(EXP = i, u1 = {: partial argument match of
  ‘EXP’ to ‘EXPR’
[,ClassW: warning in return(x@u1): partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in }, u2 = {: partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in return(x@u2): partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in }, w1 = {: partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in return(x@w1): partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in }): partial argument match of ‘EXP’ to ‘EXPR’
[<-,ClassW: warning in switch(EXP = i, u1 = {: partial argument match
  of ‘EXP’ to ‘EXPR’
[<-,ClassW: warning in x@u1 <- value: partial argument match of ‘EXP’
  to ‘EXPR’
[<-,ClassW: warning in }, u2 = {: partial argument match of ‘EXP’ to
  ‘EXPR’
[<-,ClassW: warning in x@u2 <- value: partial argument match of ‘EXP’
  to ‘EXPR’
[<-,ClassW: warning in }, w1 = {: partial argument match of ‘EXP’ to
  ‘EXPR’
[<-,ClassW: warning in x@w1 <- value: partial argument match of ‘EXP’
  to ‘EXPR’
[<-,ClassW: warning in }): partial argument match of ‘EXP’ to ‘EXPR’
paf: no visible global function definition for ‘as.formula’
paf: no visible global function definition for ‘model.response’
paf: no visible global function definition for ‘model.frame’
paf: no visible global function definition for ‘model.matrix’
plot.paf: no visible global function definition for ‘plot’
plot.paf: no visible global function definition for ‘lines’
Undefined global functions or variables:
  as.formula lines model.frame model.matrix model.response plot
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response")
to your NAMESPACE file.
CalGIF: no visible binding for global variable ‘PAGIData’
CalGIF2: no visible binding for global variable ‘PAGIData’
PAGI.Main: no visible binding for global variable ‘PAGIData’
PAGI.Main: no visible global function definition for ‘p.adjust’
PAGI.Main: no visible global function definition for ‘pt’
getclass.labels: no visible binding for global variable ‘ExampleData’
getdataset: no visible binding for global variable ‘ExampleData’
Undefined global functions or variables:
  ExampleData PAGIData p.adjust pt
Consider adding
  importFrom("stats", "p.adjust", "pt")
to your NAMESPACE file.
Rd file 'CalGIF.Rd':
  \examples lines wider than 100 characters:
     ###calculate the global influence factor (GIF) by using the random walk with restart (RWR) algorithm###
     #Each element is the GIF score and whose name correspond to gene symbol in the gene expression data. 
     #Each element is the GIF score and whose name correspond to gene symbol in the gene expression data. 

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

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

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

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

These lines will be truncated in the PDF manual.
EAMM: no visible global function definition for ‘anova’
EAMM: no visible global function definition for ‘rand’
PAMM: no visible global function definition for ‘rand’
PAMM: no visible global function definition for ‘anova’
SSF: no visible global function definition for ‘rand’
SSF: no visible global function definition for ‘anova’
Undefined global functions or variables:
  anova rand
Consider adding
  importFrom("stats", "anova")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  print.pamrcved print.pamrtrained
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘pamr/libs/pamr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
GOpredict: no visible global function definition for ‘fisher.test’
KEGGpredict: no visible global function definition for ‘fisher.test’
ProteinCluster: no visible global function definition for ‘ecdf’
ProteinCluster: no visible global function definition for ‘as.hclust’
ProteinCluster: no visible global function definition for
  ‘as.dendrogram’
ProteinCluster : addE: no visible global function definition for
  ‘is.leaf’
ProteinCluster: no visible global function definition for ‘plot’
SignificantSubcluster: no visible global function definition for
  ‘order.dendrogram’
SignificantSubcluster: no visible global function definition for
  ‘fisher.test’
SignificantSubcluster: no visible global function definition for ‘plot’
Undefined global functions or variables:
  as.dendrogram as.hclust ecdf fisher.test is.leaf order.dendrogram
  plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "as.dendrogram", "as.hclust", "ecdf",
             "fisher.test", "is.leaf", "order.dendrogram")
to your NAMESPACE file.
File ‘PanelCount/libs/PanelCount.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Paneldata.formula: no visible global function definition for
  ‘model.frame’
Paneldata.formula: no visible global function definition for
  ‘model.matrix’
Paneldata.formula: no visible global function definition for
  ‘model.response’
summary.Paneldata: no visible global function definition for ‘coef’
summary.Paneldata: no visible global function definition for ‘pt’
Undefined global functions or variables:
  coef model.frame model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.frame", "model.matrix",
             "model.response", "pt")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  predict.forest
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
grow.forest: no visible global function definition for ‘model.frame’
grow.tree: no visible global function definition for ‘model.frame’
predict.forest: no visible global function definition for ‘model.frame’
predict.tree: no visible global function definition for ‘model.frame’
predict,forest: no visible global function definition for ‘model.frame’
predict,tree: no visible global function definition for ‘model.frame’
Undefined global functions or variables:
  model.frame
Consider adding
  importFrom("stats", "model.frame")
to your NAMESPACE file.
File ‘ParallelForest/libs/ParallelForest.so’:
  Found ‘_gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘random_utils.o’
  Found ‘_gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘random_utils.o’
  Found ‘_gfortran_st_read’, possibly from ‘read’ (Fortran)
    Object: ‘random_utils.o’
File ‘ParallelForest/libs/ParallelForest.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 use Fortran I/O
nor system RNGs.
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 ‘parallelize.dynamic’ for: ‘initialize’

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

Probably some imports need to be declared in the NAMESPACE file.
'library' or 'require' call to ‘package’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘methods’ ‘parallel’ ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
parallelExport: no visible global function definition for ‘setNames’
parallelGetOptions: no visible global function definition for
  ‘setNames’
parallelStop: no visible global function definition for
  ‘getFromNamespace’
stopWithJobErrorMessages: no visible global function definition for
  ‘head’
Undefined global functions or variables:
  getFromNamespace head setNames
Consider adding
  importFrom("stats", "setNames")
  importFrom("utils", "getFromNamespace", "head")
to your NAMESPACE file.
consensusMCcov: no visible global function definition for ‘var’
consensusMCcov: no visible global function definition for ‘cov’
consensusMCindep: no visible global function definition for ‘var’
semiparamDPE: no visible binding for global variable ‘var’
semiparamDPE: no visible global function definition for ‘cov’
semiparamDPE: no visible global function definition for ‘runif’
Undefined global functions or variables:
  cov runif var
Consider adding
  importFrom("stats", "cov", "runif", "var")
to your NAMESPACE file.
parallelSVM.default: no visible binding for global variable ‘na.omit’
parallelSVM.formula: no visible binding for global variable ‘na.omit’
predict.parallelSVM: no visible binding for global variable ‘predict’
Undefined global functions or variables:
  na.omit predict
Consider adding
  importFrom("stats", "na.omit", "predict")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘paran-Ex.R’
paran: no visible global function definition for ‘cor’
paran: no visible global function definition for ‘rnorm’
paran: no visible global function definition for ‘quantile’
paran: no visible global function definition for ‘par’
paran: no visible global function definition for ‘plot.default’
paran: no visible global function definition for ‘abline’
paran: no visible global function definition for ‘points’
paran: no visible global function definition for ‘dev.copy’
paran: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  abline cor dev.copy dev.off par plot.default points quantile rnorm
Consider adding
  importFrom("grDevices", "dev.copy", "dev.off")
  importFrom("graphics", "abline", "par", "plot.default", "points")
  importFrom("stats", "cor", "quantile", "rnorm")
to your NAMESPACE file.
.formula.make: no visible global function definition for ‘formula’
regress: no visible global function definition for ‘lm’
regress: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  formula lm model.matrix
Consider adding
  importFrom("stats", "formula", "lm", "model.matrix")
to your NAMESPACE file.
adalasso: no visible global function definition for ‘predict’
lm.ridge.univariate: no visible global function definition for ‘sd’
mylars: no visible global function definition for ‘predict’
mylars: no visible binding for global variable ‘var’
performance.pcor: no visible global function definition for
  ‘ggm.test.edges’
performance.pcor: no visible global function definition for ‘var’
ridge.cv: no visible global function definition for ‘coef’
ridge.cv: no visible global function definition for ‘plot’
Undefined global functions or variables:
  coef ggm.test.edges plot predict sd var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "predict", "sd", "var")
to your NAMESPACE file.
ParentOffspring: no visible global function definition for ‘axis’
ParentOffspring: no visible global function definition for ‘abline’
ParentOffspring: no visible global function definition for ‘title’
ParentOffspring: no visible global function definition for ‘box’
Undefined global functions or variables:
  abline axis box title
Consider adding
  importFrom("graphics", "abline", "axis", "box", "title")
to your NAMESPACE file.
par.nmds : nmdscalc: no visible global function definition for ‘runif’
par.nmds : nmdscalc: no visible global function definition for ‘dist’
par.nmds: no visible binding for global variable ‘j’
par.nmds: no visible global function definition for ‘cor’
par.nmds: no visible global function definition for ‘dist’
par.spp.est: no visible binding for global variable ‘i’
par.spp.est: no visible global function definition for ‘sd’
Undefined global functions or variables:
  cor dist i j runif sd
Consider adding
  importFrom("stats", "cor", "dist", "runif", "sd")
to your NAMESPACE file.
Rd file 'par.nmds.Rd':
  \usage lines wider than 90 characters:
     par.nmds(dmat, mindim = 1, maxdim = 2, nits = 10, iconf = 0, epsilon = 1e-12, maxit = 500, trace = FALSE) 

These lines will be truncated in the PDF manual.
File ‘parma/libs/parma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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("aracne", as.double(t(mis)), as.integer(n), as.double(eps), 
       as.double(eta), res = double(n * n), PACKAGE = "parmigene", 
       DUP = FALSE)
   .C("clr", as.double(t(mis)), as.integer(n), res = double(n * 
       n), PACKAGE = "parmigene", DUP = FALSE)
   .C("mrnet", as.double(t(mis)), as.integer(n), res = double(n * 
       n), PACKAGE = "parmigene", DUP = FALSE)
DUP is no longer supported and will be ignored.
File ‘parmigene/libs/parmigene.so’:
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.o’
File ‘parmigene/libs/parmigene.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 use Fortran I/O
nor system RNGs.
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: ‘nnet’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fitOR: no visible global function definition for ‘multinom’
fitOR: no visible global function definition for ‘formula’
fitOR: no visible global function definition for ‘coef’
fitOR: no visible global function definition for ‘optim’
reportOR: no visible global function definition for ‘qnorm’
reportOR: no visible global function definition for ‘pchisq’
reportOR: no visible global function definition for ‘coef’
simData: no visible global function definition for ‘rnorm’
simData: no visible global function definition for ‘runif’
Undefined global functions or variables:
  coef formula multinom optim pchisq qnorm rnorm runif
Consider adding
  importFrom("stats", "coef", "formula", "optim", "pchisq", "qnorm",
             "rnorm", "runif")
to your NAMESPACE file.
partitionMap: no visible global function definition for ‘predict’
partitionMap: no visible global function definition for ‘rnorm’
partitionMap: no visible binding for global variable ‘sd’
partitionMap: no visible global function definition for ‘sd’
partitionMap: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  predict quantile rnorm sd
Consider adding
  importFrom("stats", "predict", "quantile", "rnorm", "sd")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from ‘partsm’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
parviol: no visible global function definition for ‘plot.new’
parviol: no visible global function definition for ‘plot.window’
parviol: no visible global function definition for ‘title’
parviol: no visible global function definition for ‘lines’
parviol: no visible global function definition for ‘text’
parviol: no visible global function definition for ‘rgb’
selecto: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines plot.new plot.window rgb text title
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "plot.new", "plot.window", "text",
             "title")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘ape’ ‘caper’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
conch: no visible global function definition for ‘read.tree’
conch: no visible global function definition for ‘reorder’
conch: no visible global function definition for ‘read.nexus’
conch: no visible global function definition for ‘.compressTipLabel’
conch: no visible global function definition for ‘drop.tip’
conch: no visible global function definition for ‘extract.clade’
conch: no visible global function definition for ‘which.edge’
conch: no visible global function definition for ‘write.tree’
pastis_main: no visible global function definition for ‘combn’
read_input: no visible global function definition for ‘read.tree’
read_input: no visible global function definition for ‘reorder’
read_input: no visible global function definition for ‘read.csv’
read_input: no visible global function definition for ‘read.dna’
Undefined global functions or variables:
  .compressTipLabel combn drop.tip extract.clade read.csv read.dna
  read.nexus read.tree reorder which.edge write.tree
Consider adding
  importFrom("stats", "reorder")
  importFrom("utils", "combn", "read.csv")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘e1071’
  Please remove these calls from your code.
SweaveAll: no visible global function definition for ‘file_test’
texi2dvi: no visible global function definition for ‘file_test’
Undefined global functions or variables:
  file_test
Consider adding
  importFrom("utils", "file_test")
to your NAMESPACE file.
File ‘patchDVI/libs/patchDVI.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘datautils’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
animatePatches: no visible global function definition for
  ‘getTimestamp’
animatePatches: no visible global function definition for ‘getElapsed’
colorPlot: no visible global function definition for ‘layout’
colorPlot: no visible global function definition for ‘par’
colorPlot: no visible global function definition for ‘image’
colorPlot: no visible global function definition for ‘axis’
drawPatches: no visible global function definition for ‘rgb’
getInterRGB: no visible global function definition for ‘col2rgb’
getInterRGB: no visible global function definition for ‘rgb’
plotGmmOverlay: no visible global function definition for ‘rgb’
plotGreyPatches : squarepatch: no visible global function definition
  for ‘rgb’
plotGreyPatches : trianglepatch: no visible global function definition
  for ‘rgb’
Undefined global functions or variables:
  axis col2rgb getElapsed getTimestamp image layout par rgb
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
  importFrom("graphics", "axis", "image", "layout", "par")
to your NAMESPACE file.
Rd file 'drawPatches.Rd':
  \usage lines wider than 90 characters:
     drawPatches(data, patches, patchSize=0.05, alpha=0.5, patchNpix=20, highlight=numeric(0), labels=rep("1", length(highlight)))

Rd file 'plotGreyPatches.Rd':
  \usage lines wider than 90 characters:
     plotGreyPatches(data, maingrey, auxgrey=NULL, patchSize=0.05, alpha=0.5, highlight=numeric(0), labels=rep("1", length(highlight)))

These lines will be truncated in the PDF manual.
Depends: includes the non-default packages:
  ‘svmpath’ ‘kernlab’ ‘affy’ ‘Biobase’ ‘ROCR’ ‘igraph’ ‘lpSolve’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' call to ‘ROCR’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Biobase’ ‘ROCR’ ‘affy’ ‘igraph’ ‘kernlab’ ‘lpSolve’ ‘svmpath’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘parallel:::detectCores’
  See the note in ?`:::` about the use of this operator.
Found the following apparent S3 methods exported but not registered:
  plot.pathClassResult predict.graphSVM predict.networkBasedSVM
  predict.rfe predict.rrfe
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Package in Depends field not imported from: ‘shape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
arrow: no visible global function definition for ‘arrows’
draw: no visible global function definition for ‘rect’
draw: no visible global function definition for ‘text’
draw: no visible global function definition for ‘plotellipse’
wall: no visible global function definition for ‘plot.new’
wall: no visible global function definition for ‘plot.window’
Undefined global functions or variables:
  arrows plot.new plot.window plotellipse rect text
Consider adding
  importFrom("graphics", "arrows", "plot.new", "plot.window", "rect",
             "text")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘plspm’ ‘tester’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
add_noise: no visible global function definition for ‘rnorm’
estimate_risk_dream6 : <anonymous>: no visible global function
  definition for ‘var’
generate_sample: no visible global function definition for ‘rnorm’
generate_sample: no visible global function definition for ‘runif’
sample_function: no visible global function definition for ‘runif’
sample_function : <anonymous>: no visible global function definition
  for ‘var’
sample_function_multi_mod_weight: no visible global function definition
  for ‘runif’
sample_function_multi_mod_weight : <anonymous>: no visible global
  function definition for ‘var’
sample_function_single_mod: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  rnorm runif var
Consider adding
  importFrom("stats", "rnorm", "runif", "var")
to your NAMESPACE file.
File ‘pauwels2014/libs/pauwels2014.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘PAWL’ for: ‘show’

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘pbdDEMO/libs/pbdDEMO.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.ddmatrix rbind.ddmatrix
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'binds':
  ‘rbind.ddmatrix’ ‘cbind.ddmatrix’

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘pbdNCDF4/libs/pbdNCDF4.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
dotplot.pbo: no visible global function definition for ‘reorder’
pbo: no visible global function definition for ‘%dopar%’
pbo: no visible global function definition for ‘foreach’
pbo: no visible global function definition for ‘lm’
xyplot.pbo: no visible global function definition for ‘ecdf’
xyplot.pbo: no visible global function definition for ‘doubleYScale’
xyplot.pbo: no visible global function definition for ‘reorder’
Undefined global functions or variables:
  %dopar% doubleYScale ecdf foreach lm reorder
Consider adding
  importFrom("stats", "ecdf", "lm", "reorder")
to your NAMESPACE file.
a_get_native: no visible global function definition for ‘par’
a_get_relative: no visible global function definition for ‘par’
brackets: no visible global function definition for ‘par’
brackets: no visible global function definition for ‘dist’
brackets: no visible global function definition for ‘lines’
Undefined global functions or variables:
  dist lines par
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "dist")
to your NAMESPACE file.
.win.appendLog: no visible binding for global variable ‘lines’
plotMC : panel: no visible global function definition for ‘points’
plotMC: no visible global function definition for ‘pairs’
plotMC: no visible global function definition for ‘mtext’
plotMC: no visible global function definition for ‘axis’
plotMC: no visible global function definition for ‘par’
readADpaths: no visible global function definition for ‘read.table’
readRep: no visible global function definition for ‘read.table’
saveADpaths: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  axis lines mtext pairs par points read.table write.table
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "pairs", "par",
             "points")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
File ‘PBSddesolve/libs/PBSddesolve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘PCA4TS/libs/PCA4TS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
draw.pcaBootPlot: no visible global function definition for ‘plot’
draw.pcaBootPlot: no visible global function definition for ‘grid’
draw.pcaBootPlot: no visible global function definition for ‘points’
draw.pcaBootPlot: no visible global function definition for ‘symbols’
draw.pcaBootPlot: no visible global function definition for ‘legend’
pcaBootPlot: no visible global function definition for ‘prcomp’
pcaBootPlot: no visible global function definition for ‘cor’
pcaBootPlot: no visible global function definition for ‘quantile’
pcaBootPlot: no visible global function definition for ‘pdf’
pcaBootPlot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  cor dev.off grid legend pdf plot points prcomp quantile symbols
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "grid", "legend", "plot", "points", "symbols")
  importFrom("stats", "cor", "prcomp", "quantile")
to your NAMESPACE file.
File ‘pcaPA/libs/pcaPA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
PCDReg.wf: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  optimize
Consider adding
  importFrom("stats", "optimize")
to your NAMESPACE file.
File ‘PCICt/libs/PCICt.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.
defineTasks: no visible global function definition for ‘par’
defineTasks: no visible global function definition for ‘abline’
plotCorCoeff: no visible global function definition for ‘hist’
plotCorCoeff: no visible global function definition for ‘plot.new’
plotCorCoeff: no visible global function definition for ‘plot.window’
plotCorCoeff: no visible global function definition for ‘rect’
plotCorCoeff: no visible global function definition for ‘axis’
plotCorCoeff: no visible global function definition for ‘title’
plotCorCoeff: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline axis hist legend par plot.new plot.window rect title
Consider adding
  importFrom("graphics", "abline", "axis", "hist", "legend", "par",
             "plot.new", "plot.window", "rect", "title")
to your NAMESPACE file.
File ‘PCIT/libs/PCIT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
PdofCSGt.bootstrap5: no visible global function definition for ‘rnorm’
PdofCSGt.bootstrap5: no visible global function definition for ‘rt’
PdofCSt.T1or2: no visible global function definition for ‘combn’
PofCSGt: no visible global function definition for ‘combn’
PofCSLt.bootstrap5: no visible global function definition for ‘rnorm’
PofCSLt.bootstrap5: no visible global function definition for ‘rt’
PofCSt: no visible global function definition for ‘pnorm’
tindep: no visible binding for global variable ‘var’
tindep: no visible global function definition for ‘pt’
Undefined global functions or variables:
  combn pnorm pt rnorm rt var
Consider adding
  importFrom("stats", "pnorm", "pt", "rnorm", "rt", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
File ‘pdc/libs/pdc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.dbs plot.kepdf plot.pdfCluster summary.dbs summary.kepdf
  summary.pdfCluster
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘pdfCluster/libs/pdfCluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
pdist: no visible global function definition for ‘dist’
pdist: no visible global function definition for ‘new’
Undefined global functions or variables:
  dist new
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dist")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘pdist/libs/pdist.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
band.chol.cv: no visible global function definition for ‘cov’
pdsoft.cv: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
File ‘PDSCE/libs/PDSCE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  spectrum.c:707:14: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:715:20: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1606:41: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1654:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1654:63: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Peaks.Rcheck/00install.out’ for details.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
prepare_Rd: SpectrumBackground.Rd:59: Dropping empty section \keyword
prepare_Rd: SpectrumBackground.Rd:54-55: Dropping empty section \seealso
prepare_Rd: SpectrumBackground.Rd:56-57: Dropping empty section \examples
prepare_Rd: SpectrumDeconvolution.Rd:87: Dropping empty section \keyword
prepare_Rd: SpectrumDeconvolution.Rd:82-83: Dropping empty section \seealso
prepare_Rd: SpectrumDeconvolution.Rd:84-85: Dropping empty section \examples
prepare_Rd: SpectrumSearch.Rd:62: Dropping empty section \keyword
prepare_Rd: SpectrumSearch.Rd:59-60: Dropping empty section \examples
prepare_Rd: SpectrumSmoothMarkov.Rd:55: Dropping empty section \keyword
prepare_Rd: SpectrumSmoothMarkov.Rd:50-51: Dropping empty section \seealso
prepare_Rd: SpectrumSmoothMarkov.Rd:52-53: Dropping empty section \examples
File ‘Peaks/libs/Peaks.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
peacf: no visible global function definition for ‘is.ts’
peacf: no visible global function definition for ‘cycle’
peacf: no visible global function definition for ‘ts.intersect’
peacf: no visible global function definition for ‘lag’
peacf: no visible global function definition for ‘ts’
peacf: no visible global function definition for ‘pchisq’
peacf.plot: no visible global function definition for ‘plot’
peacf.plot: no visible global function definition for ‘segments’
peacf.plot: no visible global function definition for ‘title’
pear: no visible global function definition for ‘cycle’
pear: no visible global function definition for ‘pchisq’
peboxplot: no visible global function definition for ‘cycle’
peboxplot: no visible global function definition for ‘boxplot’
peboxplot: no visible global function definition for ‘title’
peplot: no visible global function definition for ‘par’
peplot: no visible global function definition for ‘cycle’
peplot: no visible global function definition for ‘plot’
peplot: no visible global function definition for ‘identify’
peplot: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  boxplot cycle identify is.ts lag mtext par pchisq plot segments title
  ts ts.intersect
Consider adding
  importFrom("graphics", "boxplot", "identify", "mtext", "par", "plot",
             "segments", "title")
  importFrom("stats", "cycle", "is.ts", "lag", "pchisq", "ts",
             "ts.intersect")
to your NAMESPACE file.
The following files should probably not be installed:
  ‘addendum.tex’, ‘slplot.tex’, ‘table1.tex’, ‘table3.tex’

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

These lines will be truncated in the PDF manual.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘RcppArmadillo’ ‘ggplot2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
AssoTestProc: no visible global function definition for ‘rbinom’
AssoTestProc: no visible global function definition for ‘princomp’
AssoTestProc: no visible global function definition for ‘loadings’
AssoTestProc: no visible global function definition for ‘lm’
CNVtypeAnay: no visible global function definition for ‘cov’
ClusProc: no visible global function definition for ‘princomp’
ClusProc: no visible global function definition for ‘prcomp’
ClusProc0: no visible global function definition for ‘kmeans’
ClusProc0: no visible global function definition for ‘cov’
Inde: no visible global function definition for ‘lm’
Inde: no visible global function definition for ‘var’
STE: no visible global function definition for ‘pchisq’
STIM: no visible global function definition for ‘cor’
STIM: no visible global function definition for ‘pchisq’
plot.clust: no visible global function definition for ‘princomp’
plot.clust: no visible global function definition for ‘loadings’
plot.clust: no visible global function definition for ‘qplot’
plot.clust: no visible global function definition for ‘geom_histogram’
plot.clust: no visible global function definition for ‘aes_string’
plot.clust: no visible global function definition for ‘barplot’
plot.clust: no visible global function definition for ‘title’
plot.clust: no visible global function definition for ‘mtext’
plot.clust: no visible global function definition for ‘text’
Undefined global functions or variables:
  aes_string barplot cor cov geom_histogram kmeans lm loadings mtext
  pchisq prcomp princomp qplot rbinom text title var
Consider adding
  importFrom("graphics", "barplot", "mtext", "text", "title")
  importFrom("stats", "cor", "cov", "kmeans", "lm", "loadings", "pchisq",
             "prcomp", "princomp", "rbinom", "var")
to your NAMESPACE file.
File ‘PedCNV/libs/PedCNV.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
blup: no visible global function definition for ‘model.matrix’
blup: no visible global function definition for ‘model.frame’
blup: no visible global function definition for ‘read.table’
calcG: no visible global function definition for ‘as’
gblup: no visible global function definition for ‘model.matrix’
gblup: no visible global function definition for ‘model.frame’
Undefined global functions or variables:
  as model.frame model.matrix read.table
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "model.frame", "model.matrix")
  importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘pedigree/libs/pedigree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
PEMM_fun : find.lambda: no visible global function definition for
  ‘optimize’
PEMM_fun: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov optimize
Consider adding
  importFrom("stats", "cov", "optimize")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  plot.pencopula print.pencopula
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
grid.points: no visible global function definition for ‘quantile’
knots.order: no visible global function definition for ‘median’
new.weights: no visible global function definition for ‘ecdf’
new.weights: no visible global function definition for ‘quantile’
plot.pencopula: no visible global function definition for ‘as.formula’
Undefined global functions or variables:
  as.formula ecdf median quantile
Consider adding
  importFrom("stats", "as.formula", "ecdf", "median", "quantile")
to your NAMESPACE file.
Running examples in ‘pencopula-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pencopula-package
> ### Title: The package 'pencopula' offers routines for estimating
> ###   multivariate penalized copula densities and copula distribution.
> ### Aliases: pencopula-package
> ### Keywords: nonparametric
> 
> ### ** Examples
> 
> Y <- cbind(runif(200),runif(200))
> plot(pencopula(Y,d=4,D=4,lambda=rep(10,2),base="B-spline"))
Error in as.double(y) : 
  cannot coerce type 'environment' to vector of type 'double'
Calls: plot -> plot.default -> xy.coords
Execution halted
File ‘PenCoxFrail/libs/PenCoxFrail.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘penMSM/libs/penMSM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.data: no visible global function definition for ‘rexp’
create.data: no visible global function definition for ‘runif’
create.data: no visible global function definition for ‘rbinom’
opt.splitval: no visible global function definition for ‘na.omit’
opt2D : opt.both: no visible global function definition for ‘optim’
Undefined global functions or variables:
  na.omit optim rbinom rexp runif
Consider adding
  importFrom("stats", "na.omit", "optim", "rbinom", "rexp", "runif")
to your NAMESPACE file.
'library' or 'require' call to ‘survival’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘CoxBoost’ ‘codetools’ ‘locfit’ ‘penalized’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  PLL.CoxBoost PLL.coxph predictProb.CoxBoost predictProb.coxph
  predictProb.survfit
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'aggregation.brier.Rd':
  \usage lines wider than 90 characters:
     aggregation.brier(full.data=NULL, response, x, model, cplx=NULL,  type=c("apparent", "noinf"), 

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
performance.curves.plot: no visible global function definition for
  ‘postscript’
performance.curves.plot: no visible global function definition for
  ‘axis’
performance.curves.plot: no visible global function definition for
  ‘lines’
performance.curves.plot: no visible global function definition for
  ‘legend’
performance.curves.plot: no visible global function definition for
  ‘grid’
performance.curves.plot: no visible global function definition for
  ‘dev.off’
precision.recall.curves.plot: no visible global function definition for
  ‘postscript’
precision.recall.curves.plot: no visible global function definition for
  ‘axis’
precision.recall.curves.plot: no visible global function definition for
  ‘lines’
precision.recall.curves.plot: no visible global function definition for
  ‘legend’
precision.recall.curves.plot: no visible global function definition for
  ‘grid’
precision.recall.curves.plot: no visible global function definition for
  ‘dev.off’
Undefined global functions or variables:
  axis dev.off grid legend lines postscript
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "axis", "grid", "legend", "lines")
to your NAMESPACE file.
File ‘PerfMeas/libs/PerfMeas.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  mean.LCL mean.UCL mean.geometric mean.stderr
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘dendextendRcpp’
permalgorithm: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
ksample.pclt: no visible global function definition for ‘pchisq’
pCI: no visible global function definition for ‘qbeta’
permKS.formula: no visible global function definition for ‘terms’
permTREND.default: no visible global function definition for ‘cor’
permTREND.formula: no visible global function definition for ‘terms’
permTS.formula: no visible global function definition for ‘terms’
trend.pclt: no visible global function definition for ‘pnorm’
twosample.pclt: no visible global function definition for ‘pnorm’
twosample.pclt: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  cor pchisq pnorm qbeta terms
Consider adding
  importFrom("stats", "cor", "pchisq", "pnorm", "qbeta", "terms")
to your NAMESPACE file.
Rd file 'perm-internal.Rd':
  \usage lines wider than 90 characters:
     ksample.exact.mc(scores, group, nmc = 10^4 - 1, seed = 1234321, digits = 12, p.conf.level = 0.99, setSEED = TRUE)
     trend.exact.mc(scores, group, alternative = "two.sided", nmc = 10^3 - 1, seed = 1234321, digits = 12, p.conf.level = 0.99, setSEED = TR ... [TRUNCATED]
     twosample.exact.mc(scores, group, alternative = "two.sided", nmc = 10^4 - 1, seed = 1234321, digits = 12, p.conf.level = 0.99, setSEED  ... [TRUNCATED]

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

These lines will be truncated in the PDF manual.
hasMethod: no visible global function definition for ‘getS3method’
Undefined global functions or variables:
  getS3method
Consider adding
  importFrom("utils", "getS3method")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  print.summary.perturb
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
colldiag: no visible global function definition for ‘na.omit’
perturb : cutsp: no visible global function definition for ‘runif’
perturb: no visible global function definition for ‘terms’
perturb: no visible global function definition for ‘formula’
perturb: no visible global function definition for ‘coefficients’
perturb: no visible global function definition for ‘as.formula’
print.reclassify: no visible global function definition for
  ‘addmargins’
reclassify : best.model: no visible global function definition for
  ‘glm’
reclassify : best.model: no visible global function definition for
  ‘as.formula’
reclassify : best.model: no visible global function definition for
  ‘poisson’
reclassify : best.model: no visible global function definition for
  ‘coef’
reclassify : best.model: no visible global function definition for
  ‘model.matrix’
reclassify : assocPat: no visible global function definition for
  ‘model.matrix’
reclassify : assocPat: no visible global function definition for ‘glm’
reclassify : assocPat: no visible global function definition for
  ‘poisson’
summary.perturb: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  addmargins as.formula coef coefficients formula glm model.matrix
  na.omit poisson runif sd terms
Consider adding
  importFrom("stats", "addmargins", "as.formula", "coef", "coefficients",
             "formula", "glm", "model.matrix", "na.omit", "poisson",
             "runif", "sd", "terms")
to your NAMESPACE file.
Running examples in ‘petro.One-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_papers_count
> ### Title: Number of paper for a given query
> ### Aliases: get_papers_count
> 
> ### ** Examples
> 
> # Example 1
> url_1 <- make_search_url(query = "static gradient survey", how = "all")
> get_papers_count(url_1)
Error in open.connection(x, "rb") : 
  server certificate verification failed. CAfile: none CRLfile: none
Calls: get_papers_count -> <Anonymous> -> read_html.default
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 31-37 (document_types_of_papers.Rmd) 
Error: processing vignette ‘document_types_of_papers.Rmd’ failed with diagnostics:
server certificate verification failed. CAfile: none CRLfile: none
Execution halted
Found the following significant warnings:
  Param.cpp:55:11: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/pgbart.Rcheck/00install.out’ for details.
File ‘pgee.mixed/libs/pgee.mixed.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
pGLS: no visible global function definition for ‘model.response’
pGLS: no visible global function definition for ‘model.matrix’
pGLS: no visible global function definition for ‘pt’
Undefined global functions or variables:
  model.matrix model.response pt
Consider adding
  importFrom("stats", "model.matrix", "model.response", "pt")
to your NAMESPACE file.
prepare_Rd: data_fs.Rd:11: Dropping empty section \source
prepare_Rd: var_fs.Rd:12-14: Dropping empty section \references
File ‘pGMGM/libs/pGMGM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ph2bye/libs/ph2bye.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
PharmPow_crossover: no visible global function definition for
  ‘read.table’
PharmPow_crossover: no visible global function definition for
  ‘write.csv’
PharmPow_crossover: no visible global function definition for ‘pdf’
PharmPow_crossover: no visible global function definition for ‘dev.off’
PharmPow_parallel: no visible global function definition for
  ‘read.table’
PharmPow_parallel: no visible global function definition for
  ‘write.csv’
PharmPow_parallel: no visible global function definition for ‘pdf’
PharmPow_parallel: no visible global function definition for ‘dev.off’
fig_PharmPow_crossover: no visible global function definition for
  ‘read.csv’
fig_PharmPow_parallel: no visible global function definition for
  ‘read.csv’
Undefined global functions or variables:
  dev.off pdf read.csv read.table write.csv
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "read.csv", "read.table", "write.csv")
to your NAMESPACE file.
flowField: no visible global function definition for ‘plot’
flowField: no visible global function definition for ‘arrows’
nullclines: no visible global function definition for ‘contour’
numericalSolution: no visible global function definition for ‘locator’
numericalSolution: no visible global function definition for ‘plot’
numericalSolution: no visible global function definition for ‘lines’
phasePortrait: no visible global function definition for ‘plot’
phasePortrait: no visible global function definition for ‘arrows’
stability: no visible global function definition for ‘locator’
trajectory: no visible global function definition for ‘locator’
trajectory: no visible global function definition for ‘plot’
trajectory: no visible global function definition for ‘lines’
trajectory: no visible global function definition for ‘points’
Undefined global functions or variables:
  arrows contour lines locator plot points
Consider adding
  importFrom("graphics", "arrows", "contour", "lines", "locator", "plot",
             "points")
to your NAMESPACE file.
Found the following significant warnings:
  LJMA_arms.c:297:11: warning: comparison of array 'env->p' equal to a null pointer is always false [-Wtautological-pointer-compare]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/PhaseType.Rcheck/00install.out’ for details.
Packages in Depends field not imported from:
  ‘ggplot2’ ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plot.phtMCMC: no visible global function definition for ‘ggplot’
plot.phtMCMC: no visible global function definition for ‘melt’
plot.phtMCMC: no visible global function definition for ‘geom_line’
plot.phtMCMC: no visible global function definition for ‘aes_string’
plot.phtMCMC: no visible global function definition for ‘geom_smooth’
plot.phtMCMC: no visible global function definition for ‘facet_wrap’
plot.phtMCMC: no visible global function definition for ‘ggtitle’
plot.phtMCMC: no visible global function definition for ‘xlab’
plot.phtMCMC: no visible global function definition for ‘ylab’
plot.phtMCMC: no visible global function definition for ‘geom_density’
Undefined global functions or variables:
  aes_string facet_wrap geom_density geom_line geom_smooth ggplot
  ggtitle melt xlab ylab
File ‘PhaseType/libs/PhaseType.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘LJMA_arms.o’
File ‘PhaseType/libs/PhaseType.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 use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
deforestation: no visible global function definition for ‘model.frame’
deforestation: no visible global function definition for ‘model.matrix’
deforestation: no visible global function definition for
  ‘model.response’
deforestation: no visible global function definition for ‘vcov’
deforestation: no visible global function definition for ‘glm’
demography: no visible global function definition for ‘model.frame’
demography: no visible global function definition for ‘model.matrix’
demography: no visible global function definition for ‘model.response’
form.beta.start: no visible global function definition for ‘coef’
form.beta.start: no visible global function definition for ‘glm’
form.sigma2.start: no visible global function definition for ‘var’
form.sigma2.start: no visible global function definition for
  ‘residuals’
form.sigma2.start: no visible global function definition for ‘glm’
rinvgamma: no visible global function definition for ‘rgamma’
rwish: no visible global function definition for ‘rchisq’
rwish: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  coef glm model.frame model.matrix model.response rchisq residuals
  rgamma rnorm var vcov
Consider adding
  importFrom("stats", "coef", "glm", "model.frame", "model.matrix",
             "model.response", "rchisq", "residuals", "rgamma", "rnorm",
             "var", "vcov")
to your NAMESPACE file.
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.
File ‘phcfM/libs/phcfM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
fox: no visible binding for global variable ‘sd’
fox: no visible global function definition for ‘cor’
fox: no visible global function definition for ‘interaction.plot’
fox: no visible global function definition for ‘reorder’
fox: no visible global function definition for ‘plot’
kang: no visible global function definition for ‘var’
kang: no visible binding for global variable ‘sd’
kang: no visible global function definition for ‘cor’
kang: no visible global function definition for ‘interaction.plot’
kang: no visible global function definition for ‘reorder’
kang: no visible global function definition for ‘plot’
nahu: no visible global function definition for ‘interaction.plot’
nahu: no visible global function definition for ‘reorder’
nahu: no visible global function definition for ‘plot’
thsu: no visible global function definition for ‘median’
thsu: no visible binding for global variable ‘sd’
thsu: no visible global function definition for ‘cor’
thsu: no visible global function definition for ‘interaction.plot’
thsu: no visible global function definition for ‘reorder’
thsu: no visible global function definition for ‘plot’
Undefined global functions or variables:
  cor interaction.plot median plot reorder sd var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "cor", "interaction.plot", "median", "reorder",
             "sd", "var")
to your NAMESPACE file.
File ‘phenmod/libs/phenmod.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
pheno.ddm: no visible global function definition for ‘new’
pheno.flm.fit: no visible binding for global variable ‘na.exclude’
pheno.flm.fit: no visible global function definition for ‘terms’
pheno.flm.fit: no visible global function definition for ‘residuals’
pheno.flm.fit: no visible global function definition for ‘qt’
pheno.lad.fit: no visible binding for global variable ‘na.exclude’
pheno.mlm.fit: no visible binding for global variable ‘na.exclude’
pheno.mlm.fit: no visible global function definition for ‘residuals’
Undefined global functions or variables:
  na.exclude new qt residuals terms
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "na.exclude", "qt", "residuals", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Rd file 'pheno.mlm.fit.Rd':
  \examples lines wider than 100 characters:
             R <- pheno.mlm.fit(DWD)                                                         # parameter estimation
             summary(tr)$coef[2]                                                                     # slope of trend
             summary(tr)$coef[4]                                                                     # standard error of trend

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
incident: no visible global function definition for ‘splinefun’
incident: no visible global function definition for ‘integrate’
phytoprod: no visible global function definition for ‘approx’
phytoprod: no visible global function definition for ‘splinefun’
phytoprod: no visible global function definition for ‘integrate’
reflectance: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx integrate splinefun
Consider adding
  importFrom("stats", "approx", "integrate", "splinefun")
to your NAMESPACE file.
File which contains pragma(s) suppressing diagnostics:
  ‘src/pijavski.cpp’
File ‘Pijavski/libs/Pijavski.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.pred.int: no visible global function definition for ‘plot.default’
plot.pred.int: no visible global function definition for ‘axis’
plot.pred.int: no visible global function definition for ‘box’
plot.pred.int : cidist: no visible global function definition for
  ‘ecdf’
plot.pred.int : negcidist: no visible global function definition for
  ‘ecdf’
plot.pred.int : pi.col.fun: no visible global function definition for
  ‘gray’
plot.pred.int: no visible global function definition for ‘segments’
plot.pred.int: no visible global function definition for ‘points’
plot.pred.int: no visible global function definition for ‘abline’
pred.int: no visible binding for global variable ‘sd’
prop.test.mult: no visible global function definition for ‘qnorm’
sim.basic: no visible global function definition for ‘rbinom’
sim.basic: no visible global function definition for ‘rnorm’
t.test.mult: no visible global function definition for ‘qt’
Undefined global functions or variables:
  abline axis box ecdf gray plot.default points qnorm qt rbinom rnorm
  sd segments
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "box", "plot.default",
             "points", "segments")
  importFrom("stats", "ecdf", "qnorm", "qt", "rbinom", "rnorm", "sd")
to your NAMESPACE file.
File ‘pirate/libs/pirate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘ggsubplot’
Found the following apparent S3 methods exported but not registered:
  [<-.db.obj
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘PivotalR/libs/PivotalR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'::' or ':::' import not declared from: ‘utility’
Depends: includes the non-default packages:
  ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘lattice’ ‘rggobi’ ‘ggplot2’
  ‘proto’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘RGtk2’ ‘gWidgetsRGtk2’
A package should be listed in only one of these fields.
Package in Depends field not imported from: ‘cairoDevice’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
prepare_Rd: PKgraph.Rd:11-13: Dropping empty section \arguments
prepare_Rd: PKgraph.Rd:17-19: Dropping empty section \examples
prepare_Rd: pkdata.Rd:9-11: Dropping empty section \format
prepare_Rd: pkdata.Rd:14-16: Dropping empty section \examples
prepare_Rd: pkdata2.Rd:9-11: Dropping empty section \format
prepare_Rd: pkdata2.Rd:14-16: Dropping empty section \examples
Rd file 'RSA.Rd':
  \examples lines wider than 100 characters:
     PKI.load.OpenSSH.pubkey("ssh-rsa AAAAB3NzaC1yc2EAAAABIwAAAIEAuvOXqfZ3pJeWeqyQOIXZwmgM1RBqPUmVx3XgntpA+YtOZjKfuoJSpg3LhBuI/wXx8L2QZXNFib ... [TRUNCATED]

These lines will be truncated in the PDF manual.
PKmod: no visible global function definition for ‘deriv’
Undefined global functions or variables:
  deriv
Consider adding
  importFrom("stats", "deriv")
to your NAMESPACE file.
PKadjust: no visible binding for global variable ‘jpeg’
PKadjust: no visible binding for global variable ‘bmp’
PKadjust: no visible binding for global variable ‘png’
PKadjust: no visible binding for global variable ‘tiff’
PKadjust: no visible binding for global variable ‘dev.new’
PKadjust: no visible global function definition for ‘dev.off’
PKfigure: no visible global function definition for ‘dev.cur’
PKfigure: no visible global function definition for ‘dev.off’
PKoutput: no visible global function definition for ‘heatmap’
PKoutput: no visible global function definition for
  ‘packageDescription’
PKshow: no visible global function definition for ‘browseURL’
addList1: no visible global function definition for ‘formula’
addList1.old: no visible global function definition for ‘formula’
addList2: no visible global function definition for ‘formula’
generate.plot: no visible global function definition for ‘dev.off’
writeHTML: no visible global function definition for
  ‘packageDescription’
writeLst: no visible global function definition for
  ‘packageDescription’
writeLst.tab: no visible global function definition for
  ‘packageDescription’
writeTable: no visible global function definition for
  ‘packageDescription’
writeTable: no visible global function definition for ‘quantile’
initialize,nonmem: no visible global function definition for
  ‘read.table’
Undefined global functions or variables:
  bmp browseURL dev.cur dev.new dev.off formula heatmap jpeg
  packageDescription png quantile read.table tiff
Consider adding
  importFrom("grDevices", "bmp", "dev.cur", "dev.new", "dev.off", "jpeg",
             "png", "tiff")
  importFrom("stats", "formula", "heatmap", "quantile")
  importFrom("utils", "browseURL", "packageDescription", "read.table")
to your NAMESPACE file.
File ‘plac/libs/plac.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘planar/libs/planar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘planor-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: alias-methods
> ### Title: Summarize the Design Properties
> ### Aliases: alias,designkey-method alias.designkey alias,keymatrix-method
> ###   alias.keymatrix alias,listofdesignkeys-method alias.listofdesignkeys
> ###   alias,listofkeyrings-method alias.listofkeyrings
> ###   alias,planordesign-method alias.planordesign
> ### Keywords: methods design
> 
> ### ** Examples
> 
> ### Creation of an object of class listofkeyrings
> K0 <- planor.designkey(factors=c(LETTERS[1:4], "block"), nlevels=rep(3,5),
+ model=~block+(A+B+C+D)^2, estimate=~A+B+C+D,
+ nunits=3^3, base=~A+B+C, max.sol=2)
Preliminary step 1 : processing the model specifications
Preliminary step 2 : performing prime decompositions on the factors
*** Main step for prime p = 3 : key-matrix search
  => search for columns 4 to 5 
      first visit to column 4
      first visit to column 5
    ---    col. 5 ( j = 2) 18 selected candidates
The search is closed: max.sol = 2 solution(s) found 
> ### alias on an object of class keymatrix
> alias(K0[[1]][[1]])
Error in UseMethod("alias") : 
  no applicable method for 'alias' applied to an object of class "keymatrix"
Calls: alias
Execution halted
File ‘PlayerRatings/libs/PlayerRatings.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘latticist’
'library' or 'require' call to ‘lattice’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘latticist’ 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:
  ‘cairoDevice’ ‘gWidgetsRGtk2’ ‘grid’ ‘lattice’
  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:
  ‘lattice:::lattice.getStatus’ ‘stats:::biplot.prcomp’
  See the note in ?`:::` about the use of this operator.
Found the following apparent S3 methods exported but not registered:
  plotCoords.biplot plotCoords.plot
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'plotCoords':
  ‘plotCoords.plot’ ‘plotCoords.biplot’

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
bwfw.hmm: no visible global function definition for ‘dnorm’
bwfw1.hmm: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
Rd file 'em.hmm.Rd':
  \examples lines wider than 100 characters:
     #all.Rlts=cbind(rbind(chr1.data,chr6.data), LIS=c(chr1.L2rlts$LIS,chr6.L2rlts$LIS), gFDR=plis.rlts$aLIS, fdr001state=plis.rlts$States)

These lines will be truncated in the PDF manual.
Packages in Depends field not imported from:
  ‘Formula’ ‘sm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
nrmlepln: no visible global function definition for ‘pchisq’
nrmlerasch: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
File ‘pln/libs/pln.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘adehabitat’
plotAuto: no visible global function definition for ‘window’
plotAuto: no visible global function definition for ‘title’
plotAuto: no visible global function definition for ‘axis’
plotAuto: no visible global function definition for ‘box’
plotCumu: no visible global function definition for ‘title’
plotCumu: no visible global function definition for ‘axis’
plotCumu: no visible global function definition for ‘box’
plotDens : panel.dens: no visible global function definition for ‘var’
plotDens : panel.dens: no visible global function definition for
  ‘quantile’
plotDens : panel.dens: no visible global function definition for
  ‘median’
plotDens: no visible global function definition for ‘tail’
plotQuant: no visible global function definition for ‘par’
plotQuant: no visible binding for global variable ‘quantile’
plotQuant: no visible global function definition for ‘plot’
plotQuant: no visible global function definition for ‘lines’
plotQuant: no visible global function definition for ‘bxp’
plotQuant: no visible global function definition for ‘matplot’
plotQuant: no visible global function definition for ‘axis’
plotQuant: no visible global function definition for ‘box’
plotQuant: no visible global function definition for ‘title’
plotSplom: no visible global function definition for ‘pairs’
plotTrace : panel.trace: no visible global function definition for
  ‘var’
plotTrace : panel.trace: no visible global function definition for
  ‘median’
plotTrace: no visible global function definition for ‘tail’
Undefined global functions or variables:
  axis box bxp lines matplot median pairs par plot quantile tail title
  var window
Consider adding
  importFrom("graphics", "axis", "box", "bxp", "lines", "matplot",
             "pairs", "par", "plot", "title")
  importFrom("stats", "median", "quantile", "var", "window")
  importFrom("utils", "tail")
to your NAMESPACE file.
generateEnvelope: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Rd file 'envelopeArea_and_Perimeter.Rd':
  \examples lines wider than 100 characters:
     cat("envelope area = ", envelopeStats["area"], " perimeter = ", envelopeStats["perimeter"],"\n")        
     cat("circle area = ", pi * r^2, " = ", sum(pi * r^2), "\ncircle perimenter = ",  2 * pi * r, " = ",  2 * pi * sum(r), "\n")

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

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

These lines will be truncated in the PDF manual.
llla.bi: no visible global function definition for ‘as.formula’
llla.bi: no visible global function definition for ‘glm’
llla.bi: no visible global function definition for ‘binomial’
llla.bi: no visible binding for global variable ‘logit’
llla.bi: no visible global function definition for ‘vcov’
llla.bi: no visible global function definition for ‘coef’
llla.mc: no visible global function definition for ‘model.matrix’
llla.mc: no visible global function definition for ‘as.formula’
llla.mc: no visible global function definition for ‘coxph’
llla.mc: no visible global function definition for ‘vcov’
llla.mc: no visible global function definition for ‘coef’
llla.mle: no visible global function definition for ‘as.formula’
llla.mle: no visible global function definition for ‘glm’
llla.mle: no visible global function definition for ‘poisson’
llla.mle: no visible global function definition for ‘coef’
llla.mle: no visible global function definition for ‘vcov’
mclgen: no visible global function definition for ‘reshape’
simRasch.1D: no visible global function definition for ‘rnorm’
simRasch.1D: no visible global function definition for ‘runif’
vcov.sandwich.glm: no visible global function definition for
  ‘model.matrix’
vcov.sandwich.glm: no visible global function definition for ‘weights’
vcov.sandwich.glm: no visible global function definition for
  ‘residuals’
vcov.sandwich.glm: no visible global function definition for ‘vcov’
Undefined global functions or variables:
  as.formula binomial coef coxph glm logit model.matrix poisson reshape
  residuals rnorm runif vcov weights
Consider adding
  importFrom("stats", "as.formula", "binomial", "coef", "glm",
             "model.matrix", "poisson", "reshape", "residuals", "rnorm",
             "runif", "vcov", "weights")
to your NAMESPACE file.
Running examples in ‘plsRcox-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plsRcox
> ### Title: Partial least squares Regression generalized linear models
> ### Aliases: plsRcox plsRcoxmodel.default plsRcoxmodel.formula
> ### Keywords: models regression
> 
> ### ** Examples
> 
> data(micro.censure)
> data(Xmicro.censure_compl_imp)
> 
> X_train_micro <- apply((as.matrix(Xmicro.censure_compl_imp)),FUN="as.numeric",MARGIN=2)[1:80,]
> X_train_micro_df <- data.frame(X_train_micro)
> Y_train_micro <- micro.censure$survyear[1:80]
> C_train_micro <- micro.censure$DC[1:80]
> 
> plsRcox(X_train_micro,time=Y_train_micro,event=C_train_micro,nt=5)
Error in UseMethod("plsRcoxmodel") : 
  no applicable method for 'plsRcoxmodel' applied to an object of class "c('matrix', 'double', 'numeric')"
Calls: plsRcox
Execution halted
print.densityEHpi: no visible global function definition for ‘str’
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
File ‘plugdensity/libs/plugdensity.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 'predict.plus.Rd':
  \examples lines wider than 100 characters:
     extracted.values <- predict(object, lam = sort(object$lam.path[1:10],decreasing=TRUE), newx=object$x)

These lines will be truncated in the PDF manual.
Found the following apparent S3 methods exported but not registered:
  rbind.fill rbind.fill.matrix
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'rbind.fill':
  ‘rbind.fill’

S3 methods shown with full name in documentation object 'rbind.fill.matrix':
  ‘rbind.fill.matrix’

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 ‘plyr/libs/plyr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 assignments to the global environment:
File ‘PMA/R/CCA.xlfuns.R’:
  assign(paste("cor.", x, sep = ""), val, pos = .GlobalEnv)
.MCM: no visible global function definition for ‘runif’
.MCM: no visible global function definition for ‘rmultinom’
.MCM: no visible global function definition for ‘mahalanobis’
.MCM: no visible global function definition for ‘optimize’
.MCM : f: no visible global function definition for ‘mahalanobis’
.MCM: no visible global function definition for ‘alarm’
.igpark: no visible global function definition for ‘kmeans’
.loglik: no visible global function definition for ‘mahalanobis’
.plot.gpcm: no visible global function definition for ‘plot’
.plot.gpcm: no visible global function definition for ‘lines’
.plot.gpcm: no visible global function definition for ‘legend’
.rwgpar: no visible global function definition for ‘rexp’
.weights: no visible global function definition for ‘mahalanobis’
Undefined global functions or variables:
  alarm kmeans legend lines mahalanobis optimize plot rexp rmultinom
  runif
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "kmeans", "mahalanobis", "optimize", "rexp",
             "rmultinom", "runif")
  importFrom("utils", "alarm")
to your NAMESPACE file.
dbm: no visible global function definition for ‘optim’
dbm: no visible global function definition for ‘new’
destat: no visible global function definition for ‘weighted.mean’
local.knn: no visible global function definition for ‘sd’
local.knn: no visible global function definition for ‘optim’
mdpref: no visible global function definition for ‘sd’
mdpref: no visible global function definition for ‘text’
mdpref: no visible global function definition for ‘lines’
phicom: no visible global function definition for ‘optim’
phicom: no visible global function definition for ‘new’
pl: no visible global function definition for ‘optim’
pl: no visible global function definition for ‘new’
rol: no visible global function definition for ‘nlm’
rol: no visible global function definition for ‘new’
wdbm: no visible global function definition for ‘optim’
wdbm: no visible global function definition for ‘new’
Undefined global functions or variables:
  lines new nlm optim sd text weighted.mean
Consider adding
  importFrom("graphics", "lines", "text")
  importFrom("methods", "new")
  importFrom("stats", "nlm", "optim", "sd", "weighted.mean")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘png/libs/png.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘MASS’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘MASS’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pnmtrem1: no visible global function definition for ‘pnorm’
pnmtrem1: no visible global function definition for ‘dnorm’
pnmtrem1: no visible global function definition for ‘ginv’
pnmtrem1 : fun: no visible global function definition for ‘pnorm’
pnmtrem1 : derf: no visible global function definition for ‘dnorm’
pnmtrem1 : derf: no visible global function definition for ‘pnorm’
pnmtrem1 : fun: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm ginv pnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm")
to your NAMESPACE file.
'library' or 'require' call to ‘rgenoud’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.sigma: no visible global function definition for ‘plot’
smooth: no visible global function definition for ‘genoud’
Undefined global functions or variables:
  genoud plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  print.poicla print.poiclacv print.poidist
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
ColorDendrogram: no visible global function definition for ‘plot’
ColorDendrogram: no visible global function definition for ‘segments’
CountDataSet: no visible global function definition for ‘rexp’
CountDataSet: no visible global function definition for ‘runif’
CountDataSet: no visible global function definition for ‘rnorm’
CountDataSet: no visible global function definition for ‘rnbinom’
NullModel: no visible binding for global variable ‘quantile’
NullModel : <anonymous>: no visible global function definition for
  ‘median’
NullModelTest: no visible binding for global variable ‘quantile’
NullModelTest : <anonymous>: no visible global function definition for
  ‘median’
PoissonDistance: no visible global function definition for ‘as.dist’
permute.rows: no visible global function definition for ‘runif’
print.poiclacv: no visible global function definition for ‘write.table’
se: no visible global function definition for ‘sd’
Undefined global functions or variables:
  as.dist median plot quantile rexp rnbinom rnorm runif sd segments
  write.table
Consider adding
  importFrom("graphics", "plot", "segments")
  importFrom("stats", "as.dist", "median", "quantile", "rexp", "rnbinom",
             "rnorm", "runif", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
bipoilogMLE: no visible global function definition for ‘optim’
bipoilogMLE: no visible global function definition for ‘write.table’
poilogMLE: no visible global function definition for ‘optim’
rbipoilog : sim: no visible global function definition for ‘rnorm’
rbipoilog : sim: no visible global function definition for ‘rpois’
rpoilog : sim: no visible global function definition for ‘rnorm’
rpoilog : sim: no visible global function definition for ‘rpois’
Undefined global functions or variables:
  optim rnorm rpois write.table
Consider adding
  importFrom("stats", "optim", "rnorm", "rpois")
  importFrom("utils", "write.table")
to your NAMESPACE file.
File ‘poilog/libs/poilog.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
approxMargMLE: no visible global function definition for ‘optim’
approxMargMLECI : ciFunction: no visible global function definition for
  ‘qchisq’
approxMargMLECI: no visible global function definition for ‘uniroot’
margMLE: no visible global function definition for ‘optim’
margMLECI: no visible global function definition for ‘optim’
margMLECI : unNormLikeMinusVal: no visible global function definition
  for ‘qchisq’
margMLECI: no visible global function definition for ‘uniroot’
profMLECI : ciFunction: no visible global function definition for
  ‘qchisq’
profMLECI: no visible global function definition for ‘uniroot’
rtbinom: no visible global function definition for ‘rbinom’
rtpois: no visible global function definition for ‘rpois’
waldCI: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  optim qchisq qnorm rbinom rpois uniroot
Consider adding
  importFrom("stats", "optim", "qchisq", "qnorm", "rbinom", "rpois",
             "uniroot")
to your NAMESPACE file.
File ‘poisDoubleSamp/libs/poisDoubleSamp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘combinat’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Est.Depth: no visible global function definition for ‘quantile’
PS.FDR: no visible global function definition for ‘quantile’
Permu.Ind: no visible global function definition for ‘permn’
Permu.Ind: no visible global function definition for ‘hcube’
Trans.Data: no visible global function definition for ‘write.table’
Trans.Data: no visible global function definition for ‘predict’
Trans.Data: no visible global function definition for ‘lm’
Undefined global functions or variables:
  hcube lm permn predict quantile write.table
Consider adding
  importFrom("stats", "lm", "predict", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
rpoistweedie: no visible global function definition for ‘runif’
testOmegaPT: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
prepare_Rd: poistweedie.Rd:51: Dropping empty section \references
prepare_Rd: ppoistweedie.Rd:37: Dropping empty section \references
prepare_Rd: qpoistweedie.Rd:40: Dropping empty section \references
prepare_Rd: rpoistweedie.Rd:36: Dropping empty section \references
prepare_Rd: varpt.Rd:31: Dropping empty section \references
Rd file 'ppoistweedie.Rd':
  \examples lines wider than 100 characters:
     layout.show(1)                                                                                                                          ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Packages in Depends field not imported from:
  ‘MASS’ ‘scatterplot3d’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plot.poLCA: no visible global function definition for ‘layout’
plot.poLCA: no visible global function definition for ‘par’
poLCA: no visible global function definition for ‘model.frame’
poLCA: no visible global function definition for ‘model.response’
poLCA: no visible global function definition for ‘model.matrix’
poLCA: no visible global function definition for ‘runif’
poLCA: no visible global function definition for ‘ginv’
poLCA: no visible global function definition for ‘flush.console’
poLCA.makeplot.dich: no visible global function definition for
  ‘scatterplot3d’
poLCA.makeplot.poly: no visible global function definition for
  ‘scatterplot3d’
poLCA.se: no visible global function definition for ‘ginv’
poLCA.simdata: no visible global function definition for ‘runif’
poLCA.simdata: no visible global function definition for ‘rnorm’
poLCA.table: no visible global function definition for ‘model.frame’
print.poLCA: no visible global function definition for ‘pt’
print.poLCA: no visible global function definition for ‘flush.console’
rmulti: no visible global function definition for ‘runif’
Undefined global functions or variables:
  flush.console ginv layout model.frame model.matrix model.response par
  pt rnorm runif scatterplot3d
Consider adding
  importFrom("graphics", "layout", "par")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "pt", "rnorm", "runif")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
File ‘poLCA/libs/poLCA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
qPolyaAeppliSingle: no visible global function definition for ‘qgamma’
rPolyaAeppli: no visible global function definition for ‘rpois’
rPolyaAeppli: no visible global function definition for ‘rgeom’
Undefined global functions or variables:
  qgamma rgeom rpois
Consider adding
  importFrom("stats", "qgamma", "rgeom", "rpois")
to your NAMESPACE file.
File ‘polyfreqs/libs/polyfreqs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘matrixcalc’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘matrixcalc’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
print.mixed.pom: no visible global function definition for ‘pnorm’
print.pom: no visible global function definition for ‘pnorm’
siteocc : get.mod.matrix: no visible binding for global variable
  ‘na.pass’
siteocc : get.mod.matrix: no visible global function definition for
  ‘formula’
siteocc : get.mod.matrix: no visible global function definition for
  ‘model.matrix’
siteocc: no visible global function definition for ‘nlminb’
siteocc: no visible global function definition for
  ‘is.positive.definite’
Undefined global functions or variables:
  formula is.positive.definite model.matrix na.pass nlminb pnorm
Consider adding
  importFrom("stats", "formula", "model.matrix", "na.pass", "nlminb",
             "pnorm")
to your NAMESPACE file.
Missing or unexported object: ‘GA::gaMonitor2’
Rd file 'popgen.Rd':
  \usage lines wider than 90 characters:
     popgen(datafile, ndigit = 3, freq.overall = T, freq.by.pop = T, genetic.stats = T, pairwise.fst = T)

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

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

contributionSummaryDf,simResult : <anonymous>: no visible global
  function definition for ‘aggregate’
getSimTrades,stiFromSignal-orderable-portfolio-simData-logical: no
  visible binding for global variable ‘shares’
loadIn,simResult-character-missing: no visible binding for global
  variable ‘master.freq’
loadIn,simResult-character-missing: no visible binding for global
  variable ‘master.errors’
loadIn,simResult-character-missing: no visible binding for global
  variable ‘master.type’
loadIn,simResult-character-missing: no visible binding for global
  variable ‘master.summary.interface’
loadIn,simResultSinglePeriod-character-missing: no visible binding for
  global variable ‘x’
plot,simResult-missing: no visible global function definition for
  ‘xyplot’
runSim,portfolioSim-logical: no visible binding for global variable
  ‘id’
runSim,portfolioSim-logical: no visible global function definition for
  ‘updateSummary’
securityPerfSummaryDf,simResult: no visible global function definition
  for ‘aggregate’
summary,simResult: no visible global function definition for ‘sd’
summary,simResult: no visible global function definition for ‘head’
summary,simResult: no visible global function definition for ‘tail’
Undefined global functions or variables:
  aggregate head id master.errors master.freq master.summary.interface
  master.type sd shares tail updateSummary x xyplot
Consider adding
  importFrom("stats", "aggregate", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
File ‘POT/libs/POT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  powell.c:700:14: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  powell.c:724:12: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/powell.Rcheck/00install.out’ for details.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

powell: no visible global function definition for ‘Quote’
Undefined global functions or variables:
  Quote
Consider adding
  importFrom("methods", "Quote")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘powell/libs/powell.so’:
  Found ‘printf’, possibly from ‘printf’ (C)
    Object: ‘powell.o’
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Object: ‘powell.o’
File ‘powell/libs/powell.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 use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
fnfam: no visible global function definition for ‘qnorm’
fx: no visible global function definition for ‘qnorm’
normplot : <local> : replot: no visible global function definition for
  ‘qnorm’
normplot : <local> : replot: no visible global function definition for
  ‘pnorm’
normplot : <local> : replot: no visible global function definition for
  ‘plot’
normplot : <local> : replot: no visible global function definition for
  ‘dnorm’
normplot : <local> : replot: no visible global function definition for
  ‘points’
normplot : <local> : replot: no visible global function definition for
  ‘lines’
normplot : <local> : regen: no visible global function definition for
  ‘rnorm’
normplot : <local> : regen: no visible global function definition for
  ‘rexp’
nsibs: no visible global function definition for ‘qnorm’
ntdt: no visible global function definition for ‘uniroot’
plotDom: no visible global function definition for ‘plot’
plotNsibs: no visible global function definition for ‘plot’
plotNtdt: no visible global function definition for ‘plot’
plotNtdt: no visible global function definition for ‘lines’
plotNtdt: no visible global function definition for ‘legend’
ptdt: no visible global function definition for ‘optimize’
ptdt: no visible global function definition for ‘uniroot’
ptdt: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dnorm legend lines optimize plot pnorm points qnorm rexp rnorm
  uniroot
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("stats", "dnorm", "optimize", "pnorm", "qnorm", "rexp",
             "rnorm", "uniroot")
to your NAMESPACE file.
Found the following significant warnings:
  ppcctest_pearson3.c:19:66: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ppcc.Rcheck/00install.out’ for details.
pps1: no visible global function definition for ‘runif’
ppss: no visible global function definition for ‘runif’
ppswr: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
prepare_Rd: calif.Rd:5-6: Dropping empty section \arguments
prepare_Rd: calif.Rd:8-9: Dropping empty section \examples
prepare_Rd: califcty.Rd:5-6: Dropping empty section \arguments
prepare_Rd: califcty.Rd:8-9: Dropping empty section \examples
prepare_Rd: sizesok.Rd:12-13: Dropping empty section \examples
prepare_Rd: stratumsizes.Rd:11-12: Dropping empty section \examples
LDA.Tree : Find.proj: no visible binding for global variable ‘var’
LDA.Tree : Find.proj: no visible binding for global variable ‘IQR’
LDA.Tree : Find.proj: no visible binding for global variable ‘median’
PDA.Tree : Find.proj: no visible binding for global variable ‘var’
PDA.Tree : Find.proj: no visible binding for global variable ‘median’
PDA.Tree : Find.proj: no visible binding for global variable ‘IQR’
PP.Tree : Find.proj: no visible binding for global variable ‘var’
PP.Tree : Find.proj: no visible binding for global variable ‘median’
PP.Tree : Find.proj: no visible binding for global variable ‘IQR’
PP.optimize.Huber: no visible binding for global variable ‘sd’
PP.optimize.anneal: no visible binding for global variable ‘sd’
PP.optimize.plot: no visible binding for global variable ‘sd’
PP.optimize.plot: no visible global function definition for ‘hist’
PP.optimize.plot: no visible global function definition for ‘text’
PP.optimize.plot: no visible global function definition for ‘par’
PP.optimize.plot: no visible global function definition for ‘plot’
PP.optimize.plot: no visible global function definition for ‘colors’
PP.optimize.plot: no visible global function definition for ‘pairs’
PP.optimize.random: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  IQR colors hist median pairs par plot sd text var
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "hist", "pairs", "par", "plot", "text")
  importFrom("stats", "IQR", "median", "sd", "var")
to your NAMESPACE file.
File ‘PPtree/libs/PPtree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.alleleobject print.comprabclust print.nnclean print.prab
  print.prabclust print.summary.prabtest summary.prabtest
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
prais.winsten: no visible global function definition for ‘model.frame’
prais.winsten: no visible global function definition for ‘as.formula’
prais.winsten: no visible global function definition for ‘tail’
Undefined global functions or variables:
  as.formula model.frame tail
Consider adding
  importFrom("stats", "as.formula", "model.frame")
  importFrom("utils", "tail")
to your NAMESPACE file.
TT.test : <anonymous>: no visible global function definition for
  ‘t.test’
TT.test: no visible binding for global variable ‘sd’
TT.test: no visible global function definition for ‘setNames’
kirjelda : combo: no visible binding for global variable ‘sd’
kor.tabel: no visible binding for global variable ‘cor.test’
Undefined global functions or variables:
  cor.test sd setNames t.test
Consider adding
  importFrom("stats", "cor.test", "sd", "setNames", "t.test")
to your NAMESPACE file.
Found the following significant warnings:
  ./shared.h:67:9: warning: result of comparison of constant 2147483648 with expression of type 'int' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/praznik.Rcheck/00install.out’ for details.
File ‘prclust/libs/prclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: '%+%' is deprecated.
  Warning: '%+%' is deprecated.
  Warning: '%+%' is deprecated.
  Warning: '%+%' is deprecated.
  Warning: '%+%' is deprecated.
  Warning: '%+%' is deprecated.
  Warning: '%+%' is deprecated.
  Warning: '%+%' is deprecated.
  Warning: '%+%' is deprecated.
  Warning: '%+%' is deprecated.
  Warning: '%+%' is deprecated.
  Warning: '%+%' is deprecated.
  Warning: '%+%' is deprecated.
  Warning: '%+%' is deprecated.
  Warning: '%+%' is deprecated.
  Warning: '%+%' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
gausspred: no visible global function definition for ‘qt’
mvapred: no visible global function definition for ‘qt’
Undefined global functions or variables:
  qt
Consider adding
  importFrom("stats", "qt")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘DESCRIPTION.bck’
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘predmixcor/R/firstlib.r’:
  .First.lib calls:
    cat("predmixcor loaded\n", "COPY RIGHT: Longhai Li\n", "http://math.usask.ca/~longhai\n",     "Type ?begin.predmixcor for help\n", sep = "")

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

Predict.mix: no visible global function definition for ‘dbinom’
abs_cor: no visible global function definition for ‘cor’
gen.alpha.IGamma: no visible global function definition for ‘qgamma’
gendata.mix: no visible global function definition for ‘runif’
gendata.mix: no visible global function definition for ‘rbeta’
mh1.unif: no visible global function definition for ‘runif’
train_predict_mix: no visible global function definition for ‘dbinom’
training: no visible global function definition for ‘runif’
training: no visible global function definition for ‘dbinom’
Undefined global functions or variables:
  cor dbinom qgamma rbeta runif
Consider adding
  importFrom("stats", "cor", "dbinom", "qgamma", "rbeta", "runif")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘COPYRIGHTS’
Copyright information should be in file inst/COPYRIGHTS
Found the following hidden files and directories:
  data/.Rapp.history
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘deSolve’ which was already attached by Depends.
  Please remove these calls from your code.
LVCompGames: no visible global function definition for ‘runif’
LVCompGames: no visible global function definition for ‘plot’
LVCompGames: no visible global function definition for ‘axis’
LVCompGames: no visible global function definition for ‘box’
LVCompGames: no visible global function definition for ‘lines’
LVCompGames: no visible global function definition for ‘points’
MetaSim: no visible global function definition for ‘runif’
chesson: no visible global function definition for ‘rbeta’
chesson: no visible global function definition for ‘dbeta’
chesson : rhof: no visible global function definition for ‘dbeta’
chesson: no visible global function definition for ‘integrate’
pimmlawton: no visible global function definition for ‘runif’
Undefined global functions or variables:
  axis box dbeta integrate lines plot points rbeta runif
Consider adding
  importFrom("graphics", "axis", "box", "lines", "plot", "points")
  importFrom("stats", "dbeta", "integrate", "rbeta", "runif")
to your NAMESPACE file.
File ‘primerTree/libs/primerTree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
basisplot: no visible global function definition for ‘plot’
basisplot: no visible global function definition for ‘abline’
basisplot: no visible global function definition for ‘text’
basisplot: no visible global function definition for ‘par’
plot.prinsimp: no visible global function definition for ‘screeplot’
plot.simpart: no visible global function definition for ‘par’
position_text: no visible global function definition for ‘par’
position_text: no visible global function definition for ‘strwidth’
simpart.formula: no visible global function definition for ‘terms’
simpart.formula: no visible global function definition for
  ‘model.matrix’
varperc: no visible global function definition for ‘plot’
varperc: no visible global function definition for ‘lines’
varperc: no visible global function definition for ‘text’
varsimp: no visible global function definition for ‘plot’
varsimp: no visible global function definition for ‘points’
varsimp: no visible global function definition for ‘text’
varsimp: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline lines model.matrix par plot points screeplot strwidth terms
  text
Consider adding
  importFrom("graphics", "abline", "lines", "par", "plot", "points",
             "strwidth", "text")
  importFrom("stats", "model.matrix", "screeplot", "terms")
to your NAMESPACE file.
Package suggested but not available for checking: ‘gurobi’
pr.conditional: no visible global function definition for ‘qnorm’
pr.marginal: no visible global function definition for ‘qnorm’
prLogisticDelta: no visible global function definition for ‘glm’
prLogisticDelta: no visible binding for global variable ‘binomial’
Undefined global functions or variables:
  binomial glm qnorm
Consider adding
  importFrom("stats", "binomial", "glm", "qnorm")
to your NAMESPACE file.
.pfda.fstep: no visible global function definition for ‘dist’
.pfda.main: no visible global function definition for ‘plot’
.pfda.mstep: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov dist plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "cov", "dist")
to your NAMESPACE file.
prepare_Rd: ProbForecastGOP-package.Rd:42-43: Dropping empty section \seealso
Rd file 'Emp.variog.Rd':
  \usage lines wider than 90 characters:
     Emp.variog(day, obs, forecast, id, coord1, coord2, cut.points=NULL, max.dist=NULL, nbins=300)

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
GPois: no visible global function definition for ‘dnorm’
GPois: no visible binding for global variable ‘poisson’
GPois: no visible global function definition for ‘predict’
GPois: no visible global function definition for ‘fitted’
GPois: no visible global function definition for ‘residuals’
GPois: no visible global function definition for ‘smooth.spline’
ProDenICA: no visible global function definition for ‘rnorm’
d.gaussmix: no visible global function definition for ‘dnorm’
djordan: no visible global function definition for ‘dt’
djordan: no visible global function definition for ‘dunif’
mixmat: no visible global function definition for ‘rnorm’
mixmat: no visible global function definition for ‘runif’
plot.ProDenICA: no visible global function definition for ‘plot’
r.gaussmix: no visible global function definition for ‘rmultinom’
r.gaussmix: no visible global function definition for ‘rnorm’
rjordan: no visible global function definition for ‘rt’
rjordan: no visible global function definition for ‘runif’
rmix.dexp: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dnorm dt dunif fitted plot poisson predict residuals rmultinom rnorm
  rt runif smooth.spline
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dnorm", "dt", "dunif", "fitted", "poisson",
             "predict", "residuals", "rmultinom", "rnorm", "rt", "runif",
             "smooth.spline")
to your NAMESPACE file.
profBinary: no visible global function definition for ‘model.frame’
profBinary: no visible global function definition for ‘model.matrix’
profLinear: no visible global function definition for ‘model.frame’
profLinear: no visible global function definition for ‘model.matrix’
profLinear: no visible global function definition for ‘model.response’
profLinear: no visible global function definition for ‘model.extract’
summary.profBinary: no visible global function definition for ‘terms’
summary.profBinary: no visible global function definition for ‘qbeta’
summary.profLinear: no visible global function definition for ‘terms’
Undefined global functions or variables:
  model.extract model.frame model.matrix model.response qbeta terms
Consider adding
  importFrom("stats", "model.extract", "model.frame", "model.matrix",
             "model.response", "qbeta", "terms")
to your NAMESPACE file.
File ‘profdpm/libs/profdpm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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’ ‘nlme’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.simplify : <anonymous>: no visible binding for global variable ‘hist’
.simplify : <anonymous>: no visible binding for global variable ‘start’
.simplify: no visible binding for global variable ‘start’
.simplify: no visible binding for global variable ‘end’
ggplot.profr: no visible global function definition for ‘ggplot’
ggplot.profr: no visible global function definition for ‘geom_rect’
ggplot.profr: no visible global function definition for ‘aes’
ggplot.profr: no visible binding for global variable ‘start’
ggplot.profr: no visible binding for global variable ‘end’
ggplot.profr: no visible global function definition for ‘geom_text’
ggplot.profr: no visible binding for global variable ‘time’
ggplot.profr: no visible global function definition for
  ‘scale_y_continuous’
ggplot.profr: no visible global function definition for
  ‘scale_x_continuous’
plot.profr: no visible global function definition for ‘plot’
plot.profr: no visible global function definition for ‘rect’
plot.profr: no visible binding for global variable ‘time’
plot.profr: no visible global function definition for ‘text’
profr: no visible global function definition for ‘Rprof’
Undefined global functions or variables:
  Rprof aes end geom_rect geom_text ggplot hist plot rect
  scale_x_continuous scale_y_continuous start text time
Consider adding
  importFrom("graphics", "hist", "plot", "rect", "text")
  importFrom("stats", "end", "start", "time")
  importFrom("utils", "Rprof")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘splines’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
IndividualPROC: no visible global function definition for ‘survfit’
IndividualPROC: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile survfit
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
File ‘proj4/libs/proj4.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘__var_28_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/PropClust.Rcheck/00install.out’ for details.
addpi: no visible global function definition for ‘lines’
genPerms: no visible global function definition for ‘combn’
getVar: no visible global function definition for ‘glm’
getVar: no visible global function definition for ‘binomial’
getVar: no visible global function definition for ‘var’
pba: no visible global function definition for ‘glm’
pba: no visible global function definition for ‘binomial’
pba: no visible global function definition for ‘predict’
pba: no visible global function definition for ‘rbinom’
pcr: no visible global function definition for ‘quantile’
plotpi: no visible global function definition for ‘plot’
plotpi: no visible global function definition for ‘axis’
plotpi: no visible global function definition for ‘abline’
plotpi: no visible global function definition for ‘lines’
Undefined global functions or variables:
  abline axis binomial combn glm lines plot predict quantile rbinom var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "plot")
  importFrom("stats", "binomial", "glm", "predict", "quantile", "rbinom",
             "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
Cul: no visible global function definition for ‘qf’
blockScale: no visible binding for global variable ‘sd’
cochranTest: no visible global function definition for ‘prcomp’
cochranTest: no visible binding for global variable ‘var’
cochranTest: no visible global function definition for ‘matplot’
cochranTest: no visible global function definition for ‘legend’
continuumRemoval : crfun: no visible global function definition for
  ‘chull’
continuumRemoval : crfun: no visible global function definition for
  ‘approx’
continuumRemoval : crfun: no visible global function definition for
  ‘splinefun’
detrend: no visible binding for global variable ‘sd’
duplex: no visible global function definition for ‘prcomp’
e2m: no visible global function definition for ‘cov’
kenStone: no visible global function definition for ‘prcomp’
naes: no visible global function definition for ‘prcomp’
naes: no visible global function definition for ‘kmeans’
puchwein: no visible global function definition for ‘prcomp’
readASD: no visible global function definition for ‘read.table’
resample : resfun: no visible global function definition for ‘approx’
resample : resfun: no visible global function definition for
  ‘splinefun’
shenkWest: no visible global function definition for ‘prcomp’
spliceCorrection : extrapfun: no visible global function definition for
  ‘lm’
standardNormalVariate: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  approx chull cov kmeans legend lm matplot prcomp qf read.table sd
  splinefun var
Consider adding
  importFrom("grDevices", "chull")
  importFrom("graphics", "legend", "matplot")
  importFrom("stats", "approx", "cov", "kmeans", "lm", "prcomp", "qf",
             "sd", "splinefun", "var")
  importFrom("utils", "read.table")
to your NAMESPACE file.
File ‘prospectr/libs/prospectr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
addIonSatistics: no visible binding for global variable ‘median’
adjustOne: no visible binding for global variable ‘median’
attachModifications: no visible global function definition for
  ‘na.omit’
avrgLoadingCalculation: no visible binding for global variable ‘median’
channelResponses : estimate: no visible binding for global variable
  ‘var’
responseStatisics : func: no visible global function definition for
  ‘aggregate’
testing: no visible global function definition for ‘aov’
testingOneshot: no visible global function definition for ‘anova’
testingTukey: no visible global function definition for ‘TukeyHSD’
Undefined global functions or variables:
  TukeyHSD aggregate anova aov median na.omit var
Consider adding
  importFrom("stats", "TukeyHSD", "aggregate", "anova", "aov", "median",
             "na.omit", "var")
to your NAMESPACE file.
estimateLSEparam: no visible global function definition for ‘lm’
estimateMLEparam: no visible global function definition for ‘optim’
getCCnlL: no visible global function definition for ‘dnorm’
iterateScampi: no visible global function definition for ‘quantile’
plot.scampi: no visible global function definition for ‘hist’
plot.scampiVal: no visible global function definition for ‘par’
plot.scampiVal: no visible global function definition for ‘hist’
plot.scampiVal: no visible global function definition for ‘abline’
plot.scampiVal: no visible global function definition for ‘qqnorm’
plot.scampiVal: no visible global function definition for ‘qqline’
sampleInitialVector: no visible global function definition for ‘runif’
Undefined global functions or variables:
  abline dnorm hist lm optim par qqline qqnorm quantile runif
Consider adding
  importFrom("graphics", "abline", "hist", "par")
  importFrom("stats", "dnorm", "lm", "optim", "qqline", "qqnorm",
             "quantile", "runif")
to your NAMESPACE file.
'library' or 'require' call to ‘class’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘class’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
addcircle: no visible global function definition for ‘lines’
addclassifierboundary: no visible global function definition for ‘par’
addclassifierboundary: no visible global function definition for
  ‘contour’
plot.protoclass: no visible global function definition for ‘plot’
plot.protoclass: no visible global function definition for ‘box’
plot.protoclass: no visible global function definition for ‘rgb2hsv’
plot.protoclass: no visible global function definition for ‘col2rgb’
plot.protoclass: no visible global function definition for ‘points’
plot.protoclass: no visible global function definition for ‘hsv’
predict.protoclass: no visible global function definition for ‘knn1’
Undefined global functions or variables:
  box col2rgb contour hsv knn1 lines par plot points rgb2hsv
Consider adding
  importFrom("grDevices", "col2rgb", "hsv", "rgb2hsv")
  importFrom("graphics", "box", "contour", "lines", "par", "plot",
             "points")
to your NAMESPACE file.
plotwithprototypes: no visible global function definition for ‘plot’
plotwithprototypes: no visible global function definition for
  ‘strwidth’
plotwithprototypes: no visible global function definition for
  ‘strheight’
plotwithprototypes: no visible global function definition for ‘rect’
plotwithprototypes: no visible global function definition for ‘text’
protoclust: no visible global function definition for ‘as.dist’
protocut: no visible global function definition for ‘cutree’
Undefined global functions or variables:
  as.dist cutree plot rect strheight strwidth text
Consider adding
  importFrom("graphics", "plot", "rect", "strheight", "strwidth", "text")
  importFrom("stats", "as.dist", "cutree")
to your NAMESPACE file.
File ‘protoclust/libs/protoclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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_plant_grapevine_function: no visible global function definition
  for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
File ‘prototest/libs/prototest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘pRSR/libs/pRSR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘rpart’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
mahalanobisComposite: no visible global function definition for
  ‘princomp’
prepareComposite: no visible global function definition for ‘cov’
winsorizor : f: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  cov princomp quantile
Consider adding
  importFrom("stats", "cov", "princomp", "quantile")
to your NAMESPACE file.
File ‘psd/libs/psd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
candidate.overlap: no visible global function definition for
  ‘write.table’
fisher: no visible global function definition for ‘fisher.test’
fisher.iteration: no visible global function definition for
  ‘download.file’
fisher.iteration: no visible global function definition for
  ‘read.table’
pSI.list: no visible global function definition for ‘write.table’
specificity.index: no visible global function definition for ‘png’
specificity.index: no visible global function definition for ‘par’
specificity.index: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off download.file fisher.test par png read.table write.table
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "par")
  importFrom("stats", "fisher.test")
  importFrom("utils", "download.file", "read.table", "write.table")
to your NAMESPACE file.
'library' or 'require' call to ‘numDeriv’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
test.problem : g: no visible global function definition for ‘grad’
test.problem: no visible global function definition for ‘new’
psoptim,test.problem-missing-missing-missing-missing: no visible global
  function definition for ‘new’
show,test.result: no visible global function definition for ‘show’
show,test.result: no visible global function definition for ‘sd’
Undefined global functions or variables:
  grad new sd show
Consider adding
  importFrom("methods", "new", "show")
  importFrom("stats", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
pspearman: no visible global function definition for ‘pt’
spearman.test: no visible global function definition for
  ‘complete.cases’
spearman.test: no visible global function definition for ‘cor’
Undefined global functions or variables:
  complete.cases cor pt
Consider adding
  importFrom("stats", "complete.cases", "cor", "pt")
to your NAMESPACE file.
File ‘pspearman/libs/pspearman.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘orig’
Packages in Depends field not imported from:
  ‘EffectsRelBaseline’ ‘boot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
catEffectBootAdaptor: no visible binding for global variable ‘sumSqCat’
compExclusionFraction: no visible global function definition for
  ‘rpois’
compExclusionFraction: no visible global function definition for
  ‘t.test’
compExclusionFraction: no visible global function definition for ‘glm’
compExclusionFraction: no visible global function definition for
  ‘anova’
compPowerCatSelectivity: no visible binding for global variable
  ‘fRatioStat’
compPowerGeneralRespDetection: no visible binding for global variable
  ‘sumSqCat’
compPowerRespDetection: no visible binding for global variable
  ‘sumSqCat’
compRejectionFraction: no visible global function definition for
  ‘rpois’
compRejectionFraction: no visible global function definition for
  ‘t.test’
compRejectionFraction: no visible global function definition for ‘glm’
compRejectionFraction: no visible global function definition for
  ‘anova’
simCatResp: no visible global function definition for ‘rpois’
simNormCatResp: no visible global function definition for ‘rnorm’
testCatEffectBoot: no visible global function definition for ‘boot’
Undefined global functions or variables:
  anova boot fRatioStat glm rnorm rpois sumSqCat t.test
Consider adding
  importFrom("stats", "anova", "glm", "rnorm", "rpois", "t.test")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘multilevel’ ‘nlme’
A package should be listed in only one of these fields.
Non-standard file/directory found at top level:
  ‘README.txt’
'library' or 'require' calls to packages already attached by Depends:
  ‘multilevel’ ‘nlme’
  Please remove these calls from your code.
File ‘ptest/libs/ptest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  pinpolyhedronA.cc:594:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  pinpolyhedronA.cc:1766:5: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/ptinpoly.Rcheck/00install.out’ for details.
File ‘ptinpoly/libs/ptinpoly.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘R.utils’ ‘rmeta’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ChisqTest_expect: no visible global function definition for ‘pchisq’
plot_chase_observed_expected: no visible global function definition for
  ‘meta.MH’
plot_chase_observed_expected: no visible global function definition for
  ‘txtProgressBar’
plot_chase_observed_expected: no visible global function definition for
  ‘setTxtProgressBar’
test.one.treated: no visible global function definition for
  ‘fisher.test’
test_one: no visible global function definition for ‘rbinom’
test_one: no visible global function definition for ‘fisher.test’
Undefined global functions or variables:
  fisher.test meta.MH pchisq rbinom setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "fisher.test", "pchisq", "rbinom")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
File ‘pullword/libs/pullword.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
PurBayes: no visible global function definition for ‘update’
PurBayes: no visible global function definition for ‘sd’
plot.PurBayes: no visible global function definition for ‘plot’
plot.PurBayes: no visible global function definition for ‘quantile’
plot.PurBayes: no visible global function definition for ‘lines’
summary.PurBayes : <anonymous>: no visible global function definition
  for ‘quantile’
Undefined global functions or variables:
  lines plot quantile sd update
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "quantile", "sd", "update")
to your NAMESPACE file.
CandidateBio.getBio : <anonymous>: no visible global function
  definition for ‘na.omit’
Committee.getCommittee : <anonymous>: no visible global function
  definition for ‘na.omit’
getAllBios: no visible global function definition for ‘txtProgressBar’
getAllBios: no visible global function definition for
  ‘setTxtProgressBar’
getAllLocalOfficials: no visible global function definition for
  ‘txtProgressBar’
getAllLocalOfficials: no visible global function definition for
  ‘setTxtProgressBar’
getAllVotes: no visible global function definition for ‘txtProgressBar’
getAllVotes: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  na.omit setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
File ‘PWD/libs/PWD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.grid.matrix: no visible global function definition for ‘slot’
.matrix2grid: no visible global function definition for ‘as’
.poly2grid: no visible global function definition for ‘is’
.poly2grid: no visible global function definition for ‘slot’
.poly2grid: no visible global function definition for ‘as’
.pycno.core : smooth2D : s1d: no visible global function definition for
  ‘filter’
.pycno.core: no visible global function definition for ‘flush.console’
.pycno2matrix: no visible global function definition for ‘slot’
Undefined global functions or variables:
  as filter flush.console is slot
Consider adding
  importFrom("methods", "as", "is", "slot")
  importFrom("stats", "filter")
  importFrom("utils", "flush.console")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
pyramid: no visible global function definition for ‘plot’
pyramid: no visible global function definition for ‘segments’
pyramid: no visible global function definition for ‘lines’
pyramid: no visible global function definition for ‘text’
pyramid: no visible global function definition for ‘rect’
pyramidf: no visible global function definition for ‘segments’
pyramidf: no visible global function definition for ‘lines’
pyramidf: no visible global function definition for ‘text’
pyramidf: no visible global function definition for ‘rect’
Undefined global functions or variables:
  lines plot rect segments text
Consider adding
  importFrom("graphics", "lines", "plot", "rect", "segments", "text")
to your NAMESPACE file.
csQCAbinTest: no visible global function definition for ‘p.adjust’
fsQCApermTest: no visible global function definition for ‘p.adjust’
mvQCAbinTest: no visible global function definition for ‘p.adjust’
p.threshold.adjust: no visible global function definition for
  ‘p.adjust’
plot.fsQCApt: no visible global function definition for ‘dev.cur’
plot.fsQCApt: no visible global function definition for ‘dev.new’
plot.fsQCApt: no visible global function definition for ‘par’
plot.fsQCApt: no visible global function definition for ‘plot’
plot.fsQCApt: no visible global function definition for ‘density’
plot.fsQCApt: no visible global function definition for ‘axis’
plot.fsQCApt: no visible global function definition for ‘polygon’
plot.fsQCApt: no visible global function definition for ‘points’
plot.fsQCApt: no visible global function definition for ‘hist’
summary.csQCAbt: no visible global function definition for
  ‘printCoefmat’
summary.fsQCApt: no visible global function definition for
  ‘printCoefmat’
summary.mvQCAbt: no visible global function definition for
  ‘printCoefmat’
Undefined global functions or variables:
  axis density dev.cur dev.new hist p.adjust par plot points polygon
  printCoefmat
Consider adding
  importFrom("grDevices", "dev.cur", "dev.new")
  importFrom("graphics", "axis", "hist", "par", "plot", "points",
             "polygon")
  importFrom("stats", "density", "p.adjust", "printCoefmat")
to your NAMESPACE file.
dmm_fn: no visible global function definition for ‘dnorm’
dmm_noweights_fn: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
Package suggested but not available for checking: ‘biom’
chooseMDoubleBootstrap: no visible global function definition for
  ‘model.matrix’
chooseMDoubleBootstrap: no visible global function definition for
  ‘as.formula’
chooseMDoubleBootstrap: no visible global function definition for
  ‘model.frame’
chooseMDoubleBootstrap: no visible global function definition for ‘lm’
chooseMDoubleBootstrap: no visible global function definition for
  ‘coef’
chooseMDoubleBootstrap: no visible global function definition for
  ‘quantile’
chooseMDoubleBootstrap: no visible global function definition for
  ‘qnorm’
getModel: no visible global function definition for ‘lm’
getModel: no visible global function definition for ‘model.matrix’
getModel: no visible global function definition for ‘as.formula’
getModel: no visible global function definition for ‘model.frame’
getModel: no visible global function definition for ‘model.response’
getModel: no visible global function definition for ‘coef’
getModel: no visible global function definition for ‘qnorm’
qLearn: no visible global function definition for ‘model.matrix’
qLearn: no visible global function definition for ‘as.formula’
qLearn: no visible global function definition for ‘model.frame’
qLearn: no visible global function definition for ‘coef’
qLearn: no visible global function definition for ‘lm’
qLearn: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  as.formula coef lm model.frame model.matrix model.response qnorm
  quantile
Consider adding
  importFrom("stats", "as.formula", "coef", "lm", "model.frame",
             "model.matrix", "model.response", "qnorm", "quantile")
to your NAMESPACE file.
pcAxisCubeMake: no visible global function definition for ‘aggregate’
pcAxisCubeToCSV: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  aggregate write.csv
Consider adding
  importFrom("stats", "aggregate")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  plot.CT
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

Calc.Expr: no visible global function definition for ‘read.csv’
Calc.Expr: no visible binding for global variable ‘Type’
Calc.Expr: no visible binding for global variable ‘Identifier’
Calc.Expr: no visible binding for global variable ‘Fluor’
GroupPlot: no visible global function definition for ‘read.csv’
GroupPlot: no visible binding for global variable ‘Type’
GroupPlot: no visible global function definition for
  ‘aggregate.data.frame’
plot.CT: no visible global function definition for ‘sd’
plot.CT: no visible global function definition for ‘barplot’
plot.CT: no visible binding for global variable ‘tr_gene_name’
plot.CT : errorbars: no visible global function definition for ‘arrows’
plot.CT: no visible global function definition for ‘box’
Undefined global functions or variables:
  Fluor Identifier Type aggregate.data.frame arrows barplot box
  read.csv sd tr_gene_name
Consider adding
  importFrom("graphics", "arrows", "barplot", "box")
  importFrom("stats", "aggregate.data.frame", "sd")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
prepare_Rd: Calc.Expr.Rd:38-40: Dropping empty section \details
prepare_Rd: Calc.Expr.Rd:41-47: Dropping empty section \value
prepare_Rd: Calc.Expr.Rd:54-56: Dropping empty section \note
prepare_Rd: Calc.Expr.Rd:48-50: Dropping empty section \references
prepare_Rd: Calc.Expr.Rd:60-62: Dropping empty section \seealso
prepare_Rd: GroupPlot.Rd:34-36: Dropping empty section \details
prepare_Rd: GroupPlot.Rd:37-43: Dropping empty section \value
prepare_Rd: GroupPlot.Rd:50-52: Dropping empty section \note
prepare_Rd: GroupPlot.Rd:44-46: Dropping empty section \references
prepare_Rd: GroupPlot.Rd:56-58: Dropping empty section \seealso
prepare_Rd: cal.CT.Rd:18-20: Dropping empty section \details
prepare_Rd: cal.CT.Rd:21-23: Dropping empty section \source
prepare_Rd: cal_ct.Rd:48-50: Dropping empty section \note
prepare_Rd: cal_ct.Rd:42-44: Dropping empty section \references
prepare_Rd: cal_ct.Rd:54-56: Dropping empty section \seealso
prepare_Rd: filename.Rd:16-18: Dropping empty section \references
prepare_Rd: plot.CT.Rd:25-27: Dropping empty section \details
prepare_Rd: plot.CT.Rd:28-34: Dropping empty section \value
prepare_Rd: plot.CT.Rd:41-43: Dropping empty section \note
prepare_Rd: plot.CT.Rd:35-37: Dropping empty section \references
prepare_Rd: plot.CT.Rd:47-49: Dropping empty section \seealso
prepare_Rd: repeatnum.Rd:15-17: Dropping empty section \details
prepare_Rd: repeatnum.Rd:18-20: Dropping empty section \source
prepare_Rd: repeatnum.Rd:21-23: Dropping empty section \references
prepare_Rd: tr_gene_name.Rd:15-17: Dropping empty section \details
prepare_Rd: tr_gene_name.Rd:18-20: Dropping empty section \source
prepare_Rd: tr_gene_name.Rd:21-23: Dropping empty section \references
prepare_Rd: tr_group_name.Rd:15-17: Dropping empty section \details
prepare_Rd: tr_group_name.Rd:18-20: Dropping empty section \source
prepare_Rd: tr_group_name.Rd:21-23: Dropping empty section \references
Rd file 'Calc.Expr.Rd':
  \usage lines wider than 90 characters:
     Calc.Expr(filename, con_group_name, tr_group_name, con_gene_name = "18s", tr_gene_name, repeatnum = 3, ...)

Rd file 'GroupPlot.Rd':
  \examples lines wider than 100 characters:
     suppressWarnings(aggdata <-aggregate.data.frame(unknown, by=list(unknown$Fluor),FUN=mean, na.rm=TRUE))

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  upwindorderedv4.c:542:54: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  upwindorderedv4.c:542:72: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/QPot.Rcheck/00install.out’ for details.
File ‘QPot/libs/QPot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
File ‘QPot/libs/upwindorderedv4.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘QRM/libs/QRM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘compileMetaObject’
File ‘qtbase/libs/qtbase.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘Rf_EncodeInteger’,
    ‘Rf_EncodeLogical’, ‘Rf_EncodeReal’, ‘Rf_formatInteger’,
    ‘Rf_formatLogical’, ‘Rf_formatReal’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
ci.length: no visible global function definition for ‘qexp’
detectable.bc: no visible global function definition for ‘uniroot’
detectable.f2: no visible global function definition for ‘uniroot’
detectable.ri: no visible global function definition for ‘uniroot’
nu: no visible global function definition for ‘pnorm’
nullinfo: no visible global function definition for ‘qnorm’
nullinfo: no visible global function definition for ‘dnorm’
optselection.bc: no visible global function definition for ‘optimize’
optselection.f2: no visible global function definition for ‘optimize’
optspacing.bc: no visible global function definition for ‘optim’
optspacing.bc: no visible global function definition for ‘optimize’
optspacing.f2: no visible global function definition for ‘optim’
optspacing.f2: no visible global function definition for ‘optimize’
powercalc.bc: no visible global function definition for ‘pchisq’
powercalc.f2: no visible global function definition for ‘pchisq’
samplesize.bc: no visible global function definition for ‘uniroot’
samplesize.f2: no visible global function definition for ‘uniroot’
samplesize.ri: no visible global function definition for ‘uniroot’
tailprob: no visible global function definition for ‘pchisq’
thresh: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  dnorm optim optimize pchisq pnorm qexp qnorm uniroot
Consider adding
  importFrom("stats", "dnorm", "optim", "optimize", "pchisq", "pnorm",
             "qexp", "qnorm", "uniroot")
to your NAMESPACE file.
Note: information on .o files is not available
File ‘qtpaint/libs/qtpaint.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 ‘Rmpfr’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
adjacencyMatrix: no visible global function definition for ‘as’
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘QuACN/libs/QuACN.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.
Non-standard files/directories found at top level:
  ‘LICENSE.GPL-2’ ‘LICENSE.GPL-3’
quadp: no visible global function definition for ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
alphaf: no visible global function definition for ‘pchisq’
alphaf: no visible global function definition for ‘dbinom’
conout: no visible global function definition for ‘sd’
ibgaout: no visible global function definition for ‘qnorm’
ibgaout: no visible global function definition for ‘pnorm’
plot.qualint: no visible global function definition for ‘qnorm’
powerval: no visible global function definition for ‘rnorm’
powerval: no visible global function definition for ‘qnorm’
powerval: no visible global function definition for ‘pnorm’
print.expplot: no visible global function definition for ‘gray’
print.expplot: no visible binding for global variable ‘coef’
print.outplot: no visible global function definition for ‘gray’
print.outplot: no visible binding for global variable ‘coef’
qualint: no visible global function definition for ‘qnorm’
qualint: no visible global function definition for ‘plot’
qualval: no visible global function definition for ‘qnorm’
qualval: no visible global function definition for ‘plot’
surout: no visible global function definition for ‘tail’
surout: no visible global function definition for ‘coef’
Undefined global functions or variables:
  coef dbinom gray pchisq plot pnorm qnorm rnorm sd tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "dbinom", "pchisq", "pnorm", "qnorm",
             "rnorm", "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
Found the following calls to attach():
File ‘quantmod/R/attachSymbols.R’:
  attach(NULL, pos = pos, name = DB$name)
  attach(NULL, pos = pos, name = DB$name)
See section ‘Good practice’ in ‘?attach’.
Rd file 'graph.mod.Rd':
  \usage lines wider than 90 characters:
     graph.mod(ssmod, x, y, data, title = "", xlab = "Centered X", ylab = "Raw Y", ylimit = 1.5, ...)

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘QUIC/libs/QUIC.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘QUIC.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘QUIC.o’
File ‘QUIC/libs/QUIC.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 use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘qVarSel/libs/qVarSel.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘qVarSelH.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘qVarSelH.o’
File ‘qVarSel/libs/qVarSel.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 use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
mutualCoherence : .setOneMutualP: no visible global function definition
  for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
conf2d.default: no visible global function definition for ‘polygon’
conf2d_int: no visible global function definition for ‘contourLines’
Undefined global functions or variables:
  contourLines polygon
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "polygon")
to your NAMESPACE file.
'library' or 'require' call to ‘rgdal’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘matrixStats’ ‘rgdal’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following calls to attach():
File ‘R2OpenBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
Non-standard file/directory found at top level:
  ‘readme’
r2stl: no visible global function definition for ‘persp’
Undefined global functions or variables:
  persp
Consider adding
  importFrom("graphics", "persp")
to your NAMESPACE file.
Rd file 'r2stl.Rd':
  \usage lines wider than 90 characters:
     r2stl(x, y, z, filename = "3d-R-object.stl", object.name = "r2stl-object", z.expand = FALSE, min.height = 0.008, show.persp = FALSE, st ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Found the following calls to attach():
File ‘R2WinBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
'library' or 'require' call to ‘rgl’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘lattice’ ‘leaps’ ‘rgl’ ‘s20x’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘R4dfp/libs/R4dfp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘rpvm’
'library' or 'require' call to ‘rpvm’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
race : killSlaves.exit: no visible global function definition for
  ‘.PVM.initsend’
race : killSlaves.exit: no visible global function definition for
  ‘.PVM.send’
race : killSlaves.exit: no visible global function definition for
  ‘.PVM.exit’
race: no visible global function definition for ‘.PVM.mytid’
race: no visible global function definition for ‘.PVM.spawn’
race: no visible global function definition for ‘.PVM.initsend’
race: no visible global function definition for ‘.PVM.pkstrvec’
race: no visible global function definition for ‘.PVM.send’
race: no visible global function definition for ‘.PVM.recv’
race: no visible global function definition for ‘.PVM.bufinfo’
race: no visible global function definition for ‘.PVM.upkstrvec’
race : job.start: no visible global function definition for
  ‘.PVM.initsend’
race : job.start: no visible global function definition for
  ‘.PVM.pkint’
race : job.start: no visible global function definition for ‘.PVM.send’
race : job.wait: no visible global function definition for ‘.PVM.recv’
race : job.wait: no visible global function definition for
  ‘.PVM.bufinfo’
race : job.wait: no visible global function definition for
  ‘.PVM.upkint’
race : job.wait: no visible global function definition for
  ‘.PVM.upkdblvec’
race : aux2.friedman: no visible global function definition for
  ‘pchisq’
race : aux2.friedman: no visible global function definition for ‘qt’
race : aux.friedman: no visible global function definition for
  ‘wilcox.test’
race : aux.ttest: no visible global function definition for ‘t.test’
race : aux.ttest: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  .PVM.bufinfo .PVM.exit .PVM.initsend .PVM.mytid .PVM.pkint
  .PVM.pkstrvec .PVM.recv .PVM.send .PVM.spawn .PVM.upkdblvec
  .PVM.upkint .PVM.upkstrvec p.adjust pchisq qt t.test wilcox.test
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "qt", "t.test",
             "wilcox.test")
to your NAMESPACE file.
Found the following significant warnings:

  Warning: 'glue::collapse' is deprecated.
  Warning: 'glue::collapse' is deprecated.
  Warning: 'glue::collapse' is deprecated.
  Warning: 'glue::collapse' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
           user system elapsed
visualize 6.616  0.067   7.326
Running examples in ‘radiant.model-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: write.coeff
> ### Title: Write coefficient table for linear and logistic regression
> ### Aliases: write.coeff
> 
> ### ** Examples
> 
> regress(diamonds, rvar = "price", evar = c("carat", "clarity", "x"), check = "standardize") %>%
+   write.coeff(sort = TRUE) %>%
+   format_df(dec = 3)
Standardized coefficients selected

Warning: Unknown or uninitialised column: 'OR'.
Warning: Unknown or uninitialised column: 'coeff'.
Error in abs(object$coeff) : 
  non-numeric argument to mathematical function
Calls: %>% ... eval -> _fseq -> freduce -> <Anonymous> -> write.coeff
Execution halted
Running examples in ‘radiant.multivariate-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: summary.conjoint
> ### Title: Summary method for the conjoint function
> ### Aliases: summary.conjoint
> 
> ### ** Examples
> 
> result <- conjoint(mp3, rvar = "Rating", evar = "Memory:Shape")
> summary(result, mc_diag = TRUE)
Conjoint analysis
Data                 : mp3 
Response variable    : Rating 
Explanatory variables: Memory, Radio, Size, Price, Shape 

Conjoint part-worths:
   Attributes      Levels      PW
 Memory       4GB           0.000
 Memory       6GB           7.667
 Memory       8GB          29.667
 Radio        No            0.000
 Radio        Yes           6.111
 Size         Large         0.000
 Size         Medium        6.333
 Size         Small         8.500
 Price        $50           0.000
 Price        $100         -6.833
 Price        $150        -33.833
 Shape        Circular      0.000
 Shape        Rectangular -27.833
 Shape        Square      -13.333
 Base utility ~            58.111

Conjoint importance weights:
 Attributes    IW
     Memory 0.280
     Radio  0.058
     Size   0.080
     Price  0.319
     Shape  0.263

Conjoint regression results:

Error in sprintf(paste0("%.", dec, "f"), .) : 
  (list) object cannot be coerced to type 'double'
Calls: summary ... _fseq -> freduce -> withVisible -> <Anonymous> -> sprintf
Execution halted
getsonde: no visible global function definition for ‘read.table’
plotsonde: no visible global function definition for ‘par’
plotwind: no visible global function definition for ‘plot’
plotwind: no visible global function definition for ‘mtext’
plotwind: no visible global function definition for ‘abline’
skewt.axis: no visible global function definition for ‘par’
skewt.axis: no visible global function definition for ‘plot’
skewt.axis: no visible global function definition for ‘axis’
skewt.axis: no visible global function definition for ‘mtext’
skewt.axis: no visible global function definition for ‘segments’
skewt.axis: no visible global function definition for ‘text’
skewt.axis: no visible global function definition for ‘lines’
skewt.lines: no visible global function definition for ‘lines’
skewt.points: no visible global function definition for ‘points’
station.symbol: no visible global function definition for ‘sd’
station.symbol: no visible global function definition for ‘par’
station.symbol: no visible global function definition for ‘lines’
station.symbol: no visible global function definition for ‘polygon’
station.symbol: no visible global function definition for ‘text’
station.symbol: no visible global function definition for ‘segments’
Undefined global functions or variables:
  abline axis lines mtext par plot points polygon read.table sd
  segments text
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "mtext", "par",
             "plot", "points", "polygon", "segments", "text")
  importFrom("stats", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Rd file 'MDMnMod.Rd':
  \usage lines wider than 90 characters:
     MDMnMod(MDMn.form, data, ID, dist="MDMn", scale.covar=FALSE, est.var=TRUE, calc.resid=TRUE, trace=TRUE)
  \examples lines wider than 100 characters:
     model.nij <- MDMnMod(nij.form, data=n.data, ID=n.data$i, dist="MDMn", scale.covar=TRUE, est.var=FALSE, calc.resid=TRUE, trace=TRUE)

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
RnDif.het: no visible global function definition for ‘runif’
RnDif.hom: no visible global function definition for ‘runif’
RnDifAdv.hom: no visible global function definition for ‘runif’
SoilAdv.hom: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Package unavailable to check Rd xrefs: ‘CGHbase’
File ‘RAHRS/libs/RAHRS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
cpc_get_rawdata: 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.
Found the following apparent S3 methods exported but not registered:
  plot.rsm summary.rsm
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.rsm: no visible global function definition for ‘par’
plot.rsm: no visible global function definition for ‘abline’
plot.rsm: no visible global function definition for ‘barplot’
Undefined global functions or variables:
  abline barplot par
Consider adding
  importFrom("graphics", "abline", "barplot", "par")
to your NAMESPACE file.
Running examples in ‘Rambo-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Rambo-package
> ### Title: The Random Subgraph Model
> ### Aliases: Rambo-package Rambo RAMBO
> ### Keywords: rsm
> 
> ### ** Examples
> 
> data(Regions)
> res <- rsm(Regions$X, Regions$sub, Klist=2:4, nbredo=1, maxit=5) 
> plot(res)
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'
Calls: plot -> plot.default -> xy.coords
Execution halted
File ‘ramsvm/libs/ramsvm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘randaes/libs/randaes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘RandomFields/R/RFfit.R’:
  attach(data, name = name)
See section ‘Good practice’ in ‘?attach’.
.disableThreads: no visible global function definition for
  ‘stopCluster’
.enableThreads: no visible global function definition for ‘detectCores’
.enableThreads: no visible global function definition for
  ‘makePSOCKcluster’
.enableThreads: no visible global function definition for
  ‘clusterExport’
.enableThreads: no visible global function definition for ‘clusterCall’
.forwardSelection: no visible binding for global variable ‘var’
.forwardSelection: no visible global function definition for ‘glm’
.forwardSelection: no visible global function definition for ‘formula’
.forwardSelection: no visible global function definition for ‘binomial’
.forwardSelection: no visible global function definition for ‘lm’
.forwardSelection: no visible global function definition for ‘predict’
.predict.internal: no visible global function definition for ‘predict’
randomGLM: no visible binding for global variable ‘cor’
randomGLM: no visible binding for global variable ‘sd’
randomGLM: no visible global function definition for ‘var’
thinRandomGLM: no visible global function definition for ‘glm’
thinRandomGLM: no visible global function definition for ‘binomial’
thinRandomGLM: no visible global function definition for ‘lm’
Undefined global functions or variables:
  binomial clusterCall clusterExport cor detectCores formula glm lm
  makePSOCKcluster predict sd stopCluster var
Consider adding
  importFrom("stats", "binomial", "cor", "formula", "glm", "lm",
             "predict", "sd", "var")
to your NAMESPACE file.

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

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

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

These lines will be truncated in the PDF manual.
anovaF: no visible global function definition for ‘anova’
anovaF: no visible global function definition for ‘lm’
randInterval: no visible global function definition for ‘quantile’
randInterval : <anonymous>: no visible global function definition for
  ‘quantile’
randPlot: no visible global function definition for ‘par’
randPlot: no visible global function definition for ‘hist’
randPlot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline anova hist lm par quantile
Consider adding
  importFrom("graphics", "abline", "hist", "par")
  importFrom("stats", "anova", "lm", "quantile")
to your NAMESPACE file.
File ‘randomUniformForest/libs/randomUniformForest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
bartels.rank.test: no visible global function definition for ‘na.omit’
bartels.rank.test: no visible global function definition for ‘pbeta’
bartels.rank.test: no visible global function definition for ‘pnorm’
cox.stuart.test: no visible global function definition for ‘pbinom’
difference.sign.test: no visible global function definition for
  ‘na.omit’
difference.sign.test: no visible global function definition for ‘pnorm’
rank.test: no visible global function definition for ‘na.omit’
rank.test: no visible global function definition for ‘pnorm’
rruns: no visible global function definition for ‘runif’
runs.test: no visible global function definition for ‘median’
runs.test: no visible global function definition for ‘na.omit’
runs.test: no visible global function definition for ‘points’
runs.test: no visible global function definition for ‘abline’
runs.test: no visible global function definition for ‘gray’
runs.test: no visible global function definition for ‘pnorm’
turning.point.test: no visible global function definition for ‘embed’
turning.point.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline embed gray median na.omit pbeta pbinom pnorm points runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "points")
  importFrom("stats", "embed", "median", "na.omit", "pbeta", "pbinom",
             "pnorm", "runif")
to your NAMESPACE file.
File ‘Rankcluster/libs/Rankcluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
rank.L2R: no visible global function definition for ‘kmeans’
rank.L2R: no visible global function definition for ‘pnorm’
rank.LN: no visible global function definition for ‘kmeans’
rank.LN: no visible global function definition for ‘pnorm’
rank.gs: no visible global function definition for ‘qnorm’
rank.wald: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  kmeans pnorm qnorm
Consider adding
  importFrom("stats", "kmeans", "pnorm", "qnorm")
to your NAMESPACE file.
File ‘RANKS/libs/RANKS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘RANN.L1/libs/RANN.L1.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
CropSpatialPolygonsDataFrame: no visible global function definition for
  ‘bbox’
CropSpatialPolygonsDataFrame: no visible global function definition for
  ‘clipPolys’
DiagnoseFailure: no visible global function definition for ‘points’
Undefined global functions or variables:
  bbox clipPolys points
Consider adding
  importFrom("graphics", "points")
to your NAMESPACE file.
'library' or 'require' call to ‘BSgenome.Hsapiens.UCSC.hg19’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
File ‘RAppArmor/libs/RAppArmor.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
freq: no visible global function definition for ‘xtabs’
freq: no visible binding for global variable ‘na.pass’
freq: no visible global function definition for ‘melt’
freq: no visible global function definition for ‘complete.cases’
freq: no visible global function definition for ‘tail’
kurtosis: no visible global function definition for ‘na.omit’
label: no visible global function definition for ‘tail’
name: no visible global function definition for ‘tail’
nvalid : <anonymous>: no visible global function definition for
  ‘na.omit’
rp.desc: no visible global function definition for ‘melt.data.frame’
rp.desc: no visible global function definition for ‘cast’
rp.desc: no visible global function definition for ‘na.omit’
rp.desc : <anonymous>: no visible global function definition for ‘tail’
rp.desc : <anonymous>: no visible global function definition for ‘head’
rp.freq: no visible global function definition for ‘xtabs’
rp.freq: no visible binding for global variable ‘na.pass’
rp.freq: no visible global function definition for ‘melt’
rp.freq: no visible global function definition for ‘complete.cases’
rp.freq: no visible global function definition for ‘tail’
rp.label: no visible global function definition for ‘tail’
rp.name: no visible global function definition for ‘tail’
rp.outlier : lundcrit: no visible global function definition for ‘qf’
rp.outlier: no visible global function definition for ‘lm’
rp.outlier: no visible global function definition for ‘rstandard’
rp.valid : <anonymous>: no visible global function definition for
  ‘na.omit’
skewness: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  cast complete.cases head lm melt melt.data.frame na.omit na.pass qf
  rstandard tail xtabs
Consider adding
  importFrom("stats", "complete.cases", "lm", "na.omit", "na.pass", "qf",
             "rstandard", "xtabs")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
fnRAP: no visible global function definition for ‘chisq.test’
fnRAP: no visible global function definition for ‘combn’
Undefined global functions or variables:
  chisq.test combn
Consider adding
  importFrom("stats", "chisq.test")
  importFrom("utils", "combn")
to your NAMESPACE file.
plotarc: no visible global function definition for ‘par’
plotarc: no visible global function definition for ‘plot’
plotarc: no visible global function definition for ‘lines’
plotpoly: no visible global function definition for ‘par’
plotpoly: no visible global function definition for ‘plot’
plotpoly: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  lines par plot polygon
Consider adding
  importFrom("graphics", "lines", "par", "plot", "polygon")
to your NAMESPACE file.
File ‘RArcInfo/libs/RArcInfo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
INT_FIX: no visible global function definition for ‘rbinom’
INT_FIX: no visible global function definition for ‘glm’
INT_FIX: no visible global function definition for ‘as.formula’
INT_FIX: no visible global function definition for ‘residuals’
INT_FIX: no visible global function definition for ‘var’
INT_RAN: no visible global function definition for ‘rbinom’
INT_RAN: no visible global function definition for ‘as.formula’
INT_RAN: no visible global function definition for ‘predict’
JOINT: no visible global function definition for ‘rbinom’
JOINT: no visible global function definition for ‘glm’
JOINT: no visible global function definition for ‘as.formula’
JOINT: no visible global function definition for ‘var’
JOINT: no visible global function definition for ‘residuals’
pKuonen: no visible global function definition for ‘pchisq’
pKuonen: no visible global function definition for ‘uniroot’
pKuonen: no visible global function definition for ‘pnorm’
rareGE: no visible global function definition for ‘rbinom’
rareGE: no visible global function definition for ‘as.formula’
rareGE: no visible global function definition for ‘predict’
rareGE: no visible global function definition for ‘glm’
rareGE: no visible global function definition for ‘residuals’
rareGE: no visible global function definition for ‘var’
rareGE_joint_mc: no visible global function definition for ‘pchisq’
rareGE_joint_mc: no visible global function definition for ‘qchisq’
wuweights: no visible global function definition for ‘dbeta’
Undefined global functions or variables:
  as.formula dbeta glm pchisq pnorm predict qchisq rbinom residuals
  uniroot var
Consider adding
  importFrom("stats", "as.formula", "dbeta", "glm", "pchisq", "pnorm",
             "predict", "qchisq", "rbinom", "residuals", "uniroot",
             "var")
to your NAMESPACE file.
BiogTest.individual: no visible global function definition for ‘combn’
BiogTest.individual: no visible global function definition for ‘runif’
BiogTest.individual: no visible global function definition for ‘rlnorm’
BiogTest.individual: no visible global function definition for
  ‘rnbinom’
BiogTest.sample: no visible global function definition for ‘combn’
BiogTest.sample: no visible global function definition for ‘runif’
BiogTest.sample: no visible global function definition for ‘rlnorm’
BiogTest.sample: no visible global function definition for ‘rnbinom’
BiogTest.sample: no visible global function definition for ‘aggregate’
EcoTest.individual: no visible global function definition for ‘xtabs’
plot.BiogTest: no visible global function definition for ‘quantile’
plot.BiogTest: no visible global function definition for ‘combn’
plot.EcoTest: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  aggregate combn quantile rlnorm rnbinom runif xtabs
Consider adding
  importFrom("stats", "aggregate", "quantile", "rlnorm", "rnbinom",
             "runif", "xtabs")
  importFrom("utils", "combn")
to your NAMESPACE file.
File ‘RaschSampler/libs/RaschSampler.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
rateratio.test: no visible global function definition for
  ‘complete.cases’
rateratio.test: no visible global function definition for ‘pbinom’
rateratio.test : p.L: no visible global function definition for ‘qbeta’
rateratio.test : p.U: no visible global function definition for ‘qbeta’
Undefined global functions or variables:
  complete.cases pbinom qbeta
Consider adding
  importFrom("stats", "complete.cases", "pbinom", "qbeta")
to your NAMESPACE file.
concordance: no visible global function definition for ‘quantile’
concordance : Normal: no visible global function definition for ‘qnorm’
concordance : Normal: no visible global function definition for ‘pnorm’
concordance : MC: no visible global function definition for ‘rmultinom’
concordance : MC: no visible global function definition for ‘quantile’
concordance: no visible global function definition for ‘qnorm’
concordance: no visible global function definition for ‘pnorm’
concordance : Chisq: no visible global function definition for ‘qchisq’
concordance : Chisq: no visible global function definition for ‘pchisq’
concordance : Normal2: no visible global function definition for
  ‘qnorm’
concordance : Normal2: no visible global function definition for
  ‘pnorm’
concordance : MC2: no visible global function definition for
  ‘rmultinom’
concordance : MC2: no visible global function definition for ‘quantile’
wlin.conc: no visible global function definition for ‘quantile’
wlin.conc : MC: no visible global function definition for ‘rmultinom’
wlin.conc : MC: no visible global function definition for ‘quantile’
wquad.conc: no visible global function definition for ‘quantile’
wquad.conc : MC: no visible global function definition for ‘rmultinom’
wquad.conc : MC: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  pchisq pnorm qchisq qnorm quantile rmultinom
Consider adding
  importFrom("stats", "pchisq", "pnorm", "qchisq", "qnorm", "quantile",
             "rmultinom")
to your NAMESPACE file.
.GCD: no visible global function definition for ‘as.polynomial’
.LCM: no visible global function definition for ‘as.polynomial’
.is_zero_polynomial: no visible global function definition for ‘coef’
.poly2expr: no visible global function definition for ‘coef’
integral.rationalfun: no visible global function definition for ‘coef’
integraterf.transcendent: no visible global function definition for
  ‘coef’
rationalfun: no visible global function definition for ‘polynomial’
rationalfun.poly: no visible global function definition for
  ‘polynomial’
rationalfun.poly: no visible global function definition for
  ‘is.polynomial’
rfun: no visible global function definition for ‘polynomial’
rfun.poly: no visible global function definition for ‘polynomial’
rfun.poly: no visible global function definition for ‘is.polynomial’
simplify: no visible global function definition for ‘coef’
simplify: no visible global function definition for ‘polynomial’
Undefined global functions or variables:
  as.polynomial coef is.polynomial polynomial
Consider adding
  importFrom("stats", "coef")
to your NAMESPACE file.
Package suggested but not available for checking: ‘odfWeave’
.avisApiBusAvanzada: no visible global function definition for
  ‘read.csv’
.avisRenderMapAdmin: no visible global function definition for ‘points’
.avisRenderMapAdmin: no visible global function definition for ‘rect’
.avisRenderMapPhysical: no visible global function definition for
  ‘points’
avisMap: no visible global function definition for ‘par’
avisMap: no visible global function definition for ‘layout’
Undefined global functions or variables:
  layout par points read.csv rect
Consider adding
  importFrom("graphics", "layout", "par", "points", "rect")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Running examples in ‘rbcb-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_annual_market_expectations
> ### Title: Get annual market expectations of economic indicators
> ### Aliases: get_annual_market_expectations
> 
> ### ** Examples
> 
> indic <- c("Balanço de Pagamentos", "Fiscal")
> end_date <- "2018-01-31"
> x <- get_annual_market_expectations(indic, end_date = end_date, `$top` = 10)
Error in curl::curl_fetch_memory(url, handle = handle) : 
  GnuTLS recv error (-110): The TLS connection was non-properly terminated.
Calls: get_annual_market_expectations ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
File ‘rBeta2009/libs/rBeta2009.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
GetHistoricTradeData: no visible global function definition for
  ‘read.csv’
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Rblpapi.Rcheck/00install.out’ for details.
bn2nbn: no visible binding for global variable ‘bn.fit’
chain4chain: no visible binding for global variable ‘head’
chain4chain: no visible binding for global variable ‘tail’
estimate8arcs: no visible global function definition for ‘lm’
estimate8arcs: no visible global function definition for ‘coefficients’
estimate8nbn: no visible global function definition for ‘lm’
estimate8nbn: no visible global function definition for ‘as.formula’
estimate8nbn: no visible global function definition for ‘anova’
estimate8nbn: no visible global function definition for ‘coefficients’
generate8chain: no visible global function definition for ‘runif’
generate8chain: no visible global function definition for ‘rbinom’
generate8nbn: no visible global function definition for ‘runif’
generate8nbn: no visible global function definition for ‘rbinom’
nbn2bnfit: no visible global function definition for ‘model2network’
nbn2bnfit: no visible global function definition for ‘custom.fit’
simulate8gema: no visible global function definition for ‘rnorm’
simulate8mn: no visible global function definition for ‘mvrnorm’
simulate8nbn: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  anova as.formula bn.fit coefficients custom.fit head lm model2network
  mvrnorm rbinom rnorm runif tail
Consider adding
  importFrom("stats", "anova", "as.formula", "coefficients", "lm",
             "rbinom", "rnorm", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Found the following significant warnings:
  rcppPredict.cc:60:12: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Rborist.Rcheck/00install.out’ for details.
SumTestSens: no visible global function definition for ‘pnorm’
binarysens: no visible global function definition for ‘dbinom’
hlsens: no visible global function definition for ‘wilcox.test’
iv_sens: no visible global function definition for ‘pnorm’
mcontrol: no visible global function definition for ‘pnorm’
psens: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dbinom pnorm wilcox.test
Consider adding
  importFrom("stats", "dbinom", "pnorm", "wilcox.test")
to your NAMESPACE file.
':::' call which should be '::': ‘tools:::file_path_as_absolute’
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: ‘tools:::file_test’
  See the note in ?`:::` about the use of this operator.
Found the following apparent S3 methods exported but not registered:
  print.rbugs
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
genBugsScript: no visible global function definition for ‘runif’
getBugsOutput: no visible global function definition for ‘read.table’
rbugs2coda: no visible global function definition for ‘as.mcmc’
rbugs2coda: no visible global function definition for ‘mcmc’
rbugs2coda: no visible global function definition for ‘as.mcmc.list’
Undefined global functions or variables:
  as.mcmc as.mcmc.list mcmc read.table runif
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "read.table")
to your NAMESPACE file.
find_available_versions: no visible global function definition for
  ‘contrib.url’
find_available_versions: no visible global function definition for
  ‘available.packages’
install_version: no visible global function definition for
  ‘contrib.url’
install_version: no visible global function definition for
  ‘available.packages’
install_version: no visible global function definition for
  ‘install_url’
load_available_packages: no visible global function definition for
  ‘contrib.url’
validate_installed_package: no visible global function definition for
  ‘installed.packages’
Undefined global functions or variables:
  available.packages contrib.url install_url installed.packages
Consider adding
  importFrom("utils", "available.packages", "contrib.url",
             "installed.packages")
to your NAMESPACE file.
File ‘rbvs/libs/rbvs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘RColorBrewer’ ‘classInt’ ‘maptools’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RColorBrewer’ ‘classInt’ ‘maptools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
RC.read.table: no visible global function definition for ‘type.convert’
Undefined global functions or variables:
  type.convert
Consider adding
  importFrom("utils", "type.convert")
to your NAMESPACE file.
File ‘RCassandra/libs/RCassandra.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.onAttach: no visible global function definition for
  ‘packageDescription’
rselect.list: no visible global function definition for ‘select.list’
Undefined global functions or variables:
  packageDescription select.list
Consider adding
  importFrom("utils", "packageDescription", "select.list")
to your NAMESPACE file.
Running examples in ‘Rchoice-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: estfun.Rchoice
> ### Title: Gradient for observations
> ### Aliases: estfun.Rchoice
> 
> ### ** Examples
> 
> ## Probit model
> data("Workmroz")
> probit <- Rchoice(lfp ~ k5 + k618 + age + wc + hc + lwg + inc,  
+                   data = Workmroz , family = binomial('probit'))
> summary(probit)

Model: binomial
Model estimated on: Sun Aug 12 06:34:05 PM 2018 

Call:
Rchoice(formula = lfp ~ k5 + k618 + age + wc + hc + lwg + inc, 
    data = Workmroz, family = binomial("probit"), method = "nr")


Frequencies of categories:
y
     0      1 
0.4316 0.5684 
The estimation took: 0h:0m:0s 

Coefficients:
          Estimate Std. Error z-value Pr(>|z|)    
constant  1.918422   0.380654   5.040 4.66e-07 ***
k5       -0.874711   0.113558  -7.703 1.33e-14 ***
k618     -0.038594   0.040489  -0.953 0.340488    
age      -0.037824   0.007609  -4.971 6.67e-07 ***
wc        0.488314   0.135487   3.604 0.000313 ***
hc        0.057170   0.124005   0.461 0.644776    
lwg       0.365629   0.087779   4.165 3.11e-05 ***
inc      -0.020525   0.004777  -4.297 1.73e-05 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Optimization of log-likelihood by Newton-Raphson maximisation
Log Likelihood: -452.7
Number of observations: 753
Number of iterations: 4
Exit of MLE: gradient close to zero> 
> library(sandwich)
> estfun(probit) 
Error in UseMethod("estfun") : 
  no applicable method for 'estfun' applied to an object of class "Rchoice"
Calls: estfun
Execution halted
climdex.data.frame: no visible global function definition for
  ‘as.PCICt’
Undefined global functions or variables:
  as.PCICt
get_ClinicalCodes: no visible global function definition for ‘read.csv’
get_ClinicalCodes : <anonymous>: no visible global function definition
  for ‘read.csv’
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
cmaOptimDP: no visible global function definition for ‘flush.console’
Undefined global functions or variables:
  flush.console
Consider adding
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Depends: includes the non-default packages:
  ‘biclust’ ‘fabia’ ‘iBBiG’ ‘superbiclust’ ‘BcDiag’ ‘rqubic’ ‘BicARE’
  ‘s4vd’ ‘BiBitR’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
enterTableMHTest : onOK: no visible global function definition for
  ‘na.omit’
startStop: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Namespace with empty importFrom: ‘tcltk’
'library' or 'require' calls to packages already attached by Depends:
  ‘depthTools’ ‘tcltk’
  Please remove these calls from your code.
computeMBD : OnOutput: no visible global function definition for
  ‘tkbutton’
computeMBD: no visible global function definition for ‘tkbutton’
computeMBD : OnPlot: no visible global function definition for
  ‘tkcanvas’
computeMBD : OnPlot: no visible global function definition for
  ‘tkbutton’
computeTmean: no visible global function definition for ‘tkcanvas’
computeTmean: no visible global function definition for ‘tkbutton’
computeTmean : onOK: no visible global function definition for ‘par’
plotCentralCurves: no visible global function definition for ‘tkcanvas’
plotCentralCurves: no visible global function definition for ‘tkbutton’
plotCentralCurves : onOK: no visible global function definition for
  ‘par’
Undefined global functions or variables:
  par tkbutton tkcanvas
Consider adding
  importFrom("graphics", "par")
to your NAMESPACE file.
'library' or 'require' call to ‘FrF2.catlg128’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Rcmdr’ ‘multcomp’
  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:
  ‘Rcmdr’ ‘TeachingDemos’ ‘tseries’ ‘abind’ ‘MASS’ ‘xts’ ‘forecast’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Non-standard file/directory found at top level:
  ‘histprice2.R’
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘tseries’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘MASS’ ‘Rcmdr’ ‘TeachingDemos’ ‘abind’ ‘forecast’ ‘tseries’ ‘xts’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls in package code:
  ‘abind’ ‘e1071’ ‘qcc’
  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.numSummaryIPSUR
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Packages in Depends field not imported from:
  ‘ENmisc’ ‘Hmisc’ ‘Rcmdr’ ‘vcd’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.onAttach: no visible global function definition for ‘getRcmdr’
.onAttach: no visible global function definition for ‘closeCommander’
.onAttach: no visible global function definition for ‘Commander’
mosaicMenuItem: no visible global function definition for
  ‘mosaicSelectDialog’
mosaicMenuItem: no visible global function definition for ‘Message’
Undefined global functions or variables:
  Commander Message closeCommander getRcmdr mosaicSelectDialog
Found the following apparent S3 methods exported but not registered:
  Confint.mvr
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
BOXWP: no visible binding for global variable ‘top’
BOXWP: no visible binding for global variable ‘buttonsFrame’
HIST: no visible binding for global variable ‘top’
HIST: no visible binding for global variable ‘buttonsFrame’
QQN: no visible binding for global variable ‘top’
QQN: no visible binding for global variable ‘buttonsFrame’
Undefined global functions or variables:
  buttonsFrame top
Namespaces with empty importFrom:
  ‘stats’ ‘tcltk’
fncLRpROC: no visible global function definition for ‘palette’
fncLRpROC : onOK : convert: no visible global function definition for
  ‘col2rgb’
fncLRpROC : onOK : convert: no visible global function definition for
  ‘rgb’
fncPairedpROC: no visible global function definition for ‘palette’
fncPairedpROC : onOK : convert: no visible global function definition
  for ‘col2rgb’
fncPairedpROC : onOK : convert: no visible global function definition
  for ‘rgb’
fncUnpairedpROC: no visible global function definition for ‘palette’
fncUnpairedpROC : onOK : convert: no visible global function definition
  for ‘col2rgb’
fncUnpairedpROC : onOK : convert: no visible global function definition
  for ‘rgb’
fncvpROC: no visible global function definition for ‘palette’
fncvpROC : onOK : convert: no visible global function definition for
  ‘col2rgb’
fncvpROC : onOK : convert: no visible global function definition for
  ‘rgb’
Undefined global functions or variables:
  col2rgb palette rgb
Consider adding
  importFrom("grDevices", "col2rgb", "palette", "rgb")
to your NAMESPACE file.
SampleSizes: no visible global function definition for ‘xtabs’
SampleSizes: no visible global function definition for ‘weighted.mean’
SampleSizes: no visible global function definition for ‘reshape’
stage1Sample.fn: no visible global function definition for ‘runif’
stage2Sample.fn: no visible global function definition for ‘runif’
strata.options : onOK: no visible global function definition for
  ‘packageDescription’
Undefined global functions or variables:
  packageDescription reshape runif weighted.mean xtabs
Consider adding
  importFrom("stats", "reshape", "runif", "weighted.mean", "xtabs")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
'library' or 'require' call to ‘SLC’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘SLC’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Depends: includes the non-default packages:
  ‘Rcmdr’ ‘tcltk’ ‘car’ ‘RColorBrewer’ ‘colorspace’ ‘vcd’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' call to ‘car’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RColorBrewer’ ‘Rcmdr’ ‘car’ ‘colorspace’ ‘vcd’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rcmdr.steeptestDij : onOK: no visible binding for global variable
  ‘replications’
Rcmdr.steeptestPij : onOK: no visible binding for global variable
  ‘replications’
Undefined global functions or variables:
  replications
Consider adding
  importFrom("stats", "replications")
to your NAMESPACE file.
brewer.pal: no visible global function definition for ‘rgb’
display.brewer.all: no visible global function definition for ‘par’
display.brewer.all: no visible global function definition for ‘plot’
display.brewer.all: no visible global function definition for ‘rect’
display.brewer.all: no visible global function definition for ‘text’
display.brewer.pal: no visible global function definition for ‘image’
Undefined global functions or variables:
  image par plot rect rgb text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "image", "par", "plot", "rect", "text")
to your NAMESPACE file.
addLine: no visible global function definition for ‘abline’
ellipse: no visible global function definition for ‘approx’
ellipse: no visible global function definition for ‘tail’
Undefined global functions or variables:
  abline approx tail
Consider adding
  importFrom("graphics", "abline")
  importFrom("stats", "approx")
  importFrom("utils", "tail")
to your NAMESPACE file.
File ‘RcppBDT/libs/RcppBDT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 warnings:
  ../inst/include/blaze/math/smp/openmp/Functions.h:98:1: warning: control may reach end of non-void function [-Wreturn-type]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/RcppBlaze.Rcheck/00install.out’ for details.
File which contains pragma(s) suppressing diagnostics:
  ‘inst/include/RcppBlazeConfig.h’
File ‘RcppDL/libs/RcppDL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Files which contain pragma(s) suppressing diagnostics:
  ‘inst/include/ql/math/distributions/normaldistribution.hpp’
  ‘inst/include/ql/math/matrix.hpp’
  ‘inst/include/ql/math/optimization/levenbergmarquardt.hpp’
  ‘inst/include/ql/math/statistics/incrementalstatistics.hpp’
  ‘inst/include/ql/time/date.hpp’ ‘inst/include/ql/time/imm.hpp’
  ‘inst/include/ql/utilities/dataparsers.hpp’
  ‘inst/include/ql/utilities/null.hpp’
Registration problem:
  symbol ‘symbol’ in the local frame:
   .Call(symbol)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
File ‘RcppStreams/libs/RcppStreams.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Rcsdp/libs/Rcsdp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘Changes.html’ ‘CodeGeneration’ ‘README.windows’ ‘Todo.html’
  ‘dynGC.R’ ‘encoding.R’ ‘exampleCode’ ‘getURL.html’ ‘libcurlLicense’
  ‘post.R’ ‘postForm.html’
Packages in Depends field not imported from:
  ‘MASS’ ‘Matrix’ ‘lattice’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CUR: no visible global function definition for ‘runif’
CUR: no visible global function definition for ‘new’
plotLeverage,CURobj: no visible global function definition for ‘plot’
plotLeverage,CURobj: no visible global function definition for ‘points’
plotLeverage,CURobj: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline new plot points runif
Consider adding
  importFrom("graphics", "abline", "plot", "points")
  importFrom("methods", "new")
  importFrom("stats", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
get.datamarket.csv: no visible global function definition for
  ‘read.csv’
getUserAgent: no visible global function definition for ‘sessionInfo’
Undefined global functions or variables:
  read.csv sessionInfo
Consider adding
  importFrom("utils", "read.csv", "sessionInfo")
to your NAMESPACE file.
File ‘rDEA/libs/rDEA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
distimage: no visible binding for global variable ‘terrain.colors’
distimage: no visible global function definition for ‘filled.contour’
distimage: no visible global function definition for ‘title’
distimage: no visible global function definition for ‘axis’
distimage: no visible global function definition for ‘lines’
drawkpc: no visible global function definition for ‘plot’
drawkpc: no visible global function definition for ‘segments’
drawkpc: no visible global function definition for ‘lines’
modelimage: no visible binding for global variable ‘topo.colors’
modelimage: no visible global function definition for ‘filled.contour’
modelimage: no visible global function definition for ‘title’
modelimage: no visible global function definition for ‘axis’
modelimage: no visible global function definition for ‘lines’
sincdata: no visible global function definition for ‘runif’
sincdata: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  axis filled.contour lines plot rnorm runif segments terrain.colors
  title topo.colors
Consider adding
  importFrom("grDevices", "terrain.colors", "topo.colors")
  importFrom("graphics", "axis", "filled.contour", "lines", "plot",
             "segments", "title")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
sumry_categorical: no visible global function definition for ‘freq’
sumry_continous: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  freq quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Found the following significant warnings:
  dist.cpp:19:33: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
  dist.cpp:65:33: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
  dist.cpp:111:36: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rdist.Rcheck/00install.out’ for details.
File ‘Rdsdp/libs/Rdsdp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘synchronicity’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
ip2coordinates: no visible global function definition for ‘URLencode’
street2coordinates: no visible global function definition for
  ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
File ‘Rdtq/libs/Rdtq.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Files which contain pragma(s) suppressing diagnostics:
  ‘inst/include/re2/prog.h’ ‘inst/include/re2/re2.h’
  ‘inst/include/re2/regexp.h’ ‘src/dfa.cc’ ‘src/onepass.cc’
File ‘read.dbc/libs/read.dbc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard file/directory found at top level:
  ‘devel’
'library' or 'require' calls to packages already attached by Depends:
  ‘leaps’ ‘mgcv’
  Please remove these calls from your code.
xy: warning in assign(xname, X, env = .GlobalEnv): partial argument
  match of ‘env’ to ‘envir’
xy: warning in assign(yname, y, env = .GlobalEnv): partial argument
  match of ‘env’ to ‘envir’
bestmods: no visible global function definition for ‘abline’
bestmods: no visible global function definition for ‘axis’
bestmods: no visible global function definition for ‘lines’
cic: no visible global function definition for ‘lsfit’
cic: no visible global function definition for ‘var’
cvic: no visible global function definition for ‘lsfit’
cvic: no visible global function definition for ‘lm’
eic: no visible global function definition for ‘lsfit’
eic: no visible global function definition for ‘lm’
ic.min: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘var’
xy: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline axis lines lm lsfit rnorm var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "lm", "lsfit", "rnorm", "var")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘reams/R/xy.R’:
  assign(xname, X, env = .GlobalEnv)
  assign(yname, y, env = .GlobalEnv)
prepare_Rd: bestmods.Rd:47-49: Dropping empty section \note
prepare_Rd: bestmods.Rd:43-44: Dropping empty section \references
prepare_Rd: cic.Rd:24-26: Dropping empty section \details
prepare_Rd: cic.Rd:40-42: Dropping empty section \note
prepare_Rd: cvic.Rd:49-51: Dropping empty section \note
prepare_Rd: eic.Rd:31-33: Dropping empty section \details
prepare_Rd: eic.Rd:50-52: Dropping empty section \note
prepare_Rd: eic.Rd:56-58: Dropping empty section \seealso
prepare_Rd: ic.min.Rd:22-24: Dropping empty section \details
prepare_Rd: ic.min.Rd:47-49: Dropping empty section \note
prepare_Rd: ic.min.Rd:53-55: Dropping empty section \seealso
prepare_Rd: reams-package.Rd:16-17: Dropping empty section \references
prepare_Rd: reams-package.Rd:19-20: Dropping empty section \seealso
prepare_Rd: reams-package.Rd:21-22: Dropping empty section \examples
prepare_Rd: scoremods.Rd:26-28: Dropping empty section \details
prepare_Rd: scoremods.Rd:43-45: Dropping empty section \note
prepare_Rd: xy.Rd:46-48: Dropping empty section \note
prepare_Rd: xy.Rd:52: Dropping empty section \seealso
ReCiPa: no visible global function definition for ‘count.fields’
ReCiPa: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  count.fields read.table
Consider adding
  importFrom("utils", "count.fields", "read.table")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  [.RLBigData [.RLResult [.RecLinkData [.RecLinkResult
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘RecordLinkage/libs/RecordLinkage.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
AutoCorrelationLRtest: no visible global function definition for
  ‘logLik’
AutoCorrelationLRtest: no visible global function definition for
  ‘pchisq’
REEMtree: no visible global function definition for ‘terms’
REEMtree: no visible binding for global variable ‘SubsetVector’
REEMtree: no visible global function definition for ‘predict’
REEMtree: no visible global function definition for ‘logLik’
fitted.REEMtree: no visible global function definition for ‘fitted’
plot.REEMtree: no visible global function definition for ‘plot’
predict.REEMtree: no visible global function definition for ‘predict’
residuals.REEMtree: no visible global function definition for
  ‘residuals’
Undefined global functions or variables:
  SubsetVector fitted logLik pchisq plot predict residuals terms
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "fitted", "logLik", "pchisq", "predict",
             "residuals", "terms")
to your NAMESPACE file.
Rd file 'REEMtree.Rd':
  \usage lines wider than 90 characters:
                     ErrorTolerance=0.001, MaxIterations=1000, verbose=FALSE, tree.control=rpart.control(), 
                     lme.control=lmeControl(returnObject=TRUE), method="REML", correlation=NULL)

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

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

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

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

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

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

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
cook.outliers: no visible global function definition for ‘lm’
cook.outliers: no visible global function definition for
  ‘cooks.distance’
nonparRI: no visible global function definition for ‘quantile’
plot.interval: no visible global function definition for ‘par’
plot.interval: no visible global function definition for ‘plot.new’
plot.interval: no visible global function definition for ‘plot.window’
plot.interval: no visible global function definition for ‘segments’
plot.interval: no visible global function definition for ‘axis’
plot.interval: no visible global function definition for ‘title’
plot.interval: no visible global function definition for ‘legend’
plot.interval: no visible global function definition for ‘box’
plot.interval: no visible global function definition for ‘text’
robust: no visible global function definition for ‘qt’
singleRefLimit: no visible global function definition for ‘qnorm’
singleRefLimit: no visible global function definition for
  ‘shapiro.test’
singleRefLimit: no visible global function definition for ‘ks.test’
Undefined global functions or variables:
  axis box cooks.distance ks.test legend lm par plot.new plot.window
  qnorm qt quantile segments shapiro.test text title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "par", "plot.new",
             "plot.window", "segments", "text", "title")
  importFrom("stats", "cooks.distance", "ks.test", "lm", "qnorm", "qt",
             "quantile", "shapiro.test")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  plot.wcr plot.wnet
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Data2wd: no visible binding for global variable ‘var’
getRsq: no visible global function definition for ‘var’
plot.wcr: no visible global function definition for ‘plot’
plot.wcr: no visible global function definition for ‘image’
plot.wcr: no visible global function definition for ‘par’
plot.wnet: no visible global function definition for ‘plot’
plot.wnet: no visible global function definition for ‘image’
plot.wnet: no visible global function definition for ‘par’
waveletGetCV: no visible binding for global variable ‘median’
waveletGetCV: no visible binding for global variable ‘sd’
wcr: no visible binding for global variable ‘var’
wcr: no visible global function definition for ‘cov’
wcr: no visible global function definition for ‘lm’
wcr: no visible global function definition for ‘ginv’
wcr: no visible global function definition for ‘glm’
wnet: no visible binding for global variable ‘var’
wnet: no visible global function definition for ‘predict’
Undefined global functions or variables:
  cov ginv glm image lm median par plot predict sd var
Consider adding
  importFrom("graphics", "image", "par", "plot")
  importFrom("stats", "cov", "glm", "lm", "median", "predict", "sd",
             "var")
to your NAMESPACE file.
cluster.reg: no visible global function definition for ‘rnorm’
cluster.reg: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
.area.my: no visible global function definition for ‘density’
optimalGT : <anonymous>: no visible global function definition for
  ‘median’
optimalGT: no visible global function definition for ‘png’
optimalGT: no visible global function definition for ‘dev.off’
permutation: no visible global function definition for ‘flush.console’
plot.wls: no visible global function definition for ‘par’
plot.wls: no visible global function definition for ‘plot’
plot.wls: no visible global function definition for ‘text’
plot.wls: no visible global function definition for ‘abline’
reGenotyper: no visible global function definition for ‘flush.console’
reGenotyper: no visible binding for global variable ‘var’
reGenotyper: no visible global function definition for ‘plot’
Undefined global functions or variables:
  abline density dev.off flush.console median par plot png text var
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "abline", "par", "plot", "text")
  importFrom("stats", "density", "median", "var")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Non-standard files/directories found at top level:
  ‘prebuild.sh’ ‘regtest-Ex.R’
Warning in fun(libname, pkgname) :
  package regtest is under development and still may change considerably

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.onAttach: no visible global function definition for
  ‘packageDescription’
.relax.cv.elnet: no visible global function definition for ‘predict’
.relax.cv.elnet: no visible binding for global variable ‘weighted.mean’
.relax.cv.lognet: no visible global function definition for ‘predict’
.relax.cv.lognet: no visible binding for global variable
  ‘weighted.mean’
.relax.cvcompute: no visible binding for global variable
  ‘weighted.mean’
.single.column: no visible global function definition for ‘glm’
.single.column: no visible global function definition for ‘coef’
cv.alpha.relaxnet: no visible global function definition for
  ‘mc.reset.stream’
cv.alpha.relaxnet: no visible global function definition for ‘mclapply’
cv.relaxnet: no visible global function definition for ‘predict’
cv.relaxnet: no visible global function definition for
  ‘mc.reset.stream’
cv.relaxnet: no visible global function definition for ‘mclapply’
predict.cv.alpha.relaxnet: no visible global function definition for
  ‘predict’
predict.cv.relaxnet: no visible global function definition for
  ‘predict’
predict.relaxnet: no visible global function definition for ‘predict’
Undefined global functions or variables:
  coef glm mc.reset.stream mclapply packageDescription predict
  weighted.mean
Consider adding
  importFrom("stats", "coef", "glm", "predict", "weighted.mean")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
'library' or 'require' call to ‘lars’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘lars’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
relaxo: no visible global function definition for ‘lars’
Undefined global functions or variables:
  lars
Rd file 'cvrelaxo.Rd':
  \usage lines wider than 90 characters:
     cvrelaxo(X, Y, K = 5, phi = seq(0, 1, length = 10), max.steps = min( 2* length(Y), 2 * ncol(X)), fast = TRUE, keep.data = TRUE, warn=TR ... [TRUNCATED]

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

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

These lines will be truncated in the PDF manual.
print.summary.rem: no visible global function definition for
  ‘printCoefmat’
print.summary.rem: no visible global function definition for ‘pnorm’
print.summary.rem: no visible binding for global variable ‘quantile’
print.summary.rem: no visible global function definition for ‘pchisq’
print.summary.rem.dyad: no visible global function definition for
  ‘printCoefmat’
print.summary.rem.dyad: no visible global function definition for
  ‘pnorm’
print.summary.rem.dyad: no visible global function definition for
  ‘pchisq’
rem: no visible global function definition for ‘rnorm’
rem: no visible global function definition for ‘dnorm’
rem: no visible global function definition for ‘runif’
rem: no visible global function definition for ‘rchisq’
rem: no visible global function definition for ‘cov’
rem.dyad: no visible global function definition for ‘rnorm’
rem.dyad: no visible global function definition for ‘optim’
rem.dyad: no visible global function definition for ‘rchisq’
rem.dyad: no visible global function definition for ‘quantile’
rem.dyad: no visible global function definition for ‘sd’
rem.dyad: no visible global function definition for ‘var’
rem.dyad.lprior: no visible global function definition for ‘dnorm’
rem.dyad.lprior: no visible global function definition for ‘dt’
Undefined global functions or variables:
  cov dnorm dt optim pchisq pnorm printCoefmat quantile rchisq rnorm
  runif sd var
Consider adding
  importFrom("stats", "cov", "dnorm", "dt", "optim", "pchisq", "pnorm",
             "printCoefmat", "quantile", "rchisq", "rnorm", "runif",
             "sd", "var")
to your NAMESPACE file.
File ‘relevent/libs/relevent.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
CapDistSlope: no visible global function definition for ‘coef’
CapDistSlope: no visible global function definition for ‘lm’
EnergyEntropyDecomp: no visible global function definition for ‘legend’
FernholzDecomp: no visible global function definition for ‘legend’
Invest: no visible global function definition for ‘par’
Invest: no visible global function definition for ‘legend’
SimMarketModel: no visible global function definition for ‘rnorm’
plot.capdist: no visible global function definition for ‘plot’
plot.capdist: no visible global function definition for ‘abline’
plot.capdist: no visible global function definition for ‘lm’
plot.toymkt: no visible global function definition for ‘par’
plot.toymkt: no visible global function definition for ‘plot’
plot.toymkt: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline coef legend lm par plot rnorm
Consider adding
  importFrom("graphics", "abline", "legend", "par", "plot")
  importFrom("stats", "coef", "lm", "rnorm")
to your NAMESPACE file.
File ‘remMap/libs/remMap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
RearrangeData: no visible global function definition for ‘rainbow’
RearrangeData: no visible global function definition for ‘hclust’
RearrangeData: no visible global function definition for
  ‘as.dendrogram’
RearrangeData: no visible global function definition for ‘heatmap’
RearrangeData: no visible global function definition for ‘pdf’
RearrangeData: no visible global function definition for
  ‘colorRampPalette’
RearrangeData: no visible global function definition for ‘legend’
RearrangeData: no visible global function definition for ‘dev.off’
RearrangeJoseph: no visible global function definition for
  ‘write.table’
RearrangeJoseph: no visible global function definition for
  ‘as.dendrogram’
RearrangeJoseph: no visible global function definition for
  ‘order.dendrogram’
colorDendClass : colLab: no visible global function definition for
  ‘is.leaf’
colorDendClass: no visible global function definition for ‘dendrapply’
colorDendClass: no visible global function definition for ‘plot’
testData1: no visible global function definition for ‘runif’
testData1: no visible global function definition for ‘image’
testData2: no visible global function definition for ‘runif’
testData2: no visible global function definition for ‘image’
Undefined global functions or variables:
  as.dendrogram colorRampPalette dendrapply dev.off hclust heatmap
  image is.leaf legend order.dendrogram pdf plot rainbow runif
  write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf",
             "rainbow")
  importFrom("graphics", "image", "legend", "plot")
  importFrom("stats", "as.dendrogram", "dendrapply", "hclust", "heatmap",
             "is.leaf", "order.dendrogram", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
File ‘ReorderCluster/libs/ReorderCluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
GlobTestMissing: no visible global function definition for ‘lme’
GlobTestMissing: no visible global function definition for ‘anova’
TestStatSP: no visible global function definition for ‘pf’
TestStatSimple: no visible global function definition for ‘ginv’
TestStatSimple: no visible global function definition for ‘pf’
Undefined global functions or variables:
  anova ginv lme pf
Consider adding
  importFrom("stats", "anova", "pf")
to your NAMESPACE file.
Found the following significant warnings:
  gar.c:356:29: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  gar.c:356:80: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/repeated.Rcheck/00install.out’ for details.
File ‘repeated/libs/repeated.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
delete: no visible global function definition for ‘menu’
doc_temp: no visible global function definition for ‘menu’
html5: no visible global function definition for ‘na.omit’
install_pandoc: no visible global function definition for
  ‘download.file’
new_report: no visible global function definition for ‘tail’
new_report: no visible global function definition for ‘head’
new_report: no visible global function definition for ‘menu’
presentation: no visible global function definition for ‘head’
presentation: no visible global function definition for ‘tail’
presentation: no visible global function definition for ‘menu’
repo2github: no visible global function definition for ‘download.file’
repo2github: no visible global function definition for ‘unzip’
reveal.js: no visible global function definition for ‘na.omit’
update_bib: no visible global function definition for ‘tail’
update_bib: no visible global function definition for ‘menu’
Undefined global functions or variables:
  download.file head menu na.omit tail unzip
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "download.file", "head", "menu", "tail", "unzip")
to your NAMESPACE file.
MBoxtest: no visible global function definition for ‘var’
jrparams: no visible global function definition for ‘prcomp’
jrparams: no visible global function definition for ‘predict’
jrparams: no visible global function definition for ‘qchisq’
jrparams: no visible global function definition for ‘qf’
Undefined global functions or variables:
  prcomp predict qchisq qf var
Consider adding
  importFrom("stats", "prcomp", "predict", "qchisq", "qf", "var")
to your NAMESPACE file.
Rd file 'jrparams.Rd':
  \usage lines wider than 90 characters:
     jrparams(BLOCK.1, BLOCK.2, ncomp = min(c(dim(BLOCK.1), dim(BLOCK.2))), Cscrit=0.6, Rscrit=0.6)

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

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

These lines will be truncated in the PDF manual.
.resampleMakeFunction: no visible global function definition for ‘is’
.resampleSetSeed: no visible global function definition for ‘runif’
CI.bca: no visible global function definition for ‘is’
CI.bca: no visible global function definition for ‘qnorm’
CI.bca: no visible global function definition for ‘pnorm’
CI.t: no visible global function definition for ‘qt’
ExpandProbs: no visible global function definition for ‘pnorm’
ExpandProbs: no visible global function definition for ‘qt’
colVars : f: no visible global function definition for ‘var’
colVars: no visible global function definition for ‘var’
hist.resample: no visible global function definition for ‘density’
hist.resample: no visible global function definition for ‘lines’
hist.resample: no visible global function definition for ‘points’
hist.resample: no visible global function definition for ‘approx’
hist.resample: no visible global function definition for ‘segments’
resample: no visible global function definition for ‘is’
samp.bootknife: no visible global function definition for ‘runif’
samp.bootstrap: no visible global function definition for ‘runif’
Undefined global functions or variables:
  approx density is lines pnorm points qnorm qt runif segments var
Consider adding
  importFrom("graphics", "lines", "points", "segments")
  importFrom("methods", "is")
  importFrom("stats", "approx", "density", "pnorm", "qnorm", "qt",
             "runif", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘resemble/libs/resemble.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘load.r’
Packages in Depends field not imported from:
  ‘gWidgets’ ‘gWidgetsRGtk2’ ‘plyr’ ‘reshape2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
reshapeGUI: no visible global function definition for ‘gwindow’
reshapeGUI: no visible global function definition for ‘gnotebook’
reshapeGUI: no visible global function definition for ‘size<-’
reshapeGUI: no visible global function definition for ‘ggroup’
reshapeGUI: no visible global function definition for ‘gtable’
reshapeGUI: no visible global function definition for ‘addSpring’
reshapeGUI: no visible global function definition for ‘gbutton’
reshapeGUI: no visible global function definition for ‘glabel’
reshapeGUI: no visible global function definition for ‘gedit’
reshapeGUI: no visible global function definition for ‘gcheckbox’
reshapeGUI: no visible global function definition for ‘gdf’
reshapeGUI: no visible global function definition for ‘visible<-’
reshapeGUI: no visible global function definition for
  ‘addHandlerClicked’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘gmessage’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘svalue’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘svalue<-’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘delete’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘add’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘gdf’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘visible<-’
reshapeGUI: no visible global function definition for
  ‘addHandlerChanged’
updateMeltCodeBox: no visible global function definition for ‘svalue<-’
Undefined global functions or variables:
  add addHandlerChanged addHandlerClicked addSpring delete gbutton
  gcheckbox gdf gedit ggroup glabel gmessage gnotebook gtable gwindow
  size<- svalue svalue<- visible<-
Rd file 'array.resistance.Rd':
  \usage lines wider than 90 characters:
     array.resistance(x.offset, y.offset, rows.of.resistors, cols.of.resistors, give.pots = FALSE)

These lines will be truncated in the PDF manual.
GUI_template : onHelp: no visible global function definition for ‘help’
Undefined global functions or variables:
  help
Consider adding
  importFrom("utils", "help")
to your NAMESPACE file.
File ‘restrictedMVN/libs/restrictedMVN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘testCases.R’ [2s/2s]
Running the tests in ‘tests/testCases.R’ failed.
Complete output:
  > ## test constrained lm, rlm, glm
  > # mixing weights
  > # bootstrap standard errors
  > # models with and without intercept
  > # case weights
  > # constraints on factors and interactions
  > 
  > library(restriktor)
  This is restriktor 0.1-80.711
  restriktor is BETA software! Please report any bugs.
  > n <- 100
  > p <- 4
  > betas = c(0.1,0.2,0.3,0.4,0.5)
  > set.seed(3013073)
  > X <- cbind(mvtnorm:::rmvnorm(n, mean=rep(0,p), sigma=diag(p)), rbinom(n,1,0.5))
  > colnames(X) <- c("x1","x2","x3","x4","f1")
  > z <- X %*% betas        
  > y <- z + rnorm(n)
  > DATA <- data.frame(y, X)
  > 
  > # intercept model
  > model1 <- y ~  1 + x1 + x2 + x3 + x4
  > # no intercept model
  > model2 <- y ~ -1 + x1 + x2 + x3 + x4
  > # intercept model with interaction
  > model3 <- y ~ 1 + x1*f1 + x2*f1 + x3*f1 + x4*f1
  > # intercept model with interaction
  > model4 <- y ~ -1 + x1*f1 + x2*f1 + x3*f1 + x4*f1
  > 
  > ############################ lm #################################
  > linmod1 <- lm(model1, data = DATA)
  > linmod2 <- lm(model2, data = DATA)
  > linmod3 <- lm(model3, data = DATA)
  > linmod1wt <- lm(model1, data = DATA, weights = abs(rnorm(n)))
  > linmod2wt <- lm(model2, data = DATA, weights = abs(rnorm(n)))
  > linmod1fac <- lm(model3, data = DATA)
  > linmod2fac <- lm(model4, data = DATA)
  > 
  > constraints1 <- 'x1 > 0; x2 > 0; x3 > 0'
  > fit.restr1 <- restriktor(linmod1, constraints1)
  Error in UseMethod("conLM") : 
    no applicable method for 'conLM' applied to an object of class "lm"
  Calls: restriktor
  Execution halted
Warning: no function found corresponding to methods exports from ‘retimes’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
dexgauss: no visible global function definition for ‘pnorm’
loglik: no visible global function definition for ‘pnorm’
mexgauss: no visible global function definition for ‘sd’
rexgauss: no visible global function definition for ‘rnorm’
rexgauss: no visible global function definition for ‘rexp’
timefit: no visible global function definition for ‘optim’
timefit: no visible global function definition for ‘sd’
timefit: no visible global function definition for ‘par’
timefit: no visible global function definition for ‘hist’
timefit: no visible global function definition for ‘density’
timefit: no visible global function definition for ‘curve’
timefit: no visible global function definition for ‘new’
plot,timefit: no visible global function definition for ‘density’
plot,timefit: no visible global function definition for ‘par’
plot,timefit: no visible global function definition for ‘curve’
Undefined global functions or variables:
  curve density hist new optim par pnorm rexp rnorm sd
Consider adding
  importFrom("graphics", "curve", "hist", "par")
  importFrom("methods", "new")
  importFrom("stats", "density", "optim", "pnorm", "rexp", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘retimes/libs/retimes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.reweight: no visible global function definition for ‘par’
plot.reweight: no visible global function definition for ‘plot’
plot.reweight: no visible global function definition for ‘density’
plot.reweight: no visible global function definition for ‘rug’
reweight: no visible global function definition for ‘aggregate’
search.best.h: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  aggregate density par plot quantile rug
Consider adding
  importFrom("graphics", "par", "plot", "rug")
  importFrom("stats", "aggregate", "density", "quantile")
to your NAMESPACE file.
FDSNGetTimeSeries: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
File ‘RFgroove/libs/RFgroove.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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_author_ids : <anonymous>: no visible global function definition for
  ‘select.list’
fs_download : <anonymous>: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file select.list
Consider adding
  importFrom("utils", "download.file", "select.list")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
License components which are templates and need '+ file LICENSE':
  BSD 3-clause License
Packages in Depends field not imported from:
  ‘XML’ ‘xts’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
quoteFXTsData : function.fx: no visible global function definition for
  ‘xmlValue’
quoteFundTsData : function.fund: no visible global function definition
  for ‘xmlValue’
quoteStockTsData : function.stock: no visible global function
  definition for ‘xmlSize’
quoteStockTsData : function.stock: no visible global function
  definition for ‘xmlValue’
quoteTsData: no visible global function definition for ‘xmlRoot’
quoteTsData: no visible global function definition for ‘htmlTreeParse’
quoteTsData: no visible global function definition for
  ‘xmlErrorCumulator’
quoteTsData: no visible global function definition for ‘xmlSize’
toXts: no visible global function definition for ‘as.xts’
Undefined global functions or variables:
  as.xts htmlTreeParse xmlErrorCumulator xmlRoot xmlSize xmlValue
File ‘Rfit/libs/Rfit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
gabriel.plot: no visible global function definition for ‘barplot’
gabriel.plot: no visible global function definition for ‘arrows’
rgabriel: no visible binding for global variable ‘sd’
rgabriel : psmm_x: no visible global function definition for ‘pnorm’
rgabriel : psmm: no visible global function definition for ‘integrate’
rgabriel : qsmm: no visible global function definition for ‘qnorm’
rgabriel : qsmm: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  arrows barplot integrate pnorm qnorm sd uniroot
Consider adding
  importFrom("graphics", "arrows", "barplot")
  importFrom("stats", "integrate", "pnorm", "qnorm", "sd", "uniroot")
to your NAMESPACE file.
Package in Depends field not imported from: ‘gsl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gammaIntegral: no visible global function definition for ‘integrate’
gammaIntegral : <anonymous>: no visible global function definition for
  ‘hyperg_1F1’
gammaMLE: no visible global function definition for ‘weighted.mean’
gammaMME: no visible binding for global variable ‘sd’
gammaMME: no visible binding for global variable ‘var’
Undefined global functions or variables:
  hyperg_1F1 integrate sd var weighted.mean
Consider adding
  importFrom("stats", "integrate", "sd", "var", "weighted.mean")
to your NAMESPACE file.
File ‘rgcvpack/libs/rgcvpack.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
genoud: multiple local function definitions for ‘fn1.bfgs’ with
  different formal arguments
genoud: multiple local function definitions for ‘gr1’ with different
  formal arguments
genoud: multiple local function definitions for ‘hess.fn’ with
  different formal arguments
genoud_transform: multiple local function definitions for ‘fn1.bfgs’
  with different formal arguments
genoud_transform: multiple local function definitions for ‘gr1’ with
  different formal arguments
gexf.to.igraph: no visible global function definition for ‘rgb’
igraph.to.gexf: no visible global function definition for ‘col2rgb’
Undefined global functions or variables:
  col2rgb rgb
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
to your NAMESPACE file.
File ‘rgexf/libs/rgexf.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Rgnuplot/libs/Rgnuplot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘pmg’
Rjava.init.warning: stack size reduced from unlimited to 7953613 bytes after JVM initialization.
'library' or 'require' call to ‘gWidgetsRGtk2’ 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:
  ‘RGtk2’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘RGtk2Extras/libs/RGtk2Extras.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘RGtk2/libs/RGtk2.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_new_custom_connection’,
    ‘Rf_EncodeInteger’, ‘Rf_EncodeLogical’, ‘Rf_EncodeReal’,
    ‘Rf_formatInteger’, ‘Rf_formatLogical’, ‘Rf_formatReal’
File ‘RGtk2/libs/RGtk2.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.
.quick_fetch: no visible global function definition for ‘POST’
.quick_fetch: no visible global function definition for ‘add_headers’
.quick_fetch: no visible global function definition for
  ‘stop_for_status’
.quick_fetch: no visible global function definition for ‘content’
fetch_healthdata: no visible binding for global variable ‘resources’
fetch_healthdata : <anonymous>: no visible binding for global variable
  ‘filters’
Undefined global functions or variables:
  POST add_headers content filters resources stop_for_status
Packages in Depends field not imported from:
  ‘RCurl’ ‘XML’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ECL: no visible global function definition for ‘new’
ECLDataset: no visible global function definition for ‘new’
ECLDedUp: no visible global function definition for ‘new’
ECLDistribute: no visible global function definition for ‘new’
ECLIterate: no visible global function definition for ‘new’
ECLJoin: no visible global function definition for ‘new’
ECLOutput: no visible global function definition for ‘new’
ECLProject: no visible global function definition for ‘new’
ECLRecord: no visible global function definition for ‘new’
ECLRollUp: no visible global function definition for ‘new’
ECLSort: no visible global function definition for ‘new’
ECLTOPN: no visible global function definition for ‘new’
ECLTable: no visible global function definition for ‘new’
ECLTransform: no visible global function definition for ‘new’
eclDirectCall: no visible global function definition for ‘postForm’
parseResults: no visible global function definition for ‘xmlRoot’
parseResults: no visible global function definition for ‘xmlTreeParse’
parseResults: no visible global function definition for ‘getNodeSet’
parseResults: no visible global function definition for ‘xmlGetAttr’
parseResults: no visible global function definition for ‘xmlValue’
parseResults: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  getNodeSet new postForm write.table xmlGetAttr xmlRoot xmlTreeParse
  xmlValue
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  filterhr.c:21:11: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  filterhr.c:21:53: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  filterhr.c:21:95: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/RHRV.Rcheck/00install.out’ for details.
File ‘RHRV/libs/RHRV.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
RHT.2samp : my.HotellingT2 : my.InvCov2: no visible global function
  definition for ‘cov’
RHT.2samp : get.lambda : get.para: no visible global function
  definition for ‘optimize’
RHT.2samp : get.lambda : gg: no visible global function definition for
  ‘qchisq’
RHT.2samp : get.lambda : ggl: no visible global function definition for
  ‘qnorm’
RHT.2samp : <anonymous>: no visible global function definition for
  ‘cov’
RHT.fun : my.HotellingT : my.InvCov: no visible global function
  definition for ‘cov’
RHT.fun : get.lambda : get.para: no visible global function definition
  for ‘optimize’
RHT.fun : get.lambda : gg: no visible global function definition for
  ‘qchisq’
RHT.fun : get.lambda : ggl: no visible global function definition for
  ‘qnorm’
RHT.fun : <anonymous>: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov optimize qchisq qnorm
Consider adding
  importFrom("stats", "cov", "optimize", "qchisq", "qnorm")
to your NAMESPACE file.
File ‘RI2by2/libs/RI2by2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
FusedQDA : <anonymous>: no visible global function definition for ‘cov’
RidgeFused: no visible binding for global variable ‘cov2cor’
RidgeFusedCV : <anonymous>: no visible global function definition for
  ‘cov’
SSRidgeFused : <anonymous>: no visible global function definition for
  ‘cov’
Undefined global functions or variables:
  cov cov2cor
Consider adding
  importFrom("stats", "cov", "cov2cor")
to your NAMESPACE file.
ridit.raw: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
R2ngon: no visible global function definition for ‘approx’
plotR2pre: no visible global function definition for ‘plot’
plotR2pre: no visible global function definition for ‘points’
plotR2pre: no visible global function definition for ‘gray’
plotR2pre: no visible global function definition for ‘legend’
plotR2pre: no visible global function definition for ‘rainbow’
Undefined global functions or variables:
  approx gray legend plot points rainbow
Consider adding
  importFrom("grDevices", "gray", "rainbow")
  importFrom("graphics", "legend", "plot", "points")
  importFrom("stats", "approx")
to your NAMESPACE file.
plot.ijzip: no visible global function definition for ‘plot’
plot.ijzip : <anonymous>: no visible global function definition for
  ‘plot’
plot.ijzip: no visible global function definition for ‘axis’
read.ijzip: no visible global function definition for ‘unzip’
Undefined global functions or variables:
  axis plot unzip
Consider adding
  importFrom("graphics", "axis", "plot")
  importFrom("utils", "unzip")
to your NAMESPACE file.
Non-standard files/directories found at top level:
  ‘doc’ ‘prebuild.sh’ ‘rindex-Ex.R’
Warning in fun(libname, pkgname) :
  package rindex is under development and still may change considerably

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

Probably some imports need to be declared in the NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  !=.index !=.rindex <.index <.rindex <=.index <=.rindex ==.index
  ==.rindex >.index >.rindex >=.index >=.rindex [.index [.rindex
  [<-.index [<-.rindex c.index c.rindex is.na.index is.na.rindex
  length.index length.rindex names.index names<-.index names<-.rindex
  print.index print.rindex sort.index sort.rindex str.index str.rindex
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
indexBytes: no visible global function definition for ‘object.size’
rindexBytes: no visible global function definition for ‘object.size’
Undefined global functions or variables:
  object.size
Consider adding
  importFrom("utils", "object.size")
to your NAMESPACE file.
Rd file 'index.rd':
  \examples lines wider than 100 characters:
       cat("if the index (or index$tree) is removed, the C-tree is removed at the next garbage collection\n")
       cat("accessing the ordering is also much faster (order.index is not dispatched since order is not yet generic)\n")
       indexMatch(i,c("c","f"), findlow=TRUE)  # giving parameter findlow= suppresses the warning issued on non-unique indices

Rd file 'indexFindInterval.rd':
  \usage lines wider than 90 characters:
      indexFindInterval(obj, low = NULL, high = NULL, low.include = TRUE, high.include = TRUE, low.exact = FALSE, high.exact = FALSE, lowFUN ... [TRUNCATED]

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘RInside/libs/RInside.so’:
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLdo1’, ‘R_ReplDLLinit’,
    ‘R_RunExitFinalizers’, ‘R_SetParams’, ‘R_SignalHandlers’,
    ‘R_TempDir’, ‘Rf_endEmbeddedR’, ‘Rf_initEmbeddedR’
File ‘RInside/libs/RInside.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 use Fortran I/O
nor system RNGs.
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.
File ‘Rip46/libs/Rip46.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘doMC’ ‘doSNOW’ ‘e1071’ ‘fftw’ ‘foreach’ ‘jpeg’ ‘png’ ‘rggobi’
  ‘tkrplot’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘parallel’ ‘tcltk’
  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.imagematrix print.imagematrix
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘ripa/libs/ripa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
KM.plot: no visible global function definition for ‘plot’
KM.plot: no visible global function definition for ‘lines’
SchoenSmooth: no visible global function definition for ‘lm’
llCoxReg: no visible binding for global variable ‘time’
risksetAUC: no visible global function definition for ‘abline’
risksetROC: no visible global function definition for ‘abline’
weightedKM: no visible binding for global variable ‘time’
Undefined global functions or variables:
  abline lines lm plot time
Consider adding
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "lm", "time")
to your NAMESPACE file.
Alg2: no visible global function definition for ‘uniroot’
Alg3: no visible global function definition for ‘optim’
NVCopula: no visible global function definition for ‘rnorm’
NVCopula: no visible global function definition for ‘rgamma’
NVCopula: no visible global function definition for ‘var’
NVCopula: no visible global function definition for ‘cov’
NVCopula: no visible global function definition for ‘qnorm’
NVCopulaMT: no visible global function definition for ‘rnorm’
NVCopulaMT: no visible global function definition for ‘rgamma’
NVCopulaMT: no visible global function definition for ‘var’
NVCopulaMT: no visible global function definition for ‘cov’
NVCopulaMT: no visible global function definition for ‘qnorm’
R2X: no visible global function definition for ‘write.table’
ReturnCopula: no visible global function definition for ‘qt’
ReturnCopula: no visible global function definition for ‘pt’
SISCopula: no visible global function definition for ‘runif’
SISCopula: no visible global function definition for ‘qnorm’
SISCopula: no visible global function definition for ‘rnorm’
SISCopula: no visible global function definition for ‘qgamma’
SISCopula: no visible global function definition for ‘var’
SISCopula: no visible global function definition for ‘cov’
SISCopulaMT: no visible global function definition for ‘runif’
SISCopulaMT: no visible global function definition for ‘qnorm’
SISCopulaMT: no visible global function definition for ‘rnorm’
SISCopulaMT: no visible global function definition for ‘qgamma’
SISCopulaMT: no visible global function definition for ‘var’
SISCopulaMT: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov optim pt qgamma qnorm qt rgamma rnorm runif uniroot var
  write.table
Consider adding
  importFrom("stats", "cov", "optim", "pt", "qgamma", "qnorm", "qt",
             "rgamma", "rnorm", "runif", "uniroot", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘compiler’ ‘signal’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
NumConv: no visible global function definition for ‘pchip’
NumConv: no visible global function definition for ‘cmpfun’
NumDeconv: no visible global function definition for ‘pchip’
NumDeconv : error_function: no visible global function definition for
  ‘pchip’
NumDeconv: no visible global function definition for ‘cmpfun’
NumDeconv: no visible global function definition for ‘optim’
RivivcA: no visible global function definition for ‘lm’
Undefined global functions or variables:
  cmpfun lm optim pchip
Consider adding
  importFrom("stats", "lm", "optim")
to your NAMESPACE file.
Rd file 'NumConv.Rd':
  \usage lines wider than 90 characters:
     NumConv(impulse.matrix, input.matrix, conv.timescale = NULL, explicit.interpolation = 1000)

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

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  rivmech_characteristic_v7.cpp:323:14: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rivr.Rcheck/00install.out’ for details.
File ‘rivr/libs/rivr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rjags/libs/rjags.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘getsp.class’ ‘getsp.java’ ‘install-sh’ ‘jri’ ‘version’
Found the following possibly unsafe calls:
File ‘rJava/R/import.R’:
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File ‘rJava/R/jinit.R’:
  unlockBinding(x, .env)
  unlockBinding(x, pe)
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  jri/src/Makefile.win
  jri/src/win32/Makefile
  src/jvm-w32/Makefile
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’
File ‘rJava/libs/rJava.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 use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
cubeHelix : <anonymous>: no visible global function definition for
  ‘rgb’
rdirichlet: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  rgamma rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "rgamma")
to your NAMESPACE file.
File ‘rje/libs/rje.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.jpstat
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
getStatsData: no visible global function definition for ‘xmlRoot’
getStatsData: no visible global function definition for ‘xmlTreeParse’
getStatsData: no visible global function definition for ‘xmlValue’
getStatsData: no visible global function definition for ‘getNodeSet’
getStatsData: no visible global function definition for ‘xmlSApply’
getStatsData: no visible binding for global variable ‘xmlGetAttr’
getStatsData: no visible binding for global variable ‘xmlValue’
getStatsData: no visible global function definition for ‘new’
getStatsList: no visible global function definition for ‘xmlRoot’
getStatsList: no visible global function definition for ‘xmlTreeParse’
getStatsList: no visible global function definition for ‘xmlValue’
getStatsList: no visible binding for global variable ‘xmlGetAttr’
getStatsList : <anonymous>: no visible global function definition for
  ‘xmlValue’
getStatsList : <anonymous>: no visible global function definition for
  ‘xmlGetAttr’
print.jpstat: no visible global function definition for ‘head’
Undefined global functions or variables:
  getNodeSet head new xmlGetAttr xmlRoot xmlSApply xmlTreeParse
  xmlValue
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "head")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  libjson/Source/JSONSharedString.h:180:47: warning: field 'len' will be initialized after field '_str' [-Wreorder]
  libjson/Source/JSONSharedString.h:182:66: warning: field 'len' will be initialized after field '_str' [-Wreorder]
  JSONStream.cpp:8:130: warning: field 'state' will be initialized after field 'call' [-Wreorder]
  JSONStream.cpp:8:157: warning: field 'err_call' will be initialized after field 'buffer' [-Wreorder]
  JSONStream.cpp:12:64: warning: field 'state' will be initialized after field 'call' [-Wreorder]
  JSONStream.cpp:12:100: warning: field 'err_call' will be initialized after field 'buffer' [-Wreorder]
  internalJSONNode.cpp:78:117: warning: field '_name_encoded' will be initialized after field '_name' [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/RJSONIO.Rcheck/00install.out’ for details.
Non-standard files/directories found at top level:
  ‘Changes.html’ ‘Dependencies’ ‘README.libjson’ ‘Todo.xml’
  ‘cleanup.in’ ‘cp_libjson’ ‘libjsonFixes’ ‘libjsonNotes’
File ‘RJSONIO/libs/RJSONIO.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘rJava’ which was already attached by Depends.
  Please remove these calls from your code.
cv.coef: no visible global function definition for ‘sd’
normalize.softmax: no visible global function definition for ‘plogis’
plot.rknnBeg: no visible global function definition for ‘plot’
plot.rknnBel: no visible global function definition for ‘plot’
plot.rknnSupport: no visible global function definition for ‘dotchart’
predicted: no visible global function definition for ‘influence’
predicted: no visible global function definition for ‘fitted’
predicted: no visible global function definition for ‘resid’
pressresid: no visible global function definition for ‘influence’
pressresid: no visible global function definition for ‘resid’
Undefined global functions or variables:
  dotchart fitted influence plogis plot resid sd
Consider adding
  importFrom("graphics", "dotchart", "plot")
  importFrom("stats", "fitted", "influence", "plogis", "resid", "sd")
to your NAMESPACE file.
File ‘rkvo/libs/rkvo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 which should be '::':
  ‘stats:::dexp’ ‘stats:::dgamma’ ‘stats:::dweibull’ ‘stats:::pexp’
  ‘stats:::pgamma’ ‘stats:::pweibull’ ‘stats:::qexp’ ‘stats:::qgamma’
  ‘stats:::qweibull’ ‘stats:::rexp’ ‘stats:::rgamma’ ‘stats:::rweibull’
  See the note in ?`:::` about the use of this operator.
File ‘rlecuyer/libs/rlecuyer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 Makefile(s) without a final LF:
  src/Makevars.in
Some ‘make’ programs ignore lines not ending in LF.
File ‘rlm/libs/rlm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘RLRsim/libs/RLRsim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘msm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘EMSRb_internal’ ‘EM_internal’ ‘PD_internal’
EMSRb_internal: no visible global function definition for ‘qnorm’
EM_internal: no visible global function definition for ‘dnorm’
EM_internal: no visible global function definition for ‘pnorm’
PD_internal: no visible global function definition for ‘qtnorm’
PD_internal: no visible global function definition for ‘sd’
Undefined global functions or variables:
  dnorm pnorm qnorm qtnorm sd
Consider adding
  importFrom("stats", "dnorm", "pnorm", "qnorm", "sd")
to your NAMESPACE file.
Rd file 'EMSRb_internal.Rd':
  \usage lines wider than 90 characters:
     EMSRb_internal(Fare = Fare, Mean = Mean, Var = Var, p_up = numeric(length(Fare)), cap = cap)

These lines will be truncated in the PDF manual.
ma.filter: no visible global function definition for ‘par’
ma.filter: no visible global function definition for ‘lines’
ma.filter: no visible global function definition for ‘abline’
qn: no visible global function definition for ‘lm’
qn: no visible global function definition for ‘var’
qn: no visible global function definition for ‘resid’
ss.filter: no visible global function definition for ‘smooth.spline’
ss.filter: no visible global function definition for ‘par’
ss.filter: no visible global function definition for ‘lines’
ss.filter: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline lines lm par resid smooth.spline var
Consider adding
  importFrom("graphics", "abline", "lines", "par")
  importFrom("stats", "lm", "resid", "smooth.spline", "var")
to your NAMESPACE file.
Found an obsolete/platform-specific call in the following function:
  ‘Mallows’
Found the platform-specific device:
  ‘x11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
Mallows: no visible global function definition for ‘runif’
Mallows: no visible global function definition for ‘x11’
Mallows: no visible global function definition for ‘plot’
Mallows: no visible global function definition for ‘dev.off’
UpdateLambda: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  dev.off plot runif uniroot x11
Consider adding
  importFrom("grDevices", "dev.off", "x11")
  importFrom("graphics", "plot")
  importFrom("stats", "runif", "uniroot")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Quitting from lines 104-121 (ApplyCarryToStage.Rmd) 
Error: processing vignette ‘ApplyCarryToStage.Rmd’ failed with diagnostics:
number of items to replace is not a multiple of replacement length
Execution halted
File ‘rmgarch/libs/rmgarch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
CI: no visible global function definition for ‘sd’
CI: no visible global function definition for ‘qt’
L: no visible global function definition for ‘sd’
L: no visible global function definition for ‘residuals’
Qa: no visible global function definition for ‘logLik’
Qb: no visible global function definition for ‘residuals’
Qc: no visible global function definition for ‘residuals’
Qc: no visible global function definition for ‘logLik’
STDERR: no visible global function definition for ‘sd’
group.UCL: no visible global function definition for ‘aggregate’
lr.glover: no visible binding for global variable ‘logLik’
lr.glover: no visible binding for global variable ‘update’
lr.glover : nobs0: no visible binding for global variable ‘nobs’
lr.glover : nobs0 : nobs2: no visible global function definition for
  ‘residuals’
lr.glover : tlab: no visible global function definition for ‘terms’
lr.glover : name: no visible global function definition for ‘formula’
lr.glover : modelUpdate: no visible global function definition for
  ‘as.formula’
lr.glover: no visible global function definition for ‘model.frame’
lr.glover: no visible binding for global variable ‘AIC’
lr.glover: no visible binding for global variable ‘BIC’
summarySE : <anonymous>: no visible global function definition for ‘sd’
summarySE: no visible global function definition for ‘qt’
Undefined global functions or variables:
  AIC BIC aggregate as.formula formula logLik model.frame nobs qt
  residuals sd terms update
Consider adding
  importFrom("stats", "AIC", "BIC", "aggregate", "as.formula", "formula",
             "logLik", "model.frame", "nobs", "qt", "residuals", "sd",
             "terms", "update")
to your NAMESPACE file.
Combi: no visible global function definition for ‘new’
barplotMixCluster: no visible global function definition for ‘is’
barplotMixCluster: no visible global function definition for ‘par’
barplotMixCluster: no visible global function definition for ‘lines’
barplotMixCluster: no visible global function definition for ‘text’
barplotMixCluster: no visible global function definition for ‘title’
barplotMixCluster: no visible global function definition for ‘mtext’
histMixCluster: no visible global function definition for ‘is’
histMixCluster: no visible global function definition for ‘par’
histMixCluster: no visible global function definition for ‘dnorm’
histMixCluster: no visible global function definition for ‘lines’
mixmodEntPlot: no visible global function definition for ‘par’
mixmodEntPlot: no visible global function definition for ‘lines’
mixmodEntPlot: no visible global function definition for ‘axis’
mixmodEntPlot: no visible global function definition for ‘title’
mixmodEntPlot: no visible binding for global variable ‘par’
plot,MixmodCombi: no visible global function definition for ‘par’
plot,MixmodCombi: no visible global function definition for ‘plot.new’
plot,MixmodCombi: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis dnorm is lines mtext new par plot.new text title
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "par", "plot.new",
             "text", "title")
  importFrom("methods", "is", "new")
  importFrom("stats", "dnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.pLGP_qvec: no visible global function definition for ‘ppois’
.qLGP_pvec: no visible global function definition for ‘qpois’
.rLGP.failsafe: no visible global function definition for ‘runif’
.subdmg: no visible global function definition for ‘dbinom’
dnegbin: no visible global function definition for ‘dnbinom’
pLGP: no visible global function definition for ‘ppois’
qLGP: no visible global function definition for ‘qpois’
rLGP: no visible global function definition for ‘rpois’
rLGP: no visible global function definition for ‘rnorm’
rLGP: no visible global function definition for ‘runif’
rbinegbin: no visible global function definition for ‘rnbinom’
rmanaclash: no visible global function definition for ‘rbinom’
rmanaclash: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dbinom dnbinom ppois qpois rbinom rnbinom rnorm rpois runif
Consider adding
  importFrom("stats", "dbinom", "dnbinom", "ppois", "qpois", "rbinom",
             "rnbinom", "rnorm", "rpois", "runif")
to your NAMESPACE file.
File ‘RMKdiscrete/libs/RMKdiscrete.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
predict.MOA_trainedmodel: no visible global function definition for
  ‘delete.response’
predict.MOA_trainedmodel: no visible global function definition for
  ‘model.frame’
trainMOA: no visible binding for global variable ‘na.exclude’
Undefined global functions or variables:
  delete.response model.frame na.exclude
Consider adding
  importFrom("stats", "delete.response", "model.frame", "na.exclude")
to your NAMESPACE file.
Non-standard files/directories found at top level:
  ‘COPYING.LGPL’ ‘configure_script.R’
CoeffYWeq: no visible global function definition for ‘index’
fitdistrForPrecipitation: no visible global function definition for
  ‘fitdistr’
generate.CCGammaObject: no visible binding for global variable ‘rnorm’
generate.CCGammaObject: no visible global function definition for
  ‘pnorm’
generate.YuleWalkerCoefficientBlockmatrices: no visible binding for
  global variable ‘rnorm’
generate.YuleWalkerCoefficientBlockmatricesPerEachMonth: no visible
  binding for global variable ‘rnorm’
generatePrecipitationAmount: no visible global function definition for
  ‘str’
omega_inv: no visible global function definition for ‘uniroot’
qqfit: no visible binding for global variable ‘qexp’
qqfit: no visible global function definition for ‘ecdf’
Undefined global functions or variables:
  ecdf fitdistr index pnorm qexp rnorm str uniroot
Consider adding
  importFrom("stats", "ecdf", "pnorm", "qexp", "rnorm", "uniroot")
  importFrom("utils", "str")
to your NAMESPACE file.
Missing or unexported object: ‘base::shell.exec’
rms.pval: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
dWishartSpike: no visible global function definition for ‘dnorm’
pWishartSpike: no visible global function definition for ‘pnorm’
qWishartSpike: no visible global function definition for ‘qnorm’
rWishartSpike: no visible global function definition for ‘qnorm’
rmp: no visible global function definition for ‘runif’
rtw: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dnorm pnorm qnorm runif
Consider adding
  importFrom("stats", "dnorm", "pnorm", "qnorm", "runif")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘DESeq’ ‘seqinr’ ‘topGO’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: ‘rnaturalearthhires’
File ‘rnetcarto/libs/rnetcarto.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
well19937.validate: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
File ‘rngwell19937/libs/rngwell19937.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Nnls.trimW : fun1: no visible global function definition for ‘runif’
initM: no visible global function definition for ‘runif’
rnmf: no visible global function definition for ‘txtProgressBar’
rnmf: no visible global function definition for ‘setTxtProgressBar’
see: no visible global function definition for ‘heat.colors’
see: no visible global function definition for ‘colorRampPalette’
see: no visible global function definition for ‘grey’
see: no visible global function definition for ‘par’
see: no visible global function definition for ‘image’
see: no visible global function definition for ‘mtext’
simtum: no visible global function definition for ‘runif’
simtum: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  colorRampPalette grey heat.colors image mtext par rnorm runif
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey", "heat.colors")
  importFrom("graphics", "image", "mtext", "par")
  importFrom("stats", "rnorm", "runif")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Quitting from lines 610-631 (Roahd.Rmd) 
Error: processing vignette ‘Roahd.Rmd’ failed with diagnostics:
Must request at least one colour from a hue palette.
Execution halted
'library' or 'require' calls in package code:
  ‘robustbase’ ‘sfsmisc’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.BuildPartial: no visible global function definition for ‘as.formula’
.BuildPartial: no visible global function definition for ‘residuals’
.PairwiseCorrelation : .Standardize : <anonymous>: no visible global
  function definition for ‘na.omit’
.PairwiseCorrelation : .Standardize: no visible binding for global
  variable ‘median’
.PairwiseCorrelation: no visible global function definition for
  ‘complete.cases’
.yw: no visible global function definition for ‘toeplitz’
FastQn: no visible global function definition for ‘median’
FastQn: no visible global function definition for ‘mad’
fqn: no visible global function definition for ‘median’
fqn: no visible global function definition for ‘mad’
psdcor: no visible global function definition for ‘posdefify’
psdcor: no visible global function definition for ‘nearcor’
robar: no visible global function definition for ‘frequency’
robcor: no visible global function definition for ‘covMcd’
s_FastQn: no visible global function definition for ‘median’
Undefined global functions or variables:
  as.formula complete.cases covMcd frequency mad median na.omit nearcor
  posdefify residuals toeplitz
Consider adding
  importFrom("stats", "as.formula", "complete.cases", "frequency", "mad",
             "median", "na.omit", "residuals", "toeplitz")
to your NAMESPACE file.
Found the following significant warnings:
  ./hammock.h:369:15: warning: assigning field to itself [-Wself-assign-field]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/robfilter.Rcheck/00install.out’ for details.
RobRSVD: no visible global function definition for ‘median’
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
File ‘robustETM/libs/robustETM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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’ ‘RcppArmadillo’ ‘mgcv’ ‘robustbase’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GIC: no visible global function definition for ‘integrate’
QM.poisson: no visible global function definition for ‘ppois’
QM.poisson: no visible global function definition for ‘dpois’
cplot.robustgam: no visible global function definition for ‘plot’
expect.poisson: no visible global function definition for ‘dpois’
expect.poisson: no visible global function definition for ‘ppois’
pred.robustgam: no visible global function definition for
  ‘Predict.matrix’
robust.sigma: no visible global function definition for ‘median’
robustgam: no visible global function definition for ‘s’
robustgam: no visible global function definition for
  ‘smooth.construct.tp.smooth.spec’
robustgam: no visible global function definition for
  ‘smooth.construct.cr.smooth.spec’
robustgam: no visible global function definition for
  ‘smooth.construct.ps.smooth.spec’
robustgam : w.fun: no visible global function definition for ‘covMcd’
robustgam.GIC.optim: no visible global function definition for ‘optim’
robustgam.crossval : w.fun: no visible global function definition for
  ‘covMcd’
robustgam.crossval: no visible global function definition for
  ‘integrate’
smooth.construct.tr.smooth.spec: no visible global function definition
  for ‘quantile’
w.binomial: no visible global function definition for ‘pbinom’
w.poisson: no visible global function definition for ‘ppois’
Undefined global functions or variables:
  Predict.matrix covMcd dpois integrate median optim pbinom plot ppois
  quantile s smooth.construct.cr.smooth.spec
  smooth.construct.ps.smooth.spec smooth.construct.tp.smooth.spec
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dpois", "integrate", "median", "optim", "pbinom",
             "ppois", "quantile")
to your NAMESPACE file.
File ‘robustgam/libs/robustgam.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
aggregateRanks: no visible binding for global variable ‘median’
aggregateRanks: no visible global function definition for ‘pnorm’
betaScores: no visible global function definition for ‘pbeta’
correctBetaPvaluesExact: no visible binding for global variable ‘qbeta’
thresholdBetaScore: no visible global function definition for ‘pbeta’
Undefined global functions or variables:
  median pbeta pnorm qbeta
Consider adding
  importFrom("stats", "median", "pbeta", "pnorm", "qbeta")
to your NAMESPACE file.
File ‘robustvarComp/libs/robustvarComp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘penalized’ ‘splines’ ‘survival’ ‘survivalROC’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
boot.ROC: no visible global function definition for ‘qnorm’
boot.ROC: no visible global function definition for ‘penalized’
boot.ROC: no visible global function definition for ‘coefficients’
boot.ROC: no visible global function definition for ‘sd’
boot.ROC: no visible global function definition for ‘optL1’
boot.ROCt: no visible global function definition for ‘qnorm’
boot.ROCt: no visible global function definition for ‘penalized’
boot.ROCt: no visible global function definition for ‘Surv’
boot.ROCt: no visible global function definition for ‘coefficients’
boot.ROCt: no visible global function definition for ‘sd’
boot.ROCt: no visible global function definition for ‘survivalROC’
boot.ROCt: no visible global function definition for ‘optL1’
Undefined global functions or variables:
  Surv coefficients optL1 penalized qnorm sd survivalROC
Consider adding
  importFrom("stats", "coefficients", "qnorm", "sd")
to your NAMESPACE file.
'library' or 'require' call to ‘ROCR’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘ROCR’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
o.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of ‘level’ to ‘levels’
p.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of ‘level’ to ‘levels’
o.rocc: no visible global function definition for ‘prediction’
o.rocc: no visible global function definition for ‘performance’
o.rocc: no visible global function definition for ‘binom.test’
tr.rocc: no visible global function definition for ‘prediction’
tr.rocc: no visible global function definition for ‘performance’
Undefined global functions or variables:
  binom.test performance prediction
Consider adding
  importFrom("stats", "binom.test")
to your NAMESPACE file.
NPROCwoGS: no visible global function definition for ‘quantile’
NPROCwoGS : rdirichlet: no visible global function definition for
  ‘rgamma’
NPROCwoGS: no visible global function definition for ‘rbinom’
NPROCwoGS: no visible global function definition for ‘rbeta’
NPROCwoGS: no visible binding for global variable ‘quantile’
Undefined global functions or variables:
  quantile rbeta rbinom rgamma
Consider adding
  importFrom("stats", "quantile", "rbeta", "rbinom", "rgamma")
to your NAMESPACE file.
prepare_Rd: score.Rd:20-22: Dropping empty section \details
prepare_Rd: score.Rd:23-25: Dropping empty section \source
prepare_Rd: score.Rd:26-28: Dropping empty section \references
Rd file 'NPROCwoGS.Rd':
  \examples lines wider than 100 characters:
     AUC<- sum((ROC.est$T.Se[1,-1]+ROC.est$T.Se[1,-(ncutoff+2)])*(ROC.est$T.Sp[1,-1]-ROC.est$T.Sp[1,-(ncutoff+2)])/2)
     plot(1-ROC.est$T.Sp[1,],ROC.est$T.Se[1,],"l", xlab="1-Specificities",ylab="Sensitivities", main=paste("AUC=", format(AUC, digits=4),

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

These lines will be truncated in the PDF manual.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘RODBC’
A package should be listed in only one of these fields.
'library' or 'require' call to ‘RODBC’ which was already attached by Depends.
  Please remove these calls from your code.
File ‘rollply/libs/rollply.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
ROSE.eval: no visible global function definition for ‘methods’
ROSE.eval: no visible binding for global variable ‘model.frame’
ROSE.eval: no visible binding for global variable ‘predict’
adj.formula: no visible global function definition for ‘terms’
adj.formula: no visible global function definition for ‘as.formula’
omnibus.balancing: no visible binding for global variable ‘model.frame’
ou.sampl: no visible global function definition for ‘rbinom’
over.sampl: no visible global function definition for ‘rbinom’
plot.roc.inner: no visible global function definition for ‘plot’
roc.curve: no visible global function definition for ‘lines’
roc.curve: no visible global function definition for ‘abline’
rose.real: no visible binding for global variable ‘sd’
rose.real: no visible global function definition for ‘sd’
rose.real: no visible global function definition for ‘rnorm’
rose.sampl: no visible global function definition for ‘rbinom’
under.sampl: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  abline as.formula lines methods model.frame plot predict rbinom rnorm
  sd terms
Consider adding
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "as.formula", "model.frame", "predict", "rbinom",
             "rnorm", "sd", "terms")
  importFrom("utils", "methods")
to your NAMESPACE file.
File ‘rotations/libs/rotations.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
bestFM: no visible global function definition for ‘data’
gaRoth: no visible global function definition for ‘data’
ros: no visible global function definition for ‘na.omit’
rosunc: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  data na.omit rnorm
Consider adding
  importFrom("stats", "na.omit", "rnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
mfix : m4m: no visible global function definition for ‘median’
rrfa: no visible global function definition for ‘predict’
rrfb: no visible global function definition for ‘predict’
rrfc1: no visible global function definition for ‘predict’
rrfc2: no visible global function definition for ‘predict’
rrfc3: no visible global function definition for ‘predict’
rrfc4: no visible global function definition for ‘predict’
rrfc5 : regdat: no visible global function definition for ‘predict’
rrfc5 : regdat: no visible global function definition for ‘glm’
rrfc5: no visible global function definition for ‘predict’
rrfc6: no visible global function definition for ‘predict’
rrfc7: no visible global function definition for ‘predict’
rrfd: no visible global function definition for ‘predict’
rrfe : rdms: no visible global function definition for ‘rbinom’
rrfe: no visible global function definition for ‘predict’
Undefined global functions or variables:
  glm median predict rbinom
Consider adding
  importFrom("stats", "glm", "median", "predict", "rbinom")
to your NAMESPACE file.
.computeValueReduct: no visible global function definition for ‘combn’
.findAllReductsFromCore: no visible global function definition for
  ‘combn’
.findFirstReductsFromCore: no visible global function definition for
  ‘combn’
.findSmallestReductFamilyFromCore: no visible global function
  definition for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
File ‘RoughSets/libs/RoughSets.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.fill
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'cbind.fill':
  ‘cbind.fill’

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.
royston.test: no visible global function definition for ‘shapiro.test’
royston.test: no visible global function definition for ‘cor’
royston.test: no visible global function definition for ‘qnorm’
royston.test: no visible global function definition for ‘pnorm’
royston.test: no visible global function definition for ‘cov’
royston.test: no visible global function definition for ‘mahalanobis’
royston.test: no visible global function definition for ‘qqplot’
royston.test: no visible global function definition for ‘qchisq’
royston.test: no visible global function definition for ‘ppoints’
royston.test: no visible global function definition for ‘abline’
royston.test: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  abline cor cov mahalanobis pchisq pnorm ppoints qchisq qnorm qqplot
  shapiro.test
Consider adding
  importFrom("graphics", "abline")
  importFrom("stats", "cor", "cov", "mahalanobis", "pchisq", "pnorm",
             "ppoints", "qchisq", "qnorm", "qqplot", "shapiro.test")
to your NAMESPACE file.
Package in Depends field not imported from: ‘hash’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
P: no visible global function definition for ‘has.key’
get_rand_int: no visible global function definition for ‘runif’
last: no visible global function definition for ‘tail’
rand_partitions: no visible global function definition for ‘hash’
Undefined global functions or variables:
  has.key hash runif tail
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "tail")
to your NAMESPACE file.
File ‘rpartitions/libs/rpartitions.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
evalMedian: no visible global function definition for ‘xtabs’
evalMode: no visible global function definition for ‘xtabs’
rpartScore: no visible global function definition for ‘model.extract’
rpartScore: no visible global function definition for ‘var’
rpartScore: no visible binding for global variable ‘var’
splitAbs: no visible global function definition for ‘xtabs’
Undefined global functions or variables:
  model.extract var xtabs
Consider adding
  importFrom("stats", "model.extract", "var", "xtabs")
to your NAMESPACE file.
'library' or 'require' call to ‘RODBC’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
rpart.rules.push: no visible global function definition for ‘sqlSave’
rpart.rules.table : <anonymous>: no visible global function definition
  for ‘setNames’
rpart.subrules.table : <anonymous>: no visible global function
  definition for ‘setNames’
Undefined global functions or variables:
  setNames sqlSave
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘survival’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘MASS’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GenerateData: no visible global function definition for ‘mvrnorm’
GetVarImp : FitPenalizedModel: no visible global function definition
  for ‘clogit’
Undefined global functions or variables:
  clogit mvrnorm
Rd file 'GetVarImp.Rd':
  \examples lines wider than 100 characters:
     hist(MyResults, breaks=6, col="orange", xlab="Importance score", ylab="Number of features", main="Histogram of R-PCLR variable importan ... [TRUNCATED]
     ## Sort from most important (highest importance score) to least important feature (lowest importance score)

These lines will be truncated in the PDF manual.
File ‘Rphylopars/libs/Rphylopars.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 Makefile(s) with an include directive with a pathname using R_HOME:
  src/libpq/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
File ‘rPref/libs/rPref.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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’ [5s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Copyright (c) 2015-present, Facebook, Inc.
  > # All rights reserved.
  > #
  > # This source code is licensed under the BSD-style license found in the
  > # LICENSE file in the root directory of this source tree. An additional grant
  > # of patent rights can be found in the PATENTS file in the same directory.
  > 
  > library("testthat")
  > library("DBI")
  > library("RPresto")
  > 
  > test_check("RPresto")
  -- 1. Failure: as() works (@test-src_translate_env.R#52)  ----------------------
  translate_sql(as(x, 0), con = conn[["con"]]) not equal to dplyr::sql("CAST(\"x\" AS \"DOUBLE\")").
  1/1 mismatches
  x[1]: "AS(\"x\", 0.0)"
  y[1]: "CAST(\"x\" AS \"DOUBLE\")"
  
  -- 2. Failure: as() works (@test-src_translate_env.R#56)  ----------------------
  translate_sql(pmax(x), con = conn[["con"]]) not equal to dplyr::sql("GREATEST(\"x\")").
  1/1 mismatches
  x[1]: "MAX(\"x\")"
  y[1]: "GREATEST(\"x\")"
  
  -- 3. Failure: as() works (@test-src_translate_env.R#60)  ----------------------
  translate_sql_(...) not equal to dplyr::sql("CAST(\"x\" AS \"ARRAY<VARCHAR>\")").
  1/1 mismatches
  x[1]: "AS(\"x\", ())"
  y[1]: "CAST(\"x\" AS \"ARRAY<VARCHAR>\")"
  
  -- 4. Failure: as() works (@test-src_translate_env.R#69)  ----------------------
  translate_sql_(list(substituted.expression), con = conn[["con"]]) not equal to dplyr::sql("CAST(\"x\" AS \"DATE\")").
  1/1 mismatches
  x[1]: "AS(\"x\", '2018-08-12')"
  y[1]: "CAST(\"x\" AS \"DATE\")"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 223 SKIPPED: 28 FAILED: 4
  1. Failure: as() works (@test-src_translate_env.R#52) 
  2. Failure: as() works (@test-src_translate_env.R#56) 
  3. Failure: as() works (@test-src_translate_env.R#60) 
  4. Failure: as() works (@test-src_translate_env.R#69) 
  
  Error: testthat unit tests failed
  Execution halted
but_last: no visible global function definition for ‘head’
first: no visible global function definition for ‘head’
last: no visible global function definition for ‘tail’
preview_frames: no visible global function definition for ‘str’
print.EprimeFrame: no visible global function definition for ‘str’
print.FrameList: no visible global function definition for ‘str’
Undefined global functions or variables:
  head str tail
Consider adding
  importFrom("utils", "head", "str", "tail")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘rpsychi-Ex.R’
Rd file 'ind.prop.Rd':
  \examples lines wider than 100 characters:
     ind.prop(y~x, data=dat, lev.count=2, ref.ind=1)    #Odds for not relapse is higher in treatment than control condition.
     ind.prop(y~x, data=dat, lev.count=1, ref.ind=1)    #Odds for relapse is lower in treatment than control condition.
     ind.prop(y~x, data=dat, lev.count=2, ref.ind=2)    #Odds for not relapse is lower in control than treatment condition.
     ind.prop(y~x, data=dat, lev.count=1, ref.ind=2)    #Odds for relapse is higher in control than treatment condition.

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

These lines will be truncated in the PDF manual.
File ‘rPython/libs/rPython.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘rjpod’
rrBlupM6: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  optimize
Consider adding
  importFrom("stats", "optimize")
to your NAMESPACE file.
File ‘rrcovNA/libs/rrcovNA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rredis/libs/rredis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘glasso’ ‘matrixcalc’ ‘mvoutlier’ ‘pcaPP’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
rrest: no visible binding for global variable ‘glasso’
rrest: no visible global function definition for ‘pcout’
rrest: no visible global function definition for ‘var’
rrest: no visible global function definition for ‘mahalanobis’
rrlda : centerObservations: no visible global function definition for
  ‘l1median_NLM’
rrlda : df.L2glasso: no visible global function definition for
  ‘duplication.matrix’
rrlda : alt.df.L2glasso: no visible global function definition for
  ‘lower.triangle’
Undefined global functions or variables:
  duplication.matrix glasso l1median_NLM lower.triangle mahalanobis
  pcout var
Consider adding
  importFrom("stats", "mahalanobis", "var")
to your NAMESPACE file.
File ‘rr/libs/rr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘robustbase’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.computekappa: no visible global function definition for ‘pnorm’
.computekappa: no visible global function definition for ‘dnorm’
.initmethod : <anonymous>: no visible global function definition for
  ‘median’
.initmethod: no visible global function definition for ‘model.matrix’
.mspe: no visible global function definition for ‘rnorm’
.mspe : <anonymous>: no visible global function definition for ‘rnorm’
makedata: no visible global function definition for ‘rnorm’
makedata : addraneff: no visible global function definition for ‘rnorm’
plot.meanssaemodel: no visible global function definition for ‘par’
plot.meanssaemodel: no visible global function definition for ‘plot’
plot.meanssaemodel: no visible global function definition for ‘lines’
plot.meanssaemodel: no visible global function definition for ‘axis’
plot.meanssaemodel: no visible global function definition for ‘grid’
plot.meanssaemodel: no visible global function definition for ‘box’
plot.meanssaemodel: no visible global function definition for ‘legend’
plot.meanssaemodel: no visible global function definition for ‘arrows’
saemodel: no visible global function definition for ‘model.frame’
saemodel: no visible global function definition for ‘model.response’
saemodel: no visible global function definition for ‘model.matrix’
summary.fitsaemodel: no visible global function definition for ‘pt’
summary.fitsaemodel: no visible global function definition for
  ‘printCoefmat’
Undefined global functions or variables:
  arrows axis box dnorm grid legend lines median model.frame
  model.matrix model.response par plot pnorm printCoefmat pt rnorm
Consider adding
  importFrom("graphics", "arrows", "axis", "box", "grid", "legend",
             "lines", "par", "plot")
  importFrom("stats", "dnorm", "median", "model.frame", "model.matrix",
             "model.response", "pnorm", "printCoefmat", "pt", "rnorm")
to your NAMESPACE file.
File ‘rsae/libs/rsae.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘install_dependencies.R’ ‘install_dependencies.sh’ ‘run_tests.R’
  ‘send.sh’
'library' or 'require' calls to packages already attached by Depends:
  ‘reshape’ ‘yaml’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘reshape’ ‘yaml’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'RSAPConnect.Rd':
  \examples lines wider than 100 characters:
     con <- RSAPConnect(ashost="nplhost", sysnr="42", client="001", user="developer", passwd="developer", lang="EN", trace="1", lcheck="1")

Rd file 'RSAPExecInfoQuery.Rd':
  \examples lines wider than 100 characters:
       res <- RSAPExecInfoQuery(con, "0D_NW_T01", "20120716",chars=list("0D_NW_SORG", "0D_NW_PROD"), kfigures=list("0D_NW_NETV"))

Rd file 'RSAPReadCube.Rd':
  \examples lines wider than 100 characters:
       res <- RSAPReadCube(con, "0D_NW_T01", "20120716",chars=list("0D_NW_SORG", "0D_NW_PROD"), kfigures=list("0D_NW_NETV"))

Rd file 'RSAPReadTable.Rd':
  \examples lines wider than 100 characters:
     res <- RSAPReadTable(con, "SFLIGHTS2", options=list("CARRID = 'AA'"), fields=list('CARRID', 'CONNID', 'FLDATE', 'PRICE'))

These lines will be truncated in the PDF manual.
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/Untitled.Rnw’
(Is a VignetteBuilder field missing?)
stripslash: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
File ‘rscimark/libs/rscimark.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
convexhull: no visible global function definition for ‘chull’
convexhull: no visible global function definition for ‘rnorm’
drawcompletegraph: no visible global function definition for ‘plot’
drawcompletegraph: no visible global function definition for ‘segments’
getbag: no visible global function definition for ‘plot’
getbag: no visible global function definition for ‘chull’
getbag: no visible global function definition for ‘polygon’
getbag: no visible global function definition for ‘points’
inflate: no visible global function definition for ‘rnorm’
rsmed: no visible global function definition for ‘runif’
rsplot: no visible global function definition for ‘plot’
rsplot: no visible global function definition for ‘chull’
rsplot: no visible global function definition for ‘polygon’
rsplot: no visible global function definition for ‘points’
rsrings: no visible global function definition for ‘plot’
rsrings: no visible global function definition for ‘chull’
rsrings: no visible global function definition for ‘polygon’
rsrings: no visible global function definition for ‘points’
rstinterval: no visible global function definition for ‘plot’
rstinterval: no visible global function definition for ‘runif’
rstinterval: no visible global function definition for ‘rnorm’
rstinterval: no visible global function definition for ‘chull’
rstinterval: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  chull plot points polygon rnorm runif segments
Consider adding
  importFrom("grDevices", "chull")
  importFrom("graphics", "plot", "points", "polygon", "segments")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
File ‘rsdepth/libs/rsdepth.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
rsem: no visible global function definition for ‘write.table’
rsem.Ascov: no visible global function definition for ‘qchisq’
rsem.Ascov: no visible global function definition for ‘pchisq’
rsem.emmusig: no visible global function definition for ‘na.omit’
rsem.emmusig: no visible global function definition for ‘qchisq’
rsem.emmusig: no visible global function definition for ‘pchisq’
rsem.fit: no visible global function definition for ‘pchisq’
rsem.fit: no visible global function definition for ‘pf’
rsem.print : print.estimate: no visible global function definition for
  ‘pnorm’
rsem.weight: no visible global function definition for ‘qchisq’
rsem.weight: no visible global function definition for ‘pchisq’
semdiag.call.eqs: no visible global function definition for
  ‘write.table’
semdiag.read.eqs: no visible global function definition for ‘read.fwf’
Undefined global functions or variables:
  na.omit pchisq pf pnorm qchisq read.fwf write.table
Consider adding
  importFrom("stats", "na.omit", "pchisq", "pf", "pnorm", "qchisq")
  importFrom("utils", "read.fwf", "write.table")
to your NAMESPACE file.
Non-standard files/directories found at top level:
  ‘clients’ ‘clients.txt’ ‘version’
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’
File ‘Rserve/libs/Rserve.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 use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
addNoisyCopies: no visible global function definition for ‘rnorm’
eta: no visible global function definition for ‘var’
gaussClassifier: no visible global function definition for ‘runif’
getSigma: no visible global function definition for ‘sd’
getSigma: no visible binding for global variable ‘sd’
sfaClassify: no visible global function definition for ‘rainbow’
sfaClassify: no visible global function definition for ‘par’
sfaClassify: no visible global function definition for ‘plot’
sfaClassify: no visible global function definition for ‘points’
sfaClassify: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines par plot points rainbow rnorm runif sd var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "lines", "par", "plot", "points")
  importFrom("stats", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
Depends: includes the non-default packages:
  ‘biwt’ ‘cairoDevice’ ‘fBasics’ ‘gplots’ ‘gWidgets’ ‘gWidgetsRGtk2’
  ‘minerva’ ‘parmigene’ ‘stringr’ ‘snowfall’
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:
  ‘grDevices’ ‘snowfall’
  Please remove these calls from your code.
'library' or 'require' call to ‘ctc’ 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:
  ‘biwt’ ‘cairoDevice’ ‘fBasics’ ‘gWidgets’ ‘gWidgetsRGtk2’ ‘gplots’
  ‘minerva’ ‘parmigene’ ‘snowfall’ ‘stringr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘rsgcc/libs/rsgcc.so’:
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.o’
File ‘rsgcc/libs/rsgcc.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 use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Undocumented code objects:
  ‘lengths’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘rsolr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SolrCore-class
> ### Title: SolrCore
> ### Aliases: class:SolrCore SolrCore-class name,SolrCore-method
> ###   ndoc,SolrCore-method schema schema,SolrCore-method
> ###   fieldNames,SolrCore-method version version,SolrCore-method SolrCore
> ###   docs docs,SolrCore-method read,SolrCore-method
> ###   eval,SolrQuery,SolrCore-method
> ###   eval,TranslationRequest,SolrCore-method facets facets,SolrCore-method
> ###   groupings groupings,SolrCore-method ngroup,SolrCore-method
> ###   update,SolrCore-method delete,SolrCore-method commit
> ###   commit,SolrCore-method purgeCache,SolrCore-method
> ###   show,SolrCore-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
>      solr <- TestSolr()
>      sc <- SolrCore(solr$uri)
Error in value[[3L]](cond) : 
  Failed to retrieve schema. rsolr requires schema via REST or as XML from the admin module.
Calls: SolrCore ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
negbin.pow : negbin.disp: no visible global function definition for
  ‘rpois’
negbin.pow : negbin.disp: no visible global function definition for
  ‘rnbinom’
negbin.pow : inner.fcn: no visible global function definition for
  ‘na.omit’
negbin.pow : inner.fcn: no visible global function definition for
  ‘quantile’
negbin.pow: no visible global function definition for ‘txtProgressBar’
negbin.pow: no visible global function definition for
  ‘setTxtProgressBar’
poiss.pow : inner.fcn: no visible global function definition for
  ‘rpois’
poiss.pow : inner.fcn: no visible global function definition for
  ‘quantile’
poiss.pow: no visible global function definition for ‘txtProgressBar’
poiss.pow: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  na.omit quantile rnbinom rpois setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit", "quantile", "rnbinom", "rpois")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Package in Depends field not imported from: ‘plyr’
  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.RStorm plot.Topology print.RStorm print.Topology
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
RStorm: no visible global function definition for ‘alply’
Undefined global functions or variables:
  alply
File ‘RSvgDevice/libs/RSvgDevice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘RSVGTipsDevice/libs/RSVGTipsDevice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  Math.Sym Ops.Sym as.character.Sym deriv.Sym print.Sym solve.Sym t.Sym
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Math.Sym: no visible binding for global variable ‘transtab’
jythonStart: no visible global function definition for ‘.jinit’
jythonStart: no visible global function definition for ‘.jnew’
jythonStart: no visible binding for global variable ‘.Jython’
sympy: no visible binding for global variable ‘.Jython’
sympy: no visible global function definition for ‘.jstrVal’
sympyStart: no visible binding for global variable ‘.Jython’
Undefined global functions or variables:
  .Jython .jinit .jnew .jstrVal transtab

Found the following assignments to the global environment:
File ‘rSymPy/R/sympy.R’:
  assign(".Jython", .jnew("org.python.util.PythonInterpreter"), 
    .GlobalEnv)
  assign(".Jython", rJython(modules = system.file("Lib", package = "rSymPy")), 
    .GlobalEnv)
barplot.rtconnect: no visible global function definition for ‘rainbow’
barplot.rtconnect: no visible global function definition for ‘text’
plot.rtconnect: no visible global function definition for ‘par’
plot.rtconnect: no visible global function definition for ‘plot’
plot.rtconnect: no visible global function definition for ‘axis.Date’
rtconnect: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  axis.Date par plot rainbow read.table text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis.Date", "par", "plot", "text")
  importFrom("utils", "read.table")
to your NAMESPACE file.
File ‘rtext/libs/rtext.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
classify_model: no visible global function definition for ‘predict’
cross_validate: no visible global function definition for ‘predict’
read_data: no visible global function definition for ‘read.csv’
read_data: no visible global function definition for ‘read.delim’
Undefined global functions or variables:
  predict read.csv read.delim
Consider adding
  importFrom("stats", "predict")
  importFrom("utils", "read.csv", "read.delim")
to your NAMESPACE file.
plotGLCM: no visible global function definition for ‘plot’
plotGLCM: no visible global function definition for ‘points’
Undefined global functions or variables:
  plot points
Consider adding
  importFrom("graphics", "plot", "points")
to your NAMESPACE file.
File ‘rtiff/libs/rtiff.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Ruchardet/libs/Ruchardet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 'Runiversal-package.Rd':
  \examples lines wider than 100 characters:
     #Getting estimates from regression object as Java variables that be directly interpretable by Bean Shell.

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
HapMendlianCheck: no visible global function definition for
  ‘write.table’
rvPDT.test.sub: no visible global function definition for ‘pnorm’
whap.prehap: no visible global function definition for ‘write.table’
whap.prehap: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  pnorm read.table write.table
Consider adding
  importFrom("stats", "pnorm")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
'library' or 'require' call to ‘pixmap’ which was already attached by Depends.
  Please remove these calls from your code.
rvideopoker: warning in rp.radiogroup(mypanel, var =
  state$penny.nickel.quarter.dollar, initval = 1, values = c(1, 5, 25,
  100), title = "Bet (in Cents)", action = setbet): partial argument
  match of ‘var’ to ‘variable’
rvideopoker: warning in rp.slider(mypanel, var = state$no.of.credits,
  from = 1, to = 5, initval = 1, title = "How many Credits?",
  resolution = 1, action = creditset, showvalue = TRUE): partial
  argument match of ‘var’ to ‘variable’
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC1, action = card1check, title = "Keep Card 1?"): partial
  argument match of ‘var’ to ‘variable’
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC2, action = card2check, title = "Keep Card 2?"): partial
  argument match of ‘var’ to ‘variable’
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC3, action = card3check, title = "Keep Card 3?"): partial
  argument match of ‘var’ to ‘variable’
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC4, action = card4check, title = "Keep Card 4?"): partial
  argument match of ‘var’ to ‘variable’
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC5, action = card5check, title = "Keep Card 5?"): partial
  argument match of ‘var’ to ‘variable’
rvideopoker : plotFrame: no visible global function definition for
  ‘par’
rvideopoker : showBack: no visible global function definition for
  ‘title’
rvideopoker : showCardsInitially: no visible global function definition
  for ‘title’
Undefined global functions or variables:
  par title
Consider adding
  importFrom("graphics", "par", "title")
to your NAMESPACE file.
lc_TDT: no visible global function definition for ‘pchisq’
rvTDT: no visible global function definition for ‘dbeta’
Undefined global functions or variables:
  dbeta pchisq
Consider adding
  importFrom("stats", "dbeta", "pchisq")
to your NAMESPACE file.
LASSO: no visible global function definition for ‘lm’
LASSO: no visible global function definition for ‘anova’
LASSO: no visible global function definition for ‘glm’
LASSO: no visible global function definition for ‘pchisq’
LASSO : <anonymous>: no visible global function definition for
  ‘extractAIC’
PCR : <anonymous>: no visible global function definition for ‘cor’
PLS : <anonymous>: no visible global function definition for ‘cor’
RR : RRscore: no visible binding for global variable ‘sd’
SPLS: no visible global function definition for ‘lm’
SPLS: no visible global function definition for ‘anova’
SPLS : <anonymous>: no visible global function definition for
  ‘extractAIC’
VTWOD : getScores: no visible global function definition for ‘sd’
VTWOD : getScores: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  anova cor extractAIC glm lm pchisq pnorm sd
Consider adding
  importFrom("stats", "anova", "cor", "extractAIC", "glm", "lm",
             "pchisq", "pnorm", "sd")
to your NAMESPACE file.
check_ISO_code: no visible binding for global variable ‘NoAm_country’
check_ISO_code: no visible binding for global variable ‘SoAm_country’
check_ISO_code: no visible binding for global variable ‘Oceana_country’
check_ISO_code: no visible binding for global variable ‘Africa_country’
check_ISO_code: no visible binding for global variable ‘Asia_country’
check_ISO_code: no visible binding for global variable ‘Eur_country’
climate_map: no visible binding for global variable ‘data’
date_correct: no visible global function definition for ‘tail’
Undefined global functions or variables:
  Africa_country Asia_country Eur_country NoAm_country Oceana_country
  SoAm_country data tail
Consider adding
  importFrom("utils", "data", "tail")
to your NAMESPACE file.
RWBP.default: no visible global function definition for ‘na.omit’
RWBP.default: no visible global function definition for ‘kmeans’
RWBP.formula: no visible global function definition for ‘model.extract’
plot.RWBP: no visible global function definition for ‘plot’
predict.RWBP: no visible global function definition for ‘head’
Undefined global functions or variables:
  head kmeans model.extract na.omit plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "kmeans", "model.extract", "na.omit")
  importFrom("utils", "head")
to your NAMESPACE file.
weblogo: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
File ‘rwfec/libs/rwfec.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  qwiener.c:60:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  qwiener.c:69:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/RWiener.Rcheck/00install.out’ for details.
Found the following apparent S3 methods exported but not registered:
  lines.rief lines.riif lines.rirf plot.ifile plot.rief plot.riif
  plot.rirf plot.rtef plot.rtif plot.rtrf print.wcmd print.winsteps
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
getcolors: no visible global function definition for ‘rainbow’
lines.rief: no visible global function definition for ‘lines.default’
lines.riif: no visible global function definition for ‘lines.default’
lines.rirf: no visible global function definition for ‘lines.default’
plot.ifile: no visible global function definition for ‘plot’
plot.rief: no visible global function definition for ‘plot.default’
plot.rief: no visible global function definition for ‘lines’
plot.riif: no visible global function definition for ‘plot.default’
plot.riif: no visible global function definition for ‘lines’
plot.rirf: no visible global function definition for ‘plot.default’
plot.rirf: no visible global function definition for ‘lines’
plot.rtef: no visible global function definition for ‘plot.default’
plot.rtif: no visible global function definition for ‘plot.default’
plot.rtrf: no visible global function definition for ‘plot.default’
read.ifile: no visible global function definition for ‘read.table’
read.pfile: no visible global function definition for ‘read.table’
write.wdat: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  lines lines.default plot plot.default rainbow read.table write.table
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "lines", "lines.default", "plot",
             "plot.default")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
.dwt: no visible global function definition for ‘median’
.udwt: no visible global function definition for ‘median’
plotSignalTransformation: no visible global function definition for
  ‘plot’
plotSignalTransformation: no visible global function definition for
  ‘box’
plotSignalTransformation: no visible global function definition for
  ‘axis’
plotSignalTransformation: no visible global function definition for
  ‘lines’
plotSignalTransformation: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  axis box legend lines median plot
Consider adding
  importFrom("graphics", "axis", "box", "legend", "lines", "plot")
  importFrom("stats", "median")
to your NAMESPACE file.
Found the following significant warnings:
  nchg.c:555:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/RxCEcolInf.Rcheck/00install.out’ for details.
Non-standard file/directory found at top level:
  ‘dos2unix.sh’
Analyze: no visible global function definition for ‘runif’
Analyze: no visible global function definition for ‘mcmc’
Analyze: no visible global function definition for ‘varnames<-’
AnalyzeWithExitPoll: no visible global function definition for ‘runif’
AnalyzeWithExitPoll: no visible global function definition for ‘mcmc’
AnalyzeWithExitPoll: no visible global function definition for
  ‘varnames<-’
Tune: no visible global function definition for ‘runif’
TuneWithExitPoll: no visible global function definition for ‘runif’
form.mcmc.object: no visible global function definition for
  ‘varnames<-’
gendata.ep : rdirichlet: no visible global function definition for
  ‘rgamma’
gendata.ep : rwish: no visible global function definition for ‘rchisq’
gendata.ep : rwish: no visible global function definition for ‘rnorm’
gendata.ep: no visible global function definition for ‘rpois’
gendata.ep: no visible global function definition for ‘runif’
gendata.ep: no visible global function definition for ‘rmultinom’
gendata.ep: no visible global function definition for ‘cov2cor’
gq.summary: no visible global function definition for ‘mcmc.list’
gq.summary: no visible global function definition for ‘mcmc’
gq_diagnostics: no visible global function definition for ‘mcmc.list’
gq_diagnostics: no visible global function definition for ‘mcmc’
gq_diagnostics: no visible global function definition for ‘gelman.diag’
gq_diagnostics: no visible global function definition for ‘geweke.diag’
gq_diagnostics: no visible global function definition for ‘heidel.diag’
gq_diagnostics: no visible global function definition for
  ‘autocorr.diag’
Undefined global functions or variables:
  autocorr.diag cov2cor gelman.diag geweke.diag heidel.diag mcmc
  mcmc.list rchisq rgamma rmultinom rnorm rpois runif varnames<-
Consider adding
  importFrom("stats", "cov2cor", "rchisq", "rgamma", "rmultinom",
             "rnorm", "rpois", "runif")
to your NAMESPACE file.
File ‘RxCEcolInf/libs/RxCEcolInf.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  yacas/src/obmalloc.cpp:584:23: warning: result of comparison of constant 384307168202282325 with expression of type 'unsigned int' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Ryacas.Rcheck/00install.out’ for details.
File ‘Ryacas/libs/Ryacas.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
calculate.summary: no visible global function definition for ‘sd’
detect.saccades: no visible global function definition for ‘median’
diagnostic.plot: no visible global function definition for ‘dev.new’
diagnostic.plot: no visible global function definition for ‘par’
diagnostic.plot: no visible global function definition for ‘recordPlot’
diagnostic.plot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.new dev.off median par recordPlot sd
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "recordPlot")
  importFrom("graphics", "par")
  importFrom("stats", "median", "sd")
to your NAMESPACE file.
prepare_Rd: BootsModelTest.Rd:28-29: Dropping empty section \details
prepare_Rd: BootsModelTest.Rd:43: Dropping empty section \note
prepare_Rd: CriticalValues.Rd:38: Dropping empty section \note
prepare_Rd: Pvalues.Rd:24-25: Dropping empty section \details
prepare_Rd: Pvalues.Rd:38: Dropping empty section \note
prepare_Rd: cumsum.test.Rd:16-17: Dropping empty section \details
prepare_Rd: cumsum.test.Rd:28: Dropping empty section \note
eblupDyn: no visible global function definition for ‘model.frame’
eblupDyn: no visible global function definition for ‘model.matrix’
eblupDyn: no visible global function definition for ‘pnorm’
eblupRY: no visible global function definition for ‘model.frame’
eblupRY: no visible global function definition for ‘model.matrix’
eblupRY: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  model.frame model.matrix pnorm
Consider adding
  importFrom("stats", "model.frame", "model.matrix", "pnorm")
to your NAMESPACE file.
fit.saery.AR1: no visible global function definition for ‘qnorm’
fit.saery.MA1: no visible global function definition for ‘qnorm’
fit.saery.indep: no visible global function definition for ‘qnorm’
mse.saery.boot.AR1.typeI: no visible global function definition for
  ‘rnorm’
mse.saery.boot.AR1.typeI: no visible global function definition for
  ‘write.table’
mse.saery.boot.AR1.typeII: no visible global function definition for
  ‘rnorm’
mse.saery.boot.AR1.typeII: no visible global function definition for
  ‘write.table’
mse.saery.boot.MA1.typeI: no visible global function definition for
  ‘rnorm’
mse.saery.boot.MA1.typeI: no visible global function definition for
  ‘write.table’
mse.saery.boot.MA1.typeII: no visible global function definition for
  ‘rnorm’
mse.saery.boot.MA1.typeII: no visible global function definition for
  ‘write.table’
plot.saery: no visible global function definition for ‘devAskNewPage’
plot.saery: no visible global function definition for ‘par’
plot.saery: no visible global function definition for ‘plot’
plot.saery: no visible global function definition for ‘abline’
plot.saery: no visible global function definition for ‘title’
plot.saery: no visible global function definition for ‘axis’
plot.saery: no visible global function definition for ‘lines’
plot.saery: no visible global function definition for ‘legend’
pvalue: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline axis devAskNewPage legend lines par plot pnorm qnorm rnorm
  title write.table
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "title")
  importFrom("stats", "pnorm", "qnorm", "rnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SafeBayes.Rcheck/00install.out’ for details.
File ‘SafeBayes/libs/SafeBayes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘lpSolveAPI’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
glm: no visible binding for global variable ‘gaussian’
glm: no visible global function definition for ‘glm.control’
glm: no visible global function definition for ‘model.response’
glm: no visible global function definition for ‘is.empty.model’
glm: no visible global function definition for ‘model.matrix’
glm: no visible global function definition for ‘model.weights’
glm: no visible global function definition for ‘model.offset’
glm: no visible global function definition for ‘model.extract’
glm: no visible global function definition for ‘glm.fit’
glm: no visible global function definition for ‘.getXlevels’
separator: no visible global function definition for ‘make.lp’
separator: no visible global function definition for ‘set.column’
separator: no visible global function definition for ‘set.rhs’
separator: no visible global function definition for ‘set.constr.type’
separator: no visible global function definition for ‘set.objfn’
separator: no visible global function definition for ‘set.bounds’
separator: no visible global function definition for ‘lp.control’
separator: no visible global function definition for ‘get.variables’
separator: no visible global function definition for ‘set.basis’
separator: no visible global function definition for
  ‘get.dual.solution’
Undefined global functions or variables:
  .getXlevels gaussian get.dual.solution get.variables glm.control
  glm.fit is.empty.model lp.control make.lp model.extract model.matrix
  model.offset model.response model.weights set.basis set.bounds
  set.column set.constr.type set.objfn set.rhs
Consider adding
  importFrom("stats", ".getXlevels", "gaussian", "glm.control",
             "glm.fit", "is.empty.model", "model.extract",
             "model.matrix", "model.offset", "model.response",
             "model.weights")
to your NAMESPACE file.
File ‘SALES/libs/SALES.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SAMM/libs/SAMM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 'mudiff.acc.Rd':
  \usage lines wider than 90 characters:
     mudiff.acc(len, alpha1, beta1, alpha2, beta2, n01, n02, level = 0.95, equal = TRUE, m = 10000, mcs = 3)

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

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

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

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

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

These lines will be truncated in the PDF manual.
propdiff.acc: no visible global function definition for ‘rbeta’
propdiff.acc: no visible global function definition for ‘rbinom’
propdiff.acc: no visible global function definition for ‘pbeta’
propdiff.alc: no visible global function definition for ‘rbeta’
propdiff.alc: no visible global function definition for ‘rbinom’
propdiff.alc: no visible global function definition for ‘qbeta’
propdiff.freq: no visible global function definition for ‘qnorm’
propdiff.mblacc: no visible global function definition for ‘rbeta’
propdiff.mblacc: no visible global function definition for ‘rbinom’
propdiff.mblacc: no visible global function definition for ‘pbeta’
propdiff.mblalc: no visible global function definition for ‘rbeta’
propdiff.mblalc: no visible global function definition for ‘rbinom’
propdiff.mblalc: no visible global function definition for ‘qbeta’
propdiff.mblmodwoc: no visible global function definition for ‘qchisq’
propdiff.mblmodwoc: no visible global function definition for ‘pbeta’
propdiff.mblwoc: no visible global function definition for ‘pbeta’
propdiff.modwoc: no visible global function definition for ‘qchisq’
propdiff.modwoc: no visible global function definition for ‘pbeta’
propdiff.woc: no visible global function definition for ‘pbeta’
Undefined global functions or variables:
  pbeta qbeta qchisq qnorm rbeta rbinom
Consider adding
  importFrom("stats", "pbeta", "qbeta", "qchisq", "qnorm", "rbeta",
             "rbinom")
to your NAMESPACE file.
File ‘sampling/libs/sampling.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.samEL: no visible global function definition for ‘matplot’
plot.samHL: no visible global function definition for ‘matplot’
plot.samLL: no visible global function definition for ‘matplot’
plot.samQL: no visible global function definition for ‘matplot’
predict.samEL: no visible global function definition for ‘ns’
predict.samHL: no visible global function definition for ‘ns’
predict.samLL: no visible global function definition for ‘ns’
predict.samQL: no visible global function definition for ‘ns’
samEL: no visible global function definition for ‘ns’
samHL: no visible global function definition for ‘ns’
samHL: no visible binding for global variable ‘median’
samLL: no visible global function definition for ‘ns’
samQL: no visible global function definition for ‘ns’
Undefined global functions or variables:
  matplot median ns
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "median")
to your NAMESPACE file.
File ‘SAM/libs/SAM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
GraphBinaryForestPlot: no visible global function definition for
  ‘abline’
GraphBinaryForestPlot: no visible global function definition for ‘text’
GraphContinuousForestPlot: no visible global function definition for
  ‘abline’
GraphContinuousForestPlot: no visible global function definition for
  ‘text’
ImputeBinaryEvents: no visible global function definition for ‘rbinom’
ImputeSMD: no visible global function definition for ‘rnorm’
funnelplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline rbinom rnorm text
Consider adding
  importFrom("graphics", "abline", "text")
  importFrom("stats", "rbinom", "rnorm")
to your NAMESPACE file.
generate.sample.core: no visible global function definition for
  ‘predict’
mdh: no visible global function definition for ‘model.frame’
mdh: no visible binding for global variable ‘na.fail’
mdh: no visible global function definition for ‘.getXlevels’
mdh: no visible global function definition for ‘quantile’
mdh: no visible global function definition for ‘hist’
predict.mdh: no visible global function definition for ‘model.frame’
samur: no visible global function definition for ‘predict’
Undefined global functions or variables:
  .getXlevels hist model.frame na.fail predict quantile
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", ".getXlevels", "model.frame", "na.fail", "predict",
             "quantile")
to your NAMESPACE file.
Package suggested but not available for checking: ‘mixer’
File ‘sanitizers/libs/sanitizers.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
download.sas7bdat.sources : <anonymous>: no visible global function
  definition for ‘download.file’
generate.sas7bdat.source: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
parse.SAScii: no visible binding for global variable ‘end’
parse.SAScii: no visible binding for global variable ‘start’
read.SAScii: no visible global function definition for ‘download.file’
read.SAScii: no visible global function definition for ‘unzip’
read.SAScii: no visible global function definition for ‘read.fwf’
read.SAScii: no visible global function definition for ‘capture.output’
Undefined global functions or variables:
  capture.output download.file end read.fwf start unzip
Consider adding
  importFrom("stats", "end", "start")
  importFrom("utils", "capture.output", "download.file", "read.fwf",
             "unzip")
to your NAMESPACE file.
Rd file 'read.SAScii.Rd':
  \usage lines wider than 90 characters:
     read.SAScii( fn, sas_ri, beginline = 1, buffersize = 50, zipped = F , n = -1 , intervals.to.print = 1000 , lrecl = NULL , skip.decimal. ... [TRUNCATED]
  \examples lines wider than 100 characters:
                     paste( "http://smpbff2.dsd.census.gov/pub/sipp/2004/l04puw" , i , ".zip" , sep = "" )

These lines will be truncated in the PDF manual.
SASPECT: no visible global function definition for ‘dbinom’
my.SOnePro: missing arguments not allowed in calls to ‘c’
my.ttest: no visible global function definition for ‘var’
Undefined global functions or variables:
  dbinom var
Consider adding
  importFrom("stats", "dbinom", "var")
to your NAMESPACE file.
File ‘saturnin/libs/saturnin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
loads: no visible global function definition for ‘untar’
saves: no visible global function definition for ‘tar’
Undefined global functions or variables:
  tar untar
Consider adding
  importFrom("utils", "tar", "untar")
to your NAMESPACE file.
clogistCalc: no visible global function definition for ‘model.matrix’
clogistCalc: no visible global function definition for ‘glm.fit’
clogistCalc: no visible global function definition for ‘binomial’
clogistInfo : all.not.equal: no visible global function definition for
  ‘var’
geeUOmega: no visible global function definition for ‘model.extract’
geeUOmega: no visible global function definition for ‘model.matrix’
geeUOmega: no visible binding for global variable ‘contrasts’
mgee: no visible binding for global variable ‘gaussian’
sawsCalc: no visible global function definition for ‘pf’
sawsCalc: no visible global function definition for ‘qt’
Undefined global functions or variables:
  binomial contrasts gaussian glm.fit model.extract model.matrix pf qt
  var
Consider adding
  importFrom("stats", "binomial", "contrasts", "gaussian", "glm.fit",
             "model.extract", "model.matrix", "pf", "qt", "var")
to your NAMESPACE file.
File ‘sbfc/libs/sbfc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
K: no visible global function definition for ‘dnorm’
sBF: no visible global function definition for ‘density’
sBF: no visible global function definition for ‘txtProgressBar’
sBF: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  density dnorm setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "density", "dnorm")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
File ‘sBIC/libs/sBIC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sbmSDP/libs/sbmSDP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 Title field: should not end in a period.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
File ‘sbrl/libs/sbrl.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
fitSBSA: no visible binding for global variable ‘var’
fitSBSA: no visible global function definition for ‘var’
fitSBSA: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm var
Consider adding
  importFrom("stats", "qnorm", "var")
to your NAMESPACE file.
File ‘SBSA/libs/SBSA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘src-java’
ChooseBest: no visible global function definition for ‘head’
GetScores: no visible global function definition for ‘write.table’
ReportTable: no visible binding for global variable ‘sd’
ReportTable: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  head sd write.table
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "head", "write.table")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘MASS’ ‘lars’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  predict.scalreg print.scalreg
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
lse: no visible global function definition for ‘lm’
predict.scalreg: no visible global function definition for ‘fitted’
slassoEst: no visible global function definition for ‘qnorm’
slassoEst: no visible global function definition for ‘lars’
slassoEst: no visible global function definition for ‘predict.lars’
Undefined global functions or variables:
  fitted lars lm predict.lars qnorm
Consider adding
  importFrom("stats", "fitted", "lm", "qnorm")
to your NAMESPACE file.
plot.scair: no visible global function definition for ‘par’
plot.scair: no visible global function definition for ‘plot’
plot.scair: no visible global function definition for ‘points’
plot.scar: no visible global function definition for ‘par’
plot.scar: no visible global function definition for ‘plot’
plot.scar: no visible global function definition for ‘points’
predict.scair: no visible global function definition for ‘approx’
predict.scar: no visible global function definition for ‘approx’
scair: no visible global function definition for ‘gaussian’
scair: no visible global function definition for ‘runif’
scair: no visible global function definition for ‘rnorm’
scar: no visible global function definition for ‘gaussian’
scar: no visible global function definition for ‘glm.fit’
scar: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx gaussian glm.fit par plot points rnorm runif
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "approx", "gaussian", "glm.fit", "rnorm", "runif")
to your NAMESPACE file.
File ‘scar/libs/scar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
prime.factor: no visible global function definition for ‘data’
prime.factor: no visible binding for global variable ‘primlist’
Undefined global functions or variables:
  data primlist
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘schoolmath/R/prime.factor.R’:
  data(primlist)
See section ‘Good practice’ in ‘?data’.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/scio.Rcheck/00install.out’ for details.
'library' or 'require' call to ‘QUIC’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
scio.cv: no visible global function definition for ‘cov’
scio.refit: no visible global function definition for ‘QUIC’
Undefined global functions or variables:
  QUIC cov
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
File ‘scio/libs/scio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
score.GGUM: no visible global function definition for ‘dnorm’
score.GGUM: no visible global function definition for ‘hist’
score.GGUM: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  dnorm hist write.table
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "dnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
CreatePssm: no visible binding for global variable ‘training’
Undefined global functions or variables:
  training
File ‘scorer/libs/scorer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
License components which are templates and need '+ file LICENSE':
  MIT License
'library' or 'require' calls to packages already attached by Depends:
  ‘RCurl’ ‘XML’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RCurl’ ‘XML’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
scrape: no visible global function definition for ‘getURLAsynchronous’
scrape: no visible global function definition for ‘runif’
scrape: no visible global function definition for ‘capture.output’
scrape: no visible binding for global variable ‘xmlParse’
scrape: no visible binding for global variable ‘htmlParse’
Undefined global functions or variables:
  capture.output getURLAsynchronous htmlParse runif xmlParse
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘MASS’ ‘oligoClasses’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following calls to attach():
File ‘scriptests/R/source.pkg.R’:
  attach(NULL, pos = pos, name = paste("pkgcode", pkg.name, sep = ":"))
  attach(envir, pos = pos, name = paste("pkgcode", pkg.name, sep = ":"))
See section ‘Good practice’ in ‘?attach’.
File ‘scs/libs/scs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
lahiri.design: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
estimateTimeToComputeTargetDefinition: no visible global function
  definition for ‘flush.console’
estimateTimeToComputeTargetDefinition: no visible global function
  definition for ‘combn’
initialize,sdcTargetDefinitionClass: no visible global function
  definition for ‘flush.console’
initialize,sdcTargetDefinitionClass: no visible global function
  definition for ‘combn’
initialize,sdcTargetDefinitionClass: no visible global function
  definition for ‘quantile’
initialize,sdcTargetMatrixClass: no visible global function definition
  for ‘flush.console’
Undefined global functions or variables:
  combn flush.console quantile
Consider adding
  importFrom("stats", "quantile")
  importFrom("utils", "combn", "flush.console")
to your NAMESPACE file.
File ‘SDDE/libs/SDDE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: sdd.Rd:46-47: Dropping empty section \seealso
prepare_Rd: sddpack-package.Rd:31-32: Dropping empty section \seealso
prepare_Rd: sddsolve.Rd:29-30: Dropping empty section \references
prepare_Rd: sddsolve.Rd:38-39: Dropping empty section \seealso
prepare_Rd: sddsolve.Rd:40-41: Dropping empty section \examples
File ‘sde/libs/sde.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 significant warnings:
  pointinpolygon.c:60:7: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  slope.aspect.c:128:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  slope.aspect.c:128:33: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  vincenty.geodesics.c:50:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  vincenty.geodesics.c:126:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SDMTools.Rcheck/00install.out’ for details.
'library' or 'require' calls in package code:
  ‘raster’ ‘sp’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
File ‘SDMTools/libs/SDMTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sdnet/libs/sdnet.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 ‘sdprisk/libs/sdprisk.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘__var_1_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/sdwd.Rcheck/00install.out’ for details.
File ‘sdwd/libs/sdwd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘lars’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
sealasso: no visible global function definition for ‘lars’
weight.calc: no visible global function definition for ‘lars’
Undefined global functions or variables:
  lars
Rd file 'createTree.Rd':
  \usage lines wider than 90 characters:
     createTree(data, treeType = "quad", dataType = "point", columns = if (dataType=="point") 1:2 else 1:4, ...)

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
adx: no visible global function definition for ‘abline’
adx: no visible global function definition for ‘legend’
dx: no visible global function definition for ‘abline’
dx: no visible global function definition for ‘legend’
maxd: no visible global function definition for ‘abline’
maxd: no visible global function definition for ‘legend’
pc: no visible global function definition for ‘rainbow’
pc: no visible global function definition for ‘plot’
pc: no visible global function definition for ‘abline’
pc: no visible global function definition for ‘legend’
pc: no visible global function definition for ‘points’
pcu: no visible global function definition for ‘rainbow’
pcu: no visible global function definition for ‘plot’
pcu: no visible global function definition for ‘abline’
pcu: no visible global function definition for ‘legend’
pcu: no visible global function definition for ‘points’
rmsd: no visible global function definition for ‘abline’
rmsd: no visible global function definition for ‘legend’
rsd: no visible global function definition for ‘abline’
rsd: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline legend plot points rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "legend", "plot", "points")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘NADA’ ‘lubridate’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package in Depends field not imported from: ‘JM’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SEchart: no visible global function definition for ‘plot’
SEchart: no visible global function definition for ‘rect’
SEchart: no visible global function definition for ‘par’
SEchart: no visible global function definition for ‘grid’
SEchart: no visible global function definition for ‘axis’
SEchart: no visible global function definition for ‘text’
SEchart: no visible global function definition for ‘lines’
SEchart: no visible global function definition for ‘heat.colors’
SEchart: no visible global function definition for ‘topo.colors’
SEchart: no visible global function definition for ‘cm.colors’
SEchart: no visible global function definition for ‘terrain.colors’
SEchart: no visible global function definition for ‘gray.colors’
SEchart: no visible global function definition for ‘rainbow’
SEchart: no visible global function definition for ‘points’
SEchart: no visible global function definition for ‘legend’
Undefined global functions or variables:
  axis cm.colors gray.colors grid heat.colors legend lines par plot
  points rainbow rect terrain.colors text topo.colors
Consider adding
  importFrom("grDevices", "cm.colors", "gray.colors", "heat.colors",
             "rainbow", "terrain.colors", "topo.colors")
  importFrom("graphics", "axis", "grid", "legend", "lines", "par",
             "plot", "points", "rect", "text")
to your NAMESPACE file.
fdc2s: no visible global function definition for ‘lm’
fdc3s: no visible global function definition for ‘lm’
fds2s: no visible global function definition for ‘lm’
fds3s: no visible global function definition for ‘lm’
Undefined global functions or variables:
  lm
Consider adding
  importFrom("stats", "lm")
to your NAMESPACE file.
.read.SeerStatTXT: no visible global function definition for
  ‘read.table’
.write.SeerStatTXT: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
prepare_Rd: SEER2RTestdata.Rd:77-78: Dropping empty section \source
Rd file 'SEER2R-package.Rd':
  \examples lines wider than 100 characters:
     #load testing data: there are three data objects, i.e. SEER2RTestData1,SEER2RTestData2,SEER2RTestData3 
     dicinfoused = write.SeerStat(SEER2RTestData2, DICfileName = "testrun1.dic",UseVarLabelsInTxtFile=FALSE);

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

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

These lines will be truncated in the PDF manual.
File ‘segmag/libs/segmag.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  BinNegative.cpp:108:5: warning: assigning field to itself [-Wself-assign-field]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/Segmentor3IsBack.Rcheck/00install.out’ for details.
File ‘Segmentor3IsBack/libs/Segmentor3IsBack.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘rgdal’ ‘spdep’ ‘spgrass6’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.use.spgrass6: no visible global function definition for ‘listw2mat’
.use.spgrass6: no visible global function definition for ‘sn2listw’
conprof: no visible global function definition for ‘axis’
conprof: no visible global function definition for ‘lines’
isp: no visible global function definition for ‘combn’
points.SegLocal: no visible global function definition for ‘points’
Undefined global functions or variables:
  axis combn lines listw2mat points sn2listw
Consider adding
  importFrom("graphics", "axis", "lines", "points")
  importFrom("utils", "combn")
to your NAMESPACE file.
File ‘seg/libs/seg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
get_statistics_from_file: no visible global function definition for
  ‘read.csv’
glm_anova: no visible global function definition for ‘aov’
glm_anova: no visible global function definition for ‘glm’
glm_anova: no visible global function definition for ‘gaussian’
glm_anova: no visible global function definition for ‘anova’
glm_anova: no visible global function definition for ‘quasipoisson’
glm_anova: no visible global function definition for ‘sd’
glm_anova: no visible global function definition for ‘p.adjust’
ttest_cohens_d: no visible global function definition for ‘t.test’
ttest_cohens_d: no visible global function definition for ‘sd’
Undefined global functions or variables:
  anova aov gaussian glm p.adjust quasipoisson read.csv sd t.test
Consider adding
  importFrom("stats", "anova", "aov", "gaussian", "glm", "p.adjust",
             "quasipoisson", "sd", "t.test")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
predict.SEL: warning in splineDesign(newdata, knots = knts, ord =
  object$nord, deriv = rep(deriv, length(newdata)), outer.ok = TRUE):
  partial argument match of ‘deriv’ to ‘derivs’
getbinPost: no visible binding for global variable ‘dbeta’
getbinPost: no visible binding for global variable ‘pbeta’
getbinPost : fu: no visible global function definition for ‘dbinom’
getbinPost : fu: no visible global function definition for ‘predict’
getbinPost: no visible global function definition for ‘integrate’
getbinPost: no visible global function definition for ‘splinefun’
int.funct: no visible global function definition for ‘integrate’
int.funct2: no visible global function definition for ‘integrate’
min.abs: no visible global function definition for ‘uniroot’
plot.SEL: no visible global function definition for ‘plot’
print.SEL: no visible global function definition for ‘integrate’
print.summary.SEL : foo1: no visible global function definition for
  ‘predict’
print.summary.SEL : foo2: no visible global function definition for
  ‘predict’
print.summary.SEL: no visible global function definition for
  ‘integrate’
quantSEL: no visible global function definition for ‘predict’
quantSEL: no visible global function definition for ‘splinefun’
rvSEL: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dbeta dbinom integrate pbeta plot predict runif splinefun uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dbeta", "dbinom", "integrate", "pbeta", "predict",
             "runif", "splinefun", "uniroot")
to your NAMESPACE file.
File ‘SEL/libs/SEL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘sem’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'semdiag.Rd':
  \usage lines wider than 90 characters:
     semdiag(x,  EQSmodel, varphi=0.1, EQSdata='data.txt', D='E', delete=integer(0), max_it=1000, EQSprog='C:/Progra~1/EQS61/WINEQS',serial= ... [TRUNCATED]

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

These lines will be truncated in the PDF manual.
Found the following apparent S3 methods exported but not registered:
  chisqNull.objectiveML print.summaryGOF
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
ChiSquaredLRTest: no visible global function definition for ‘na.omit’
ChiSquaredLRTest: no visible global function definition for ‘cov’
ChiSquaredLRTest: no visible global function definition for ‘dmvnorm’
ChiSquaredLRTest: no visible global function definition for ‘pchisq’
NormalTheoryLRTest: no visible global function definition for ‘na.omit’
NormalTheoryLRTest: no visible global function definition for ‘cov’
NormalTheoryLRTest: no visible global function definition for ‘dmvnorm’
NormalTheoryLRTest: no visible global function definition for ‘sd’
NormalTheoryLRTest: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  cov dmvnorm na.omit pchisq pnorm sd
Consider adding
  importFrom("stats", "cov", "na.omit", "pchisq", "pnorm", "sd")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘XML’ ‘boot’ ‘sem’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  ‘boot:::const’ ‘stats:::AIC.logLik’ ‘stats:::BIC.logLik’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘addPath.plsm’ ‘endogenous’ ‘predecessors’ ‘qSquared’ ‘reorder’
  ‘resempls’ ‘residuals.sempls’
File ‘semver/libs/semver.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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_attachment: no visible global function definition for ‘dev.off’
.update_list: no visible global function definition for ‘modifyList’
mime_part.data.frame: no visible global function definition for
  ‘write.table’
mime_part.ggplot: no visible binding for global variable ‘pdf’
mime_part.matrix: no visible global function definition for
  ‘write.table’
mime_part.trellis: no visible binding for global variable ‘pdf’
Undefined global functions or variables:
  dev.off modifyList pdf write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "modifyList", "write.table")
to your NAMESPACE file.
'library' or 'require' call to ‘rtiff’ which was already attached by Depends.
  Please remove these calls from your code.
Rd file 'addDefault.Rd':
  \examples lines wider than 100 characters:
     plot.calls = c("boxplot(count ~ spray, data = InsectSprays, col = 'lightgray')", "plot(1:3,1:3, col='blue', xlab='', ylab=''); points(1 ... [TRUNCATED]
     plt.extras=list(figure1= "rect(xleft=c(3,1), ytop=c(25,5),xright=c(4,2),  ybottom=c(20,0));title(main='A', cex=3)", figure2="polygon(x= ... [TRUNCATED]
     Splot = addDefault(Splot, data=c("This is default", "data2"), data.labels=c("label", "d2"), links=c("http://www.buffalo.edu, http://www ... [TRUNCATED]

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

These lines will be truncated in the PDF manual.
gconv: no visible global function definition for ‘convolve’
sens.analysis.aberrant.rank: no visible global function definition for
  ‘pnorm’
sens.analysis.mh: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  convolve pnorm
Consider adding
  importFrom("stats", "convolve", "pnorm")
to your NAMESPACE file.
mscorev: no visible global function definition for ‘quantile’
senmwCI : funcCI: no visible global function definition for ‘qnorm’
senmwCI : funcCI2: no visible global function definition for ‘qnorm’
separable1k: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm quantile
Consider adding
  importFrom("stats", "pnorm", "qnorm", "quantile")
to your NAMESPACE file.
plot.sensitivity.2.0d: no visible global function definition for ‘gray’
sensitivitySGD: no visible global function definition for ‘tail’
sensitivitySGL: no visible global function definition for ‘tail’
Undefined global functions or variables:
  gray tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("utils", "tail")
to your NAMESPACE file.
File ‘sensitivityPStrat/libs/sensitivityPStrat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
separationplot: no visible global function definition for ‘dev.new’
separationplot: no visible global function definition for ‘pdf’
separationplot: no visible global function definition for ‘par’
separationplot: no visible global function definition for ‘plot’
separationplot: no visible global function definition for ‘title’
separationplot: no visible global function definition for ‘segments’
separationplot: no visible global function definition for ‘rect’
separationplot: no visible global function definition for ‘points’
separationplot: no visible global function definition for ‘lines’
separationplot: no visible global function definition for
  ‘colorRampPalette’
separationplot: no visible global function definition for ‘layout’
separationplot: no visible global function definition for ‘plot.new’
separationplot: no visible global function definition for ‘legend’
separationplot: no visible global function definition for ‘dev.off’
separationplot: no visible global function definition for ‘locator’
sp.categorical: no visible global function definition for ‘dev.new’
sp.categorical: no visible global function definition for ‘pdf’
sp.categorical: no visible global function definition for ‘par’
sp.categorical: no visible global function definition for ‘layout’
sp.categorical: no visible global function definition for ‘plot’
sp.categorical: no visible global function definition for ‘text’
sp.categorical: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  colorRampPalette dev.new dev.off layout legend lines locator par pdf
  plot plot.new points rect segments text title
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.new", "dev.off",
             "pdf")
  importFrom("graphics", "layout", "legend", "lines", "locator", "par",
             "plot", "plot.new", "points", "rect", "segments", "text",
             "title")
to your NAMESPACE file.
Rd file 'sp.categorical.Rd':
  \examples lines wider than 100 characters:
       read.dta("http://www2.lse.ac.uk/dataFiles/geographyAndEnvironment/Replication/Article%20for%20JCR%20(Human%20Rights).dta")

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
GammaDist: no visible binding for global variable ‘rgamma’
VEpowerPP: no visible global function definition for ‘qnorm’
applyStopRules: no visible global function definition for ‘qnorm’
finalLogRankTest: no visible global function definition for ‘qnorm’
finalLogRankTest: no visible global function definition for ‘pchisq’
generateDropout: no visible global function definition for ‘rexp’
generateEnrollment: no visible global function definition for ‘rpois’
generateEnrollment: no visible global function definition for ‘runif’
generateInfection: no visible global function definition for ‘rexp’
generateInfection : <anonymous>: no visible global function definition
  for ‘rexp’
getAlphaPerTest: no visible global function definition for ‘uniroot’
getHarmBound: no visible global function definition for ‘dbinom’
getHarmBound: no visible global function definition for ‘write.csv’
getTreatmentAssignment : <anonymous>: no visible global function
  definition for ‘runif’
getTreatmentAssignment: no visible global function definition for
  ‘runif’
simTrial: no visible global function definition for ‘runif’
sumTrialOneTrtArm: no visible global function definition for ‘quantile’
testVE: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  dbinom pchisq qnorm quantile rexp rgamma rpois runif uniroot
  write.csv
Consider adding
  importFrom("stats", "dbinom", "pchisq", "qnorm", "quantile", "rexp",
             "rgamma", "rpois", "runif", "uniroot")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
File ‘seqMeta/libs/seqMeta.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  vcf.c:253:15: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/seqminer.Rcheck/00install.out’ for details.
plotenz : addmark: no visible global function definition for ‘par’
plotenz : addmark: no visible global function definition for ‘plot’
plotenz : addmark: no visible global function definition for ‘text’
plotenz : addmark: no visible global function definition for ‘segments’
plotenz : addband: no visible global function definition for ‘segments’
plotenz : addband: no visible global function definition for ‘text’
plotenz: no visible global function definition for ‘layout’
plotenz: no visible global function definition for ‘text’
plotenz: no visible global function definition for ‘dev.new’
Undefined global functions or variables:
  dev.new layout par plot segments text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "layout", "par", "plot", "segments", "text")
to your NAMESPACE file.
Rd file 'plotenz.Rd':
  \usage lines wider than 90 characters:
     plotenz(sequences, enznames, enzdata, side = TRUE, type = c("RFLP", "TRFLP"), Terminal = c("T5", "T3"))

These lines will be truncated in the PDF manual.
File ‘sequences/libs/sequences.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: Array reference at (1) out of bounds (43 > 42) in loop beginning at (2)
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/sequoia.Rcheck/00install.out’ for details.
File ‘sequoia/libs/sequoia.so’:
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Object: ‘sequoia.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
capture: no visible binding for global variable ‘resultText’
restore.session: no visible binding for global variable
  ‘.save.session.packages’
restore.session: no visible binding for global variable
  ‘.save.session.search’
save.session: no visible global function definition for ‘dev.list’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.search’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.packages’
Undefined global functions or variables:
  .save.session.packages .save.session.search dev.list resultText
Consider adding
  importFrom("grDevices", "dev.list")
to your NAMESPACE file.

Found the following calls to attach():
File ‘session/R/session.R’:
  attach(sub("file:", "", i))
See section ‘Good practice’ in ‘?attach’.
setpath: no visible global function definition for ‘cov’
setpath: no visible global function definition for ‘median’
setpath: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  cov median pchisq
Consider adding
  importFrom("stats", "cov", "median", "pchisq")
to your NAMESPACE file.
random.number.test: no visible global function definition for ‘runif’
random.number.test: no visible global function definition for ‘rnorm’
setRNG: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: ‘loomR’
'library' or 'require' call to ‘graphics’ which was already attached by Depends.
  Please remove these calls from your code.
severity: no visible global function definition for ‘qnorm’
severity: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  print.extmod print.simpextmod
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
L_exp: no visible global function definition for ‘pnorm’
L_hNV: no visible global function definition for ‘pnorm’
L_trunc: no visible global function definition for ‘pnorm’
L_trunc_mufest: no visible global function definition for ‘pnorm’
dgp: no visible global function definition for ‘runif’
dgp: no visible global function definition for ‘rnorm’
eff.sfa: no visible global function definition for ‘predict’
fitted.sfa: no visible global function definition for ‘predict’
predict.sfa: no visible global function definition for ‘coef’
print.sfa: no visible global function definition for ‘coef’
residuals.sfa: no visible global function definition for ‘fitted’
sfa: no visible global function definition for ‘model.frame’
sfa: no visible global function definition for ‘model.response’
sfa.fit: no visible global function definition for ‘lm’
sfa.fit: no visible global function definition for ‘resid’
sfa.fit: no visible global function definition for ‘var’
sfa.fit: no visible global function definition for ‘optim’
summary.sfa: no visible global function definition for ‘logLik’
summary.sfa: no visible global function definition for ‘pchisq’
te.eff.sfa: no visible global function definition for ‘residuals’
te.eff.sfa: no visible global function definition for ‘pnorm’
u.sfa: no visible global function definition for ‘residuals’
u.sfa: no visible global function definition for ‘dnorm’
u.sfa: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  coef dnorm fitted lm logLik model.frame model.response optim pchisq
  pnorm predict resid residuals rnorm runif var
Consider adding
  importFrom("stats", "coef", "dnorm", "fitted", "lm", "logLik",
             "model.frame", "model.response", "optim", "pchisq", "pnorm",
             "predict", "resid", "residuals", "rnorm", "runif", "var")
to your NAMESPACE file.
File ‘sgeostat/libs/sgeostat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
coxCrossVal: no visible binding for global variable ‘sd’
error.bars: no visible global function definition for ‘segments’
linCrossVal: no visible binding for global variable ‘sd’
logitCrossVal: no visible binding for global variable ‘sd’
plot.cv.SGL: no visible global function definition for ‘points’
Undefined global functions or variables:
  points sd segments
Consider adding
  importFrom("graphics", "points", "segments")
  importFrom("stats", "sd")
to your NAMESPACE file.
Rd file 'SGL.Rd':
  \usage lines wider than 90 characters:
     SGL(data, index, type = "linear", maxit = 1000, thresh = 0.001, min.frac = 0.1, nlam = 20, gamma = 0.8, standardize = TRUE, verbose = F ... [TRUNCATED]

Rd file 'cvSGL.Rd':
  \usage lines wider than 90 characters:
     cvSGL(data, index, type = "linear", maxit = 1000, thresh = 0.001, min.frac = 0.05, nlam = 20, gamma = 0.8, nfold = 10, standardize = TR ... [TRUNCATED]

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.computePStar: no visible global function definition for ‘uniroot’
plotBoundary: no visible global function definition for
  ‘scale_y_continuous’
Undefined global functions or variables:
  scale_y_continuous uniroot
Consider adding
  importFrom("stats", "uniroot")
to your NAMESPACE file.
amse: no visible global function definition for ‘na.omit’
arb: no visible global function definition for ‘na.omit’
rdatagen: no visible global function definition for ‘qnorm’
rdatagen: no visible global function definition for ‘pbinom’
rdatagen: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  na.omit pbinom pnorm qnorm
Consider adding
  importFrom("stats", "na.omit", "pbinom", "pnorm", "qnorm")
to your NAMESPACE file.
UQnormalize.count: no visible binding for global variable ‘quantile’
plotNScores: no visible global function definition for ‘par’
plotNScores: no visible global function definition for ‘hist’
plotNScores: no visible global function definition for ‘title’
plotScores: no visible global function definition for ‘par’
plotScores: no visible global function definition for ‘hist’
plotScores: no visible global function definition for ‘title’
sgRSEA: no visible binding for global variable ‘sd’
sgRSEA: no visible global function definition for ‘p.adjust’
sgRSEA.mean: no visible binding for global variable ‘sd’
sgRSEA.mean: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  hist p.adjust par quantile sd title
Consider adding
  importFrom("graphics", "hist", "par", "title")
  importFrom("stats", "p.adjust", "quantile", "sd")
to your NAMESPACE file.
'library' or 'require' call to ‘foreign’ which was already attached by Depends.
  Please remove these calls from your code.
File ‘sharpeRratio/libs/sharpeRratio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
popify: no visible global function definition for ‘runif’
tipify: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
get_selected_names: no visible global function definition for ‘tail’
get_selected_names: no visible global function definition for ‘head’
Undefined global functions or variables:
  head tail
Consider adding
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
shrink.estim: no visible global function definition for ‘cov’
shrink.estim: no visible global function definition for ‘cor’
shrink.estim: no visible global function definition for ‘cov2cor’
targetCor: no visible global function definition for ‘cor.test’
targetCor: no visible global function definition for ‘cor’
targetCor: no visible global function definition for ‘sd’
targetCor: no visible global function definition for ‘cov’
targetD: no visible binding for global variable ‘var’
targetF: no visible global function definition for ‘cov’
targetF: no visible global function definition for ‘cor’
targetG: no visible global function definition for ‘cor’
targetG: no visible global function definition for ‘sd’
targetG: no visible global function definition for ‘cov’
targetGpos: no visible global function definition for ‘cor’
targetGpos: no visible global function definition for ‘sd’
targetGpos: no visible global function definition for ‘cov’
targetGstar: no visible global function definition for ‘cor’
targetGstar: no visible global function definition for ‘sd’
targetGstar: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cor cor.test cov cov2cor sd var
Consider adding
  importFrom("stats", "cor", "cor.test", "cov", "cov2cor", "sd", "var")
to your NAMESPACE file.
.params: no visible binding for global variable ‘URLencode’
.params: no visible global function definition for ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
Depends: includes the non-default packages:
  ‘hdrcde’ ‘coda’ ‘MASS’ ‘bayesm’ ‘mnormt’ ‘spatstat’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  ‘MASS’ ‘bayesm’ ‘coda’ ‘hdrcde’ ‘mnormt’ ‘spatstat’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'siarmcmcdirichletv4.Rd':
  \usage lines wider than 90 characters:
     siarmcmcdirichletv4(data, sources, corrections = 0, concdep = 0, iterations=200000, burnin=50000, howmany=10000, thinby=15, prior = rep ... [TRUNCATED]

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

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

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

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

These lines will be truncated in the PDF manual.
File ‘siar/libs/siar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘ade4’ ‘corpcor’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
filter.PCA.default: no visible global function definition for
  ‘princomp’
filter.mRMR.default: no visible global function definition for
  ‘discretize’
gaussian.default: no visible global function definition for ‘cov’
gaussian.default: no visible global function definition for
  ‘cov.shrink’
plot.verify.cv: no visible global function definition for ‘plot’
plot.verify.cv: no visible global function definition for ‘points’
plot.verify.ho: no visible global function definition for ‘plot’
plot.verify.ho: no visible global function definition for ‘points’
plot.verify.loo: no visible global function definition for ‘plot’
plot.verify.loo: no visible global function definition for ‘points’
predict.dpa1: no visible global function definition for ‘cor’
predict.filter.PCA: no visible global function definition for ‘predict’
predict.filter.RegressionTreeFilter: no visible global function
  definition for ‘is.struct’
predict.filter.RegressionTreeFilter: no visible global function
  definition for ‘var’
simulator.Simple1: no visible global function definition for ‘rnorm’
verify.ho.default: no visible global function definition for ‘predict’
verify.loo.default: no visible global function definition for ‘predict’
Undefined global functions or variables:
  cor cov cov.shrink discretize is.struct plot points predict princomp
  rnorm var
Consider adding
  importFrom("graphics", "plot", "points")
  importFrom("stats", "cor", "cov", "predict", "princomp", "rnorm",
             "var")
to your NAMESPACE file.
Rd file 'plot.verify.ho.Rd':
  \examples lines wider than 100 characters:
     attack=verify.ho(model=gaussian,filter=filter.PCA,Xlearn=traces[1:128,],Ylearn=key[1:128],Xval=traces[129:256,],Yval=key[129:256],nbreV ... [TRUNCATED]

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

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

These lines will be truncated in the PDF manual.
dSepAdji: no visible global function definition for ‘as’
dag2cpdagAdj: no visible global function definition for ‘as’
randomDAG: no visible global function definition for ‘rbinom’
structIntervDist: no visible global function definition for ‘as’
Undefined global functions or variables:
  as rbinom
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "rbinom")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.cluster: no visible global function definition for ‘kmeans’
.plot.sigclust: no visible global function definition for ‘par’
.plot.sigclust: no visible global function definition for ‘density’
.plot.sigclust: no visible global function definition for ‘runif’
.plot.sigclust: no visible global function definition for ‘dnorm’
.plot.sigclust: no visible global function definition for ‘lines’
.plot.sigclust: no visible global function definition for ‘points’
.plot.sigclust: no visible global function definition for ‘title’
.plot.sigclust: no visible global function definition for ‘text’
.plot.sigclust: no visible global function definition for ‘qnorm’
.plot.sigclust: no visible global function definition for ‘abline’
.plot.sigclust: no visible global function definition for ‘quantile’
.plot.sigclust: no visible global function definition for ‘legend’
.simnull: no visible global function definition for ‘rnorm’
.vareigen: no visible global function definition for ‘mad’
.vareigen: no visible global function definition for ‘cov’
sigclust: no visible global function definition for ‘sd’
sigclust: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline cov density dnorm kmeans legend lines mad par pnorm points
  qnorm quantile rnorm runif sd text title
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "points",
             "text", "title")
  importFrom("stats", "cov", "density", "dnorm", "kmeans", "mad",
             "pnorm", "qnorm", "quantile", "rnorm", "runif", "sd")
to your NAMESPACE file.
Sight.Est: no visible global function definition for ‘glm’
Sight.Est: no visible global function definition for ‘binomial’
Sight.Est: no visible global function definition for ‘coef’
Sight.Est: no visible global function definition for ‘terms’
Sight.Est: no visible binding for global variable ‘binomial’
covtheta: no visible global function definition for ‘cov’
print.sightest: no visible global function definition for ‘qnorm’
summary.sightest: no visible global function definition for ‘qnorm’
vardiff: no visible global function definition for ‘vcov’
vardiff: no visible global function definition for ‘coef’
vardiff: no visible global function definition for ‘terms’
varlog.lam: no visible global function definition for ‘vcov’
varlog.lam: no visible global function definition for ‘coef’
varlog.lam: no visible global function definition for ‘terms’
Undefined global functions or variables:
  binomial coef cov glm qnorm terms vcov
Consider adding
  importFrom("stats", "binomial", "coef", "cov", "glm", "qnorm", "terms",
             "vcov")
to your NAMESPACE file.
File ‘signalHsmm/libs/signalHsmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
signmedian.test: no visible global function definition for ‘median’
signmedian.test: no visible global function definition for ‘binom.test’
signmedian.test: no visible global function definition for ‘pbinom’
signmedian.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  binom.test median pbinom pnorm
Consider adding
  importFrom("stats", "binom.test", "median", "pbinom", "pnorm")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘gdata’ ‘splines’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.SII: no visible global function definition for ‘plot’
plot.SII: no visible global function definition for ‘lines’
plot.SII: no visible global function definition for ‘abline’
plot.SII: no visible global function definition for ‘legend’
sii : approx.l: no visible global function definition for ‘approx’
sii.excel: no visible global function definition for ‘predict’
sii.excel : approx.l: no visible global function definition for
  ‘approx’
Undefined global functions or variables:
  abline approx legend lines plot predict
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "plot")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
Packages suggested but not available for checking: ‘tmlenet’ ‘ltmle’
'::' or ':::' import not declared from: ‘devtools’
'library' or 'require' calls not declared from:
  ‘devtools’ ‘roxygen2’
Found the following apparent S3 methods exported but not registered:
  print.simexaft summary.simexaft
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
linearextrapolation: no visible global function definition for ‘coef’
linearextrapolation: no visible global function definition for ‘lm’
plotsimexaft: no visible global function definition for ‘plot’
plotsimexaft: no visible global function definition for ‘lm’
plotsimexaft: no visible global function definition for ‘predict’
plotsimexaft: no visible global function definition for ‘lines’
plotsimexaft: no visible global function definition for ‘points’
plotsimexaft: no visible global function definition for ‘legend’
print.simexaft: no visible global function definition for ‘coef’
quadraticextrapolation: no visible global function definition for
  ‘coef’
quadraticextrapolation: no visible global function definition for ‘lm’
simexaft: no visible global function definition for ‘terms’
simexaft: no visible global function definition for ‘rnorm’
simexaft: no visible binding for global variable ‘var’
simexaft: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  coef legend lines lm plot pnorm points predict rnorm terms var
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("stats", "coef", "lm", "pnorm", "predict", "rnorm", "terms",
             "var")
to your NAMESPACE file.
getFormula: no visible global function definition for ‘as.formula’
internalSimXyplot : f: no visible global function definition for
  ‘median’
runSimulation: no visible global function definition for ‘runif’
setup: no visible global function definition for ‘runif’
clusterSetup,ANY-data.frame-SampleControl: no visible binding for
  global variable ‘cnam’
clusterSetup,ANY-data.frame-TwoStageControl: no visible binding for
  global variable ‘cnam’
initialize,DCARContControl: no visible binding for global variable
  ‘rnorm’
initialize,DataControl: no visible binding for global variable ‘rnorm’
Undefined global functions or variables:
  as.formula cnam median rnorm runif
Consider adding
  importFrom("stats", "as.formula", "median", "rnorm", "runif")
to your NAMESPACE file.
File ‘simFrame/libs/simFrame.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘simLife/libs/simLife.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.
cumallcausehr: no visible global function definition for ‘integrate’
plotbe: no visible global function definition for ‘plot’
plotbe: no visible global function definition for ‘lines’
plotbe: no visible global function definition for ‘legend’
plotcph: no visible global function definition for ‘confint’
plotcph: no visible global function definition for ‘plot’
plotcph: no visible global function definition for ‘abline’
plotcph: no visible global function definition for ‘axis’
plotcph: no visible global function definition for ‘polygon’
plotcph: no visible global function definition for ‘lines’
plotnae: no visible global function definition for ‘plot’
simCR: no visible global function definition for ‘rnorm’
simEBMT: no visible global function definition for ‘model.matrix’
simexit: no visible global function definition for ‘runif’
simexitinner: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  abline axis confint integrate legend lines model.matrix plot polygon
  rnorm runif uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "plot",
             "polygon")
  importFrom("stats", "confint", "integrate", "model.matrix", "rnorm",
             "runif", "uniroot")
to your NAMESPACE file.
'library' or 'require' call to ‘boot’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘boot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  pairs.boot
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘simpleboot/R/zzz.R’:
  .onLoad calls:
    require(boot)

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

lo.boot.resample: warning in sample(1:nrow(orig.data), rep = TRUE, prob
  = weights): partial argument match of ‘rep’ to ‘replace’
lo.boot.resample: warning in sample(res, rep = TRUE, prob = weights):
  partial argument match of ‘rep’ to ‘replace’
S3 methods shown with full name in documentation object 'pairs.boot':
  ‘pairs.boot’

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.
randInitializeWeights: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  ‘HISTORY’
File ‘simplexreg/libs/simplexreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘mclust’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Simpsons: no visible global function definition for ‘Mclust’
Simpsons: no visible global function definition for ‘lm’
Simpsons: no visible global function definition for ‘plot’
Simpsons: no visible global function definition for ‘abline’
Simpsons: no visible global function definition for ‘par’
Simpsons: no visible global function definition for ‘legend’
Simpsons: no visible global function definition for ‘txtProgressBar’
Simpsons: no visible global function definition for ‘setTxtProgressBar’
Simpsons: no visible global function definition for ‘quantile’
plot.Simpson: no visible global function definition for ‘plot’
plot.Simpson: no visible global function definition for ‘lm’
plot.Simpson: no visible global function definition for ‘abline’
plot.Simpson: no visible global function definition for ‘par’
plot.Simpson: no visible global function definition for ‘legend’
Undefined global functions or variables:
  Mclust abline legend lm par plot quantile setTxtProgressBar
  txtProgressBar
Consider adding
  importFrom("graphics", "abline", "legend", "par", "plot")
  importFrom("stats", "lm", "quantile")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
File ‘SimReg/libs/SimReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
simrel: no visible global function definition for ‘runif’
simrel: no visible global function definition for ‘rnorm’
simrelplot: no visible global function definition for ‘par’
simrelplot: no visible global function definition for ‘layout’
simrelplot: no visible global function definition for ‘devAskNewPage’
simrelplot: no visible global function definition for ‘dev.hold’
simrelplot: no visible global function definition for ‘plot’
simrelplot: no visible global function definition for ‘abline’
simrelplot: no visible global function definition for ‘dev.flush’
simrelplot: no visible global function definition for ‘points’
simrelplot: no visible global function definition for ‘axis’
simrelplot: no visible global function definition for ‘mtext’
simrelplot: no visible global function definition for ‘box’
simrelplot: no visible global function definition for ‘cov’
Undefined global functions or variables:
  abline axis box cov dev.flush dev.hold devAskNewPage layout mtext par
  plot points rnorm runif
Consider adding
  importFrom("grDevices", "dev.flush", "dev.hold", "devAskNewPage")
  importFrom("graphics", "abline", "axis", "box", "layout", "mtext",
             "par", "plot", "points")
  importFrom("stats", "cov", "rnorm", "runif")
to your NAMESPACE file.
Found the following hidden files and directories:
  vignettes/.Rhistory
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘abind’ ‘svUnit’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
simSummary: no visible global function definition for ‘abind’
simSummary_unitTests: no visible global function definition for
  ‘clearLog’
simSummary_unitTests: no visible global function definition for
  ‘runTest’
simSummary_unitTests: no visible global function definition for
  ‘svSuite’
simSummary_unitTests: no visible global function definition for ‘Log’
simSummary_unitTests: no visible global function definition for ‘stats’
simSummary_unitTests: no visible global function definition for
  ‘metadata’
simSummary_unitTests: no visible global function definition for
  ‘errorLog’
Undefined global functions or variables:
  Log abind clearLog errorLog metadata runTest stats svSuite
Found the following apparent S3 methods exported but not registered:
  plot.siRSM plot.siRSM.default plot.siRSM.default print.siRSM
  print.siRSM.default print.siRSM.default siRSM.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
cvskda: no visible global function definition for ‘detectCores’
cvskda: no visible global function definition for ‘makeCluster’
cvskda: no visible global function definition for ‘clusterApplyLB’
cvskda: no visible global function definition for ‘mclapply’
cvskda: no visible global function definition for ‘stopCluster’
Undefined global functions or variables:
  clusterApplyLB detectCores makeCluster mclapply stopCluster
File ‘skda/libs/skda.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.skewhypFit
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
dskt: no visible global function definition for ‘dt’
pskt: no visible global function definition for ‘pt’
qskt: no visible global function definition for ‘qt’
rskt: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dt pt qt runif
Consider adding
  importFrom("stats", "dt", "pt", "qt", "runif")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘kmndirs’
Unavailable namespace imported from by a ':::' call: ‘kmndirs’
  See the note in ?`:::` about the use of this operator.
File ‘skm/libs/skm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘smco/R/smco.R’:
  .onAttach calls:
    cat(paste("This is smco package", version, "\n"))

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

smco: no visible global function definition for ‘runif’
smco: no visible global function definition for ‘rnorm’
smco: no visible global function definition for ‘qnorm’
smco: no visible global function definition for ‘pnorm’
smco: no visible global function definition for ‘optim’
Undefined global functions or variables:
  optim pnorm qnorm rnorm runif
Consider adding
  importFrom("stats", "optim", "pnorm", "qnorm", "rnorm", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  MCP_efficient.c:114:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  MCP_efficient.c:134:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  MCP_efficient.c:154:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SMCP.Rcheck/00install.out’ for details.
SMCP : fun: no visible global function definition for ‘cor’
manipulate : fun: no visible global function definition for ‘sd’
sp: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  cor sd
Consider adding
  importFrom("stats", "cor", "sd")
to your NAMESPACE file.
File ‘SMCP/libs/SMCP.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 ‘SMC/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage("##\n", "## Sequential Monte Carlo Package (SMC)\n",     "##\n", "## Functionality: sequential Monte Carlo (SMC) or sequential importance\n",     "## sampling (SIS) or hidden Markov models (HMM), particle filter (PF)\n",     "## and auxiliary particle filter (APF)\n", "##\n", "## Use: \"help(package = SMC)\" at the R prompt for more info\n",     "##\n", "## Copyright (C) 2006-", this.year, " Gopi Goswami\n",     "##\n", "##    Created by: Gopi Goswami <goswami@stat.harvard.edu>\n",     "## Maintained by: Gopi Goswami <grgoswami@gmail.com>\n",     "##\n")

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

.MHUpdateFuncGen.PF : MHUpdateFunc: no visible global function
  definition for ‘runif’
MarkovSwitchingFuncGenerator : generateNextStreamsFunc: no visible
  global function definition for ‘runif’
MarkovSwitchingFuncGenerator: no visible global function definition for
  ‘rnorm’
MarkovSwitchingFuncGenerator: no visible global function definition for
  ‘runif’
MarkovSwitchingFuncGenerator : logObsDensFunc: no visible global
  function definition for ‘dnorm’
MarkovSwitchingFuncGenerator : propagateFunc: no visible global
  function definition for ‘dnorm’
MarkovSwitchingFuncGenerator : propagateFunc: no visible global
  function definition for ‘runif’
Undefined global functions or variables:
  dnorm rnorm runif
Consider adding
  importFrom("stats", "dnorm", "rnorm", "runif")
to your NAMESPACE file.
File ‘SMC/libs/SMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
em: no visible global function definition for ‘coxph’
em: no visible global function definition for ‘optim’
plotpredictsmcure: no visible global function definition for ‘plot’
plotpredictsmcure: no visible global function definition for ‘matplot’
plotpredictsmcure: no visible global function definition for ‘lines’
smcure: no visible binding for global variable ‘na.omit’
smcure: no visible global function definition for ‘model.frame’
smcure: no visible global function definition for ‘model.extract’
smcure: no visible global function definition for ‘model.matrix’
smcure: no visible global function definition for ‘coxph’
smcure: no visible global function definition for ‘survreg’
smcure: no visible binding for global variable ‘var’
smcure: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  coxph lines matplot model.extract model.frame model.matrix na.omit
  optim plot pnorm survreg var
Consider adding
  importFrom("graphics", "lines", "matplot", "plot")
  importFrom("stats", "model.extract", "model.frame", "model.matrix",
             "na.omit", "optim", "pnorm", "var")
to your NAMESPACE file.
branching.resample: no visible global function definition for ‘rbinom’
cov.weights: no visible global function definition for ‘var’
inverse.cdf.weights: no visible global function definition for ‘runif’
multinomial.resample: no visible global function definition for ‘runif’
stratified.resample: no visible global function definition for ‘runif’
systematic.resample: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rbinom runif var
Consider adding
  importFrom("stats", "rbinom", "runif", "var")
to your NAMESPACE file.
Rd file 'resampling.Rd':
  \usage lines wider than 90 characters:
     residual.resample(   weights, num.samples = length(weights), engine="R", rrf = "stratified")

These lines will be truncated in the PDF manual.
File ‘smcUtils/libs/smcUtils.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘proxy’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘proxy’ ‘tm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
normalize: no visible binding for global variable ‘sd’
simDic: no visible global function definition for ‘simil’
simDoc: no visible global function definition for ‘simil’
Undefined global functions or variables:
  sd simil
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Rd file 'simDic.Rd':
  \usage lines wider than 90 characters:
     simDic(docMatrix1, docMatrix2, scoreDict, breaks = seq(-1, 1, length = 11), norm = FALSE, method = "cosine", scoreFunc = mean)

These lines will be truncated in the PDF manual.
Grad.sph: no visible global function definition for ‘dist’
IMDS: no visible global function definition for ‘cmdscale’
IMDS: no visible global function definition for ‘as.dist’
IMDS: no visible global function definition for ‘runif’
IMDS: no visible global function definition for ‘optim’
idistSph: no visible global function definition for ‘dist’
obj.sph: no visible global function definition for ‘dist’
plot.imds: no visible binding for global variable ‘lines’
plot.imds: no visible global function definition for ‘plot’
plot.imds: no visible global function definition for ‘text’
plot.imds: no visible global function definition for ‘rect’
Undefined global functions or variables:
  as.dist cmdscale dist lines optim plot rect runif text
Consider adding
  importFrom("graphics", "lines", "plot", "rect", "text")
  importFrom("stats", "as.dist", "cmdscale", "dist", "optim", "runif")
to your NAMESPACE file.
File ‘smds/libs/smds.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘ggplot2’ ‘reshape’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘corpcor’ ‘ggplot2’ ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘smfsb/libs/smfsb.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
lines.SmithWilsonYieldCurve: no visible global function definition for
  ‘lines’
plot.SmithWilsonYieldCurve: no visible global function definition for
  ‘plot’
points.SmithWilsonYieldCurve: no visible global function definition for
  ‘points’
Undefined global functions or variables:
  lines plot points
Consider adding
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
Fourier2d: no visible global function definition for ‘fft’
kernel2dsmooth: no visible global function definition for ‘fft’
Undefined global functions or variables:
  fft
Consider adding
  importFrom("stats", "fft")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  pairs.mod plot.glm.diag
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'plot.glm.diag.Rd':
  \usage lines wider than 90 characters:
     plot(x, glmdiag = glm.diag(x), subset = NULL, iden = FALSE, labels = NULL, ret = FALSE, ...)

Rd file 'poi.beta.laplace.Rd':
  \usage lines wider than 90 characters:
     poi.beta.laplace(data, alpha = get.alpha(data), phi = 1, nu = 0.1, beta = seq(from = 0, to = 7, length = 1000))

These lines will be truncated in the PDF manual.
dNMR: no visible global function definition for ‘pnorm’
dNMR: no visible global function definition for ‘dnorm’
pNMR: no visible global function definition for ‘pnorm’
pNMR: no visible global function definition for ‘dnorm’
rMR: no visible global function definition for ‘rnorm’
rMR: no visible global function definition for ‘rchisq’
Undefined global functions or variables:
  dnorm pnorm rchisq rnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm", "rchisq", "rnorm")
to your NAMESPACE file.
SMVar.paired : <anonymous>: no visible global function definition for
  ‘var’
SMVar.paired: no visible global function definition for ‘var’
SMVar.paired: no visible global function definition for ‘pt’
SMVar.paired: no visible global function definition for ‘p.adjust’
SMVar.paired: no visible global function definition for ‘write.table’
SMVar.unpaired : <anonymous>: no visible global function definition for
  ‘var’
SMVar.unpaired: no visible global function definition for ‘var’
SMVar.unpaired: no visible global function definition for ‘pt’
SMVar.unpaired: no visible global function definition for ‘p.adjust’
SMVar.unpaired: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  p.adjust pt var write.table
Consider adding
  importFrom("stats", "p.adjust", "pt", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Rd file 'SMVar.paired.Rd':
  \usage lines wider than 90 characters:
     SMVar.paired(geneNumbers, logratio, fileexport = NULL, minrep = 2, method = "BH", threshold = 0.05)

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

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘snowboot/libs/snowboot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘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:
  [.cluster
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
KS.test: no visible global function definition for ‘quantile’
KS.test : Fgaus: no visible global function definition for ‘pnorm’
KS.test: no visible global function definition for ‘setNames’
cs.test: no visible global function definition for ‘pbinom’
cs.test: no visible global function definition for ‘pnorm’
cs.test: no visible global function definition for ‘setNames’
kde: no visible global function definition for ‘quantile’
kde : Fgaus: no visible global function definition for ‘pnorm’
kde: no visible global function definition for ‘par’
kre: no visible global function definition for ‘quantile’
kre: no visible global function definition for ‘lines’
ns.test: no visible global function definition for ‘complete.cases’
ns.test: no visible global function definition for ‘qnorm’
ns.test: no visible global function definition for ‘pnorm’
ns.test: no visible global function definition for ‘pchisq’
ns.test: no visible global function definition for ‘setNames’
ns.test: no visible global function definition for ‘qt’
quant.test: no visible global function definition for ‘complete.cases’
quant.test: no visible global function definition for ‘pbinom’
quant.test: no visible global function definition for ‘pnorm’
quant.test: no visible global function definition for ‘setNames’
quant.test: no visible global function definition for ‘quantile’
quant.test: no visible global function definition for ‘phyper’
runs.test: no visible global function definition for ‘median’
runs.test: no visible global function definition for ‘setNames’
runs.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  complete.cases lines median par pbinom pchisq phyper pnorm qnorm qt
  quantile setNames
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "complete.cases", "median", "pbinom", "pchisq",
             "phyper", "pnorm", "qnorm", "qt", "quantile", "setNames")
to your NAMESPACE file.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘mvtnorm’ ‘combinat’
A package should be listed in only one of these fields.
chisq.test.a: no visible global function definition for ‘chisq.test’
maxsel: no visible global function definition for ‘complete.cases’
maxsel.asymp.test: no visible global function definition for
  ‘complete.cases’
Undefined global functions or variables:
  chisq.test complete.cases
Consider adding
  importFrom("stats", "chisq.test", "complete.cases")
to your NAMESPACE file.
prepare_Rd: maxsel.rd:27-29: Dropping empty section \details
prepare_Rd: transf.inter.rd:23-25: Dropping empty section \details
MDSplot: no visible global function definition for ‘par’
MDSplot: no visible global function definition for ‘rainbow’
MDSplot: no visible global function definition for ‘plot’
MDSplot: no visible global function definition for ‘pairs’
classCenter : <anonymous>: no visible binding for global variable
  ‘median’
grow.snpRF: no visible global function definition for ‘update’
na.roughfix.data.frame : roughfix: no visible global function
  definition for ‘median’
na.roughfix.default: no visible global function definition for ‘median’
outlier.default: no visible global function definition for ‘median’
outlier.default: no visible global function definition for ‘mad’
plot.margin: no visible global function definition for
  ‘installed.packages’
plot.margin: no visible global function definition for ‘rainbow’
plot.margin: no visible global function definition for ‘plot.default’
plot.snpRF: no visible global function definition for ‘matplot’
tuneSnpRF: no visible global function definition for ‘axis’
varImpPlot: no visible global function definition for ‘par’
varImpPlot: no visible global function definition for ‘dotchart’
varImpPlot: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  axis dotchart installed.packages mad matplot median mtext pairs par
  plot plot.default rainbow update
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "dotchart", "matplot", "mtext", "pairs",
             "par", "plot", "plot.default")
  importFrom("stats", "mad", "median", "update")
  importFrom("utils", "installed.packages")
to your NAMESPACE file.
File ‘snpRF/libs/snpRF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘colorspace’ ‘snpStats’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
check.args: no visible global function definition for ‘is’
write.sbams: no visible global function definition for ‘as’
write.sbams: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  as is write.table
Consider adding
  importFrom("methods", "as", "is")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘snpStatsWriter/libs/snpStatsWriter.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘SOAR/R/SOAR.R’:
  attach(NULL, pos, basename(directory))
See section ‘Good practice’ in ‘?attach’.
calculate.areas: no visible global function definition for ‘runif’
calculate.gradedareas: no visible global function definition for
  ‘rnorm’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
File ‘SocialNetworks/libs/SocialNetworks.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘SoDA’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing or unexported object: ‘base::WHAT’
Call with DUP:
   .Fortran("GEODISTV", as.double(lat1), as.double(lon1), as.double(lat2), 
       as.double(lon2), dist = double(nok), as.integer(nok), DUP = DUP, 
       PACKAGE = "SoDA")
DUP is no longer supported and will be ignored.
File ‘SoDA/libs/SoDA.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.
Packages in Depends field not imported from:
  ‘MASS’ ‘magic’ ‘ppls’ ‘psych’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
get.hnx.B.initialW: no visible global function definition for
  ‘normalize.vector’
get.hnx.B.initialW: no visible global function definition for ‘adiag’
hclust.wrap: no visible global function definition for ‘hclust’
hclust.wrap: no visible global function definition for ‘dist’
hclust.wrap: no visible global function definition for ‘cutree’
my.normdata.gen: no visible global function definition for ‘mvrnorm’
my.normdata.gen: no visible global function definition for ‘rnorm’
odc.clust: no visible binding for global variable ‘kmeans’
odc.cv: no visible global function definition for ‘ginv’
odc.optimallambda2: no visible global function definition for ‘tr’
odc.optimallambda2: no visible global function definition for ‘ginv’
odc.optimallambda2: no visible binding for global variable ‘sd’
sodc.clust: no visible binding for global variable ‘kmeans’
Undefined global functions or variables:
  adiag cutree dist ginv hclust kmeans mvrnorm normalize.vector rnorm
  sd tr
Consider adding
  importFrom("stats", "cutree", "dist", "hclust", "kmeans", "rnorm",
             "sd")
to your NAMESPACE file.
HardKMeansDemo: no visible global function definition for
  ‘graphics.off’
HardKMeansDemo: no visible global function definition for ‘plot’
HardKMeansDemo: no visible global function definition for ‘points’
initializeMeansMatrix: no visible global function definition for
  ‘runif’
initializeMeansMatrix: no visible global function definition for ‘dist’
normalizeMatrix: no visible global function definition for ‘sd’
plotRoughKMeans: no visible global function definition for
  ‘graphics.off’
plotRoughKMeans: no visible global function definition for ‘plot’
plotRoughKMeans: no visible global function definition for ‘points’
Undefined global functions or variables:
  dist graphics.off plot points runif sd
Consider adding
  importFrom("grDevices", "graphics.off")
  importFrom("graphics", "plot", "points")
  importFrom("stats", "dist", "runif", "sd")
to your NAMESPACE file.
Ssimpute.als: no visible global function definition for ‘rnorm’
Ssvd.als: no visible global function definition for ‘rnorm’
cs.default: no visible binding for global variable ‘weighted.mean’
simpute.als: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm weighted.mean
Consider adding
  importFrom("stats", "rnorm", "weighted.mean")
to your NAMESPACE file.
File ‘softImpute/libs/softImpute.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘chemometrics’ ‘spatstat’
  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.Spectra plot.ken.sto plot.trans predict.SpectraPoints
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.soma: no visible global function definition for ‘plot’
soma: no visible global function definition for ‘runif’
Undefined global functions or variables:
  plot runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
to your NAMESPACE file.
bm: no visible global function definition for ‘rnorm’
bm: no visible global function definition for ‘ts’
fbm: no visible global function definition for ‘fft’
fbm: no visible global function definition for ‘rnorm’
fbm: no visible global function definition for ‘ts’
gbm: no visible global function definition for ‘rnorm’
gbm: no visible global function definition for ‘ts’
Undefined global functions or variables:
  fft rnorm ts
Consider adding
  importFrom("stats", "fft", "rnorm", "ts")
to your NAMESPACE file.
getAlpha: no visible global function definition for ‘pbinom’
kfweOrd: no visible global function definition for ‘qnbinom’
Undefined global functions or variables:
  pbinom qnbinom
Consider adding
  importFrom("stats", "pbinom", "qnbinom")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from ‘someMTP’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
'library' or 'require' call to ‘hexbin’ which was already attached by Depends.
  Please remove these calls from your code.
hexbinpie: no visible global function definition for ‘quantile’
hexbinpie: no visible global function definition for ‘polygon’
hexbinpie: no visible global function definition for ‘text’
makehexbinplot: no visible global function definition for ‘rainbow’
makehexbinplot: no visible global function definition for ‘col2rgb’
makehexbinplot: no visible global function definition for ‘edit’
makehexbinplot: no visible global function definition for ‘dev.new’
makehexbinplot: no visible global function definition for ‘plot.new’
makehexbinplot: no visible global function definition for ‘plot.window’
makehexbinplot: no visible global function definition for ‘box’
makehexbinplot: no visible global function definition for ‘axis’
makehexbinplot: no visible global function definition for ‘legend’
som.plot: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  axis box col2rgb dev.new edit legend plot.new plot.window polygon
  quantile rainbow read.table text
Consider adding
  importFrom("grDevices", "col2rgb", "dev.new", "rainbow")
  importFrom("graphics", "axis", "box", "legend", "plot.new",
             "plot.window", "polygon", "text")
  importFrom("stats", "quantile")
  importFrom("utils", "edit", "read.table")
to your NAMESPACE file.
File ‘som/libs/som.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
dfrag: no visible global function definition for ‘qgeom’
dfrag: no visible global function definition for ‘plogis’
dfrag: no visible global function definition for ‘dgeom’
estAbund: no visible global function definition for ‘xtabs’
mmN : <anonymous>: no visible global function definition for ‘uniroot’
pfrag: no visible global function definition for ‘qgeom’
phi.deriv.default: no visible global function definition for
  ‘model.matrix’
phi.deriv.default: no visible binding for global variable ‘sd’
phi.update.default: no visible global function definition for ‘glm’
phi.update.default: no visible binding for global variable
  ‘quasipoisson’
phi.update.default: no visible global function definition for ‘predict’
phi.update.lframe: no visible global function definition for ‘glm’
phi.update.lframe: no visible binding for global variable
  ‘quasipoisson’
phi.update.lframe: no visible global function definition for ‘predict’
pr.y.given.x : <anonymous>: no visible global function definition for
  ‘dpois’
pr.y.given.x : <anonymous> : <anonymous>: no visible global function
  definition for ‘dpois’
pr.y.given.x : <anonymous>: no visible global function definition for
  ‘convolve’
qfrag: no visible global function definition for ‘qgeom’
rfrag: no visible global function definition for ‘qgeom’
simSonic: no visible global function definition for ‘rpois’
Undefined global functions or variables:
  convolve dgeom dpois glm model.matrix plogis predict qgeom
  quasipoisson rpois sd uniroot xtabs
Consider adding
  importFrom("stats", "convolve", "dgeom", "dpois", "glm",
             "model.matrix", "plogis", "predict", "qgeom",
             "quasipoisson", "rpois", "sd", "uniroot", "xtabs")
to your NAMESPACE file.
plot.soo_function: no visible global function definition for
  ‘terrain.colors’
plot.soo_function: no visible binding for global variable ‘image’
plot.soo_function: no visible binding for global variable ‘contour’
plot3d: no visible global function definition for ‘persp3d’
plot3d: no visible global function definition for ‘terrain.colors’
random_parameters.soo_function: no visible global function definition
  for ‘runif’
random_rotation_matrix: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  contour image persp3d runif terrain.colors
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "contour", "image")
  importFrom("stats", "runif")
to your NAMESPACE file.
File ‘soobench/libs/soobench.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.markdown’ ‘build_package.sh’ ‘upload.sh’
simdata_contaminated : <anonymous>: no visible global function
  definition for ‘rbinom’
simdata_uniform : multivariate_uniform : <anonymous>: no visible global
  function definition for ‘runif’
which_min: no visible global function definition for ‘head’
which_min: no visible global function definition for ‘tail’
Undefined global functions or variables:
  head rbinom runif tail
Consider adding
  importFrom("stats", "rbinom", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
convert_municipality_names: no visible global function definition for
  ‘read.csv’
regression_plot: no visible binding for global variable ‘loess’
regression_plot: no visible global function definition for
  ‘colorRampPalette’
regression_plot: no visible global function definition for
  ‘loess.control’
regression_plot: no visible global function definition for ‘predict’
regression_plot : <anonymous>: no visible global function definition
  for ‘quantile’
regression_plot : <anonymous>: no visible global function definition
  for ‘pnorm’
regression_plot: no visible global function definition for
  ‘flush.console’
regression_plot: no visible global function definition for ‘density’
Undefined global functions or variables:
  colorRampPalette density flush.console loess loess.control pnorm
  predict quantile read.csv
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "density", "loess", "loess.control", "pnorm",
             "predict", "quantile")
  importFrom("utils", "flush.console", "read.csv")
to your NAMESPACE file.
Package suggested but not available for checking: ‘SciencesPo’
File ‘SoundexBR/libs/SoundexBR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘r2cytoscape’
analyzeSP23Design: no visible global function definition for ‘plot’
exploreSP23Design: no visible global function definition for
  ‘txtProgressBar’
exploreSP23Design: no visible global function definition for
  ‘setTxtProgressBar’
generateClinicalTrialData : <anonymous>: no visible global function
  definition for ‘runif’
generateClinicalTrialData: no visible global function definition for
  ‘rbinom’
generateClinicalTrialData: no visible global function definition for
  ‘rexp’
mHP.b : crossingProbDiff: no visible global function definition for
  ‘pnorm’
mHP.b : crossingProbDiff: no visible global function definition for
  ‘Miwa’
mHP.b: no visible global function definition for ‘qnorm’
mHP.b: no visible global function definition for ‘uniroot’
mHP.c : crossingProbDiff: no visible global function definition for
  ‘Miwa’
mHP.c: no visible global function definition for ‘uniroot’
mHP.c: no visible global function definition for ‘qnorm’
performInterimLook: no visible global function definition for ‘optim’
performInterimLook: no visible global function definition for
  ‘constrOptim’
performInterimLook: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  Miwa constrOptim optim plot pnorm qnorm rbinom rexp runif
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "constrOptim", "optim", "pnorm", "qnorm", "rbinom",
             "rexp", "runif", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
SPA: no visible global function definition for ‘var’
Score.Test.Interact: no visible global function definition for ‘pchisq’
Score.Test.Overall: no visible global function definition for ‘var’
Score.Test.Overall: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq var
Consider adding
  importFrom("stats", "pchisq", "var")
to your NAMESPACE file.
File ‘SpaCCr/libs/SpaCCr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘Matrix’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Matrix’ ‘igraph’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'SJ.Rd':
  \examples lines wider than 100 characters:
     #with standard deviations of 1, 0.5 and 0.5, (i.e. giving more weight to linear association than quadratic or cubic)
     #Fit conditional independence graph at one lambda , using the default basis functions (cubic polynomials).
     plot(g, layout=mylayout, edge.color = "gray50", vertex.color = "red", vertex.size = 3, vertex.label = NA, edge.arrow.size = 0.4, main=" ... [TRUNCATED]

Rd file 'generate.dag.data.Rd':
  \usage lines wider than 90 characters:
     generate.dag.data(g, n, basesd = 1, basemean = 0, bfuns = function(x){cbind(x, x^2, x^3)}, 
  \examples lines wider than 100 characters:
     #with standard deviations of 1, 0.5 and 0.5, (i.e. giving more weight to linear association than quadratic or cubic)

Rd file 'spacejam-package.Rd':
  \examples lines wider than 100 characters:
     #with standard deviations of 1, 0.5 and 0.5, (i.e. giving more weight to linear association than quadratic or cubic)
     plot(g, layout=mylayout, edge.color = "gray50", vertex.color = "red", vertex.size = 3, vertex.label = NA, edge.arrow.size = 0.4, main=" ... [TRUNCATED]

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
GenPar: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Rd file 'space.joint.Rd':
  \examples lines wider than 100 characters:
     #################### view the network corresponding to the parcial correlation matrix in the simulation example
     #plot(temp, vertex.size=3, vertex.frame.color="white",layout=layout.fruchterman.reingold, vertex.label=NA, edge.color=grey(0.5))

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

These lines will be truncated in the PDF manual.
File ‘space/libs/space.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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’ ‘colorspace’ ‘picante’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'phy.dotplot.Rd':
  \usage lines wider than 90 characters:
     phy.dotplot(sp.plot, phy, edge.width = 0.2, lab.adj = c(0, 0), tips.adj = c(0.5, 3), tips.cex = 1.0, pch = 21, print.labs = FALSE, outf ... [TRUNCATED]

Rd file 'spacodi.by.nodes.Rd':
  \usage lines wider than 90 characters:
     spacodi.by.nodes(sp.plot, phy, sp.parm = "Bst", obs.only = FALSE, return.all = TRUE, n.rep = 10, method = "1s", parm = NULL, dmat = NUL ... [TRUNCATED]

Rd file 'spacodi.calc.Rd':
  \usage lines wider than 90 characters:
     spacodi.calc(sp.plot, phy = NULL, sp.traits = NULL, all.together = TRUE, prune = TRUE, pairwise = FALSE, ...)

Rd file 'spacodi.permutplot.Rd':
  \usage lines wider than 90 characters:
       spacodi.permutplot(spacodi.permutations, cex=list(pch=1.5, rand=0.1, node=0.5, legend=0.75), transp=0.8, col = list("black", "lightgr ... [TRUNCATED]
       bg = list("white", "lightgray", "black"), all.points = TRUE, add.id = TRUE, sig.plot = TRUE, cut.off = 0.05, envelope = FALSE, outfil ... [TRUNCATED]

Rd file 'spacodi.treeplot.Rd':
  \usage lines wider than 90 characters:
     spacodi.treeplot(spacodi.permutations, phy, cex=list(pch = 1.5, tip = 0.5, legend = 0.75), transp=0.8, sig.plot = TRUE, cut.off = 0.05, ... [TRUNCATED]

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
hausman: no visible global function definition for ‘pchisq’
span.formula: no visible global function definition for ‘model.frame’
span.formula: no visible global function definition for ‘model.matrix’
span.formula: no visible global function definition for
  ‘model.response’
spbe: no visible global function definition for ‘cor’
spbe: no visible global function definition for ‘pt’
spfe: no visible global function definition for ‘cor’
spfe: no visible global function definition for ‘pt’
sprandom: no visible global function definition for ‘cor’
sprandom: no visible global function definition for ‘pt’
summary.span: no visible global function definition for ‘printCoefmat’
Undefined global functions or variables:
  cor model.frame model.matrix model.response pchisq printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.frame", "model.matrix",
             "model.response", "pchisq", "printCoefmat", "pt")
to your NAMESPACE file.
plot.spa: no visible global function definition for ‘plot’
plot.spa: no visible global function definition for ‘lines’
plot.spa: no visible global function definition for ‘points’
plot.spa: no visible global function definition for ‘gray’
plot.spa: no visible global function definition for ‘box’
predict.spa: no visible global function definition for ‘fitted’
predict.spa: no visible global function definition for ‘coef’
spa.gcv: no visible global function definition for ‘density’
spa.gcv: no visible global function definition for ‘quantile’
spa.sim: no visible global function definition for ‘runif’
spa.sim: no visible global function definition for ‘rnorm’
spa.sim: no visible global function definition for ‘rbinom’
update.spa: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  box coef density fitted gray lines plot points quantile rbinom rnorm
  runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "box", "lines", "plot", "points")
  importFrom("stats", "coef", "density", "fitted", "quantile", "rbinom",
             "rnorm", "runif")
to your NAMESPACE file.
Rd file 'predict.spa.Rd':
  \examples lines wider than 100 characters:
     title(switch(attr(dat,"type"),moon="Two Moon Simulated Data",supervised="Supervised Border Simulated set"))

These lines will be truncated in the PDF manual.
File ‘sparc/libs/sparc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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’ ‘XML’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SPARQL : <anonymous>: no visible global function definition for
  ‘URLencode’
SPARQL: no visible binding for global variable ‘getURL’
SPARQL: no visible global function definition for ‘URLencode’
SPARQL: no visible binding for global variable ‘xmlParse’
SPARQL: no visible global function definition for ‘getNodeSet’
SPARQL: no visible global function definition for ‘xpathApply’
SPARQL: no visible binding for global variable ‘postForm’
get_attr: no visible global function definition for ‘getNodeSet’
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for ‘getNodeSet’
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for ‘xmlDoc’
get_value: no visible global function definition for ‘xmlDoc’
get_value: no visible global function definition for ‘xpathSApply’
get_value: no visible binding for global variable ‘xmlValue’
get_value: no visible global function definition for ‘xpathApply’
get_value: no visible binding for global variable ‘xmlGetAttr’
readCSVstring: no visible global function definition for ‘read.csv’
readTSVstring: no visible global function definition for ‘read.delim’
Undefined global functions or variables:
  URLencode getNodeSet getURL postForm read.csv read.delim xmlDoc
  xmlGetAttr xmlParse xmlValue xpathApply xpathSApply
Consider adding
  importFrom("utils", "URLencode", "read.csv", "read.delim")
to your NAMESPACE file.
f.I2.cont: no visible global function definition for ‘combn’
f.I2.dich: no visible global function definition for ‘combn’
f.pstar.cont: no visible global function definition for ‘combn’
f.pstar.dich: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
image.matrixBC: no visible global function definition for ‘dev.new’
image.matrixBC: no visible global function definition for ‘image’
image.matrixBC: no visible global function definition for ‘heat.colors’
image.matrixBC: no visible global function definition for ‘axis’
image.matrixBC: no visible global function definition for ‘title’
image.sparseBC: no visible global function definition for ‘dev.new’
image.sparseBC: no visible global function definition for ‘image’
image.sparseBC: no visible global function definition for ‘heat.colors’
image.sparseBC: no visible global function definition for ‘axis’
image.sparseBC: no visible global function definition for ‘tail’
image.sparseBC: no visible global function definition for ‘title’
matrixBC: no visible global function definition for ‘kmeans’
sparseBC: no visible global function definition for ‘kmeans’
sparseBC.choosekr: no visible global function definition for ‘kmeans’
sparseBC.choosekr: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  axis dev.new heat.colors image kmeans sd tail title
Consider adding
  importFrom("grDevices", "dev.new", "heat.colors")
  importFrom("graphics", "axis", "image", "title")
  importFrom("stats", "kmeans", "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
File ‘SparseFactorAnalysis/libs/SparseFactorAnalysis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
gev.impute: no visible global function definition for ‘rnorm’
gev.init: no visible global function definition for ‘rbinom’
gev.init: no visible global function definition for ‘var’
gev.init: no visible global function definition for ‘optimize’
gev.logscore: no visible global function definition for ‘density’
gev.logscore: no visible global function definition for ‘splinefun’
gev.update.M: no visible global function definition for ‘runif’
gev.update.hyper: no visible global function definition for ‘rgamma’
gev.update.lambda: no visible global function definition for ‘rnorm’
gev.update.lambda: no visible global function definition for ‘dgamma’
gev.update.lambda: no visible global function definition for ‘dnorm’
gev.update.lambda: no visible global function definition for ‘runif’
gev.update.tau.kappa: no visible global function definition for ‘rnorm’
gev.update.tau.kappa: no visible global function definition for ‘dnorm’
gev.update.tau.kappa: no visible global function definition for ‘runif’
gev.update.tau.mu: no visible global function definition for ‘rnorm’
gev.update.tau.mu: no visible global function definition for ‘dnorm’
gev.update.tau.mu: no visible global function definition for ‘runif’
gev.update.tau.xi: no visible global function definition for ‘rnorm’
gev.update.tau.xi: no visible global function definition for ‘dnorm’
gev.update.tau.xi: no visible global function definition for ‘runif’
gev.update.theta: no visible global function definition for ‘rnorm’
gp.like.lambda: no visible global function definition for ‘dgamma’
Undefined global functions or variables:
  density dgamma dnorm optimize rbinom rgamma rnorm runif splinefun var
Consider adding
  importFrom("stats", "density", "dgamma", "dnorm", "optimize", "rbinom",
             "rgamma", "rnorm", "runif", "splinefun", "var")
to your NAMESPACE file.
I2BR: no visible global function definition for ‘pnorm’
I2SmD2: no visible global function definition for ‘pnorm’
IBR: no visible global function definition for ‘pnorm’
ISmD2: no visible global function definition for ‘pnorm’
MestimatorBR: no visible global function definition for ‘optim’
MestimatorSmith: no visible global function definition for ‘optim’
psidotBR: no visible global function definition for ‘dnorm’
psidotBR: no visible global function definition for ‘pnorm’
psidotSmD2: no visible global function definition for ‘dnorm’
psidotSmD2: no visible global function definition for ‘pnorm’
tailBRInt: no visible global function definition for ‘pnorm’
tailSmithInt: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dnorm optim pnorm
Consider adding
  importFrom("stats", "dnorm", "optim", "pnorm")
to your NAMESPACE file.
File ‘spatialTailDep/libs/spatialTailDep.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
GenerateCliquesCovariance: no visible global function definition for
  ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
File ‘spcr/libs/spcr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘spDataLarge’
bartlett: no visible global function definition for ‘pchisq’
local.rbfdot: no visible binding for global variable ‘sd’
local.rbfdot: no visible global function definition for ‘dist’
local.rbfdot : <anonymous>: no visible global function definition for
  ‘median’
speccalt: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  dist kmeans median pchisq sd
Consider adding
  importFrom("stats", "dist", "kmeans", "median", "pchisq", "sd")
to your NAMESPACE file.
File ‘SpeciesMix/libs/SpeciesMix.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
ChaoBunge: no visible global function definition for ‘qnorm’
ChaoLee1992: no visible global function definition for ‘qnorm’
Pmix: no visible global function definition for ‘dpois’
PmixSCon: no visible global function definition for ‘dbeta’
bootPCG: no visible global function definition for ‘flush.console’
bootPCG: no visible global function definition for ‘quantile’
bootPnpmle: no visible global function definition for ‘flush.console’
bootPnpmle: no visible global function definition for ‘quantile’
bootUnpmle: no visible global function definition for ‘flush.console’
bootUnpmle: no visible global function definition for ‘quantile’
chao1984: no visible global function definition for ‘qnorm’
jackknife: no visible global function definition for ‘dbinom’
jackknife: no visible global function definition for ‘qnorm’
pcg: no visible global function definition for ‘flush.console’
unpmle: no visible global function definition for ‘flush.console’
untrunPmix: no visible global function definition for ‘dpois’
Undefined global functions or variables:
  dbeta dbinom dpois flush.console qnorm quantile
Consider adding
  importFrom("stats", "dbeta", "dbinom", "dpois", "qnorm", "quantile")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
File ‘SPECIES/libs/SPECIES.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘rcytoscapejs’
File ‘spectral/libs/spectral.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘leaps’ which was already attached by Depends.
  Please remove these calls from your code.
modSearch: no visible global function definition for ‘glm’
modSearch: no visible binding for global variable ‘binomial’
modSearch: no visible global function definition for ‘na.omit’
modSearch: no visible global function definition for ‘as.formula’
speff: no visible binding for global variable ‘na.pass’
speff: no visible global function definition for ‘model.matrix’
speff: no visible global function definition for ‘terms’
speff: no visible global function definition for ‘model.response’
speff: no visible global function definition for ‘as.formula’
speff: no visible global function definition for ‘predict’
speff: no visible global function definition for ‘na.omit’
speff: no visible global function definition for ‘glm’
speff: no visible binding for global variable ‘na.omit’
speffSurv: no visible global function definition for ‘model.matrix’
speffSurv: no visible global function definition for ‘terms’
speffSurv: no visible global function definition for ‘model.response’
speffSurv: no visible global function definition for ‘as.formula’
speffSurv: no visible global function definition for ‘uniroot’
summary.speff: no visible global function definition for ‘qnorm’
summary.speff: no visible global function definition for ‘pnorm’
summary.speffSurv: no visible global function definition for ‘qnorm’
summary.speffSurv: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as.formula binomial glm model.matrix model.response na.omit na.pass
  pnorm predict qnorm terms uniroot
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "model.matrix",
             "model.response", "na.omit", "na.pass", "pnorm", "predict",
             "qnorm", "terms", "uniroot")
to your NAMESPACE file.
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of ‘nr’ to ‘nrow’
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of ‘nc’ to ‘ncol’
spe: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
File ‘spe/libs/spe.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘rgl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pointsphere: no visible global function definition for ‘runif’
rgl.sphMW: no visible global function definition for ‘plot3d’
rgl.sphcirc: no visible global function definition for ‘rotate3d’
rgl.sphcirc: no visible global function definition for ‘lines3d’
rgl.sphgrid: no visible global function definition for ‘open3d’
rgl.sphgrid: no visible global function definition for ‘plot3d’
rgl.sphgrid: no visible global function definition for ‘lines3d’
rgl.sphgrid: no visible global function definition for ‘text3d’
rgl.sphpoints: no visible global function definition for ‘points3d’
rgl.sphsun: no visible global function definition for ‘plot3d’
rgl.sphtext: no visible global function definition for ‘text3d’
Undefined global functions or variables:
  lines3d open3d plot3d points3d rotate3d runif text3d
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
File ‘spikeSlabGAM/libs/spikeSlabGAM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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’ ‘parallel’ ‘randomForest’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘spikeslab/libs/spikeslab.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘quadprog’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘quadprog’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SPIn: no visible global function definition for ‘density’
SPIn: no visible global function definition for ‘quantile’
SPIn: no visible global function definition for ‘solve.QP’
bootSPIn: no visible global function definition for ‘runif’
plot.SPIn: no visible global function definition for ‘hist’
plot.SPIn: no visible global function definition for ‘lines’
plot.SPIn: no visible global function definition for ‘text’
plot.SPIn: no visible global function definition for ‘quantile’
plot.SPIn: no visible global function definition for ‘legend’
Undefined global functions or variables:
  density hist legend lines quantile runif solve.QP text
Consider adding
  importFrom("graphics", "hist", "legend", "lines", "text")
  importFrom("stats", "density", "quantile", "runif")
to your NAMESPACE file.
spi: no visible global function definition for ‘read.table’
spi: no visible global function definition for ‘ecdf’
spi: no visible global function definition for ‘qnorm’
spi: no visible global function definition for ‘colorRampPalette’
spi: no visible global function definition for ‘filled.contour’
spi: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis colorRampPalette ecdf filled.contour qnorm read.table
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "filled.contour")
  importFrom("stats", "ecdf", "qnorm")
  importFrom("utils", "read.table")
to your NAMESPACE file.
prepare_Rd: spi.Rd:117-119: Dropping empty section \note
prepare_Rd: spi.Rd:123-125: Dropping empty section \seealso
Rd file 'spi.Rd':
  \examples lines wider than 100 characters:
     spi(7,"spi.txt",1963,2010,"Standardized Precipitation Index - Rio Grande do Norte State",1,"years","months")

These lines will be truncated in the PDF manual.
File ‘splus2R/libs/splus2R.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
R2.global: no visible global function definition for ‘var’
calculer.var.exp: no visible global function definition for ‘var’
creer.noeud: no visible global function definition for ‘var’
ponderer.classe: no visible global function definition for ‘var’
ponderer.classe: no visible global function definition for ‘cov’
spodt: no visible global function definition for ‘model.frame’
spodt.tree: no visible global function definition for ‘plot.new’
spodt.tree: no visible global function definition for ‘par’
spodt.tree: no visible global function definition for ‘plot.window’
spodt.tree: no visible global function definition for ‘text’
spodt.tree: no visible global function definition for ‘segments’
test.spodt: no visible global function definition for ‘model.frame’
test.spodt: no visible global function definition for ‘hist’
test.spodt: no visible global function definition for ‘abline’
tracer.noeud: no visible global function definition for ‘text’
tracer.noeud: no visible global function definition for ‘segments’
Undefined global functions or variables:
  abline cov hist model.frame par plot.new plot.window segments text
  var
Consider adding
  importFrom("graphics", "abline", "hist", "par", "plot.new",
             "plot.window", "segments", "text")
  importFrom("stats", "cov", "model.frame", "var")
to your NAMESPACE file.
File ‘SPODT/libs/SPODT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Ell.Theta: no visible global function definition for ‘ell.theta’
confid.int.theta: no visible global function definition for ‘qchisq’
confid.int.theta : sim.c: no visible global function definition for
  ‘runif’
confid.int.theta: no visible global function definition for ‘quantile’
dd.est: no visible global function definition for ‘ecdf’
ks.sporm : Simul: no visible global function definition for ‘runif’
ks.stat: no visible global function definition for ‘ecdf’
plotor: no visible global function definition for ‘ecdf’
plotor: no visible global function definition for ‘plot’
test.theta: no visible global function definition for ‘ecdf’
test.theta : sim: no visible global function definition for ‘runif’
Undefined global functions or variables:
  ecdf ell.theta plot qchisq quantile runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "ecdf", "qchisq", "quantile", "runif")
to your NAMESPACE file.
prepare_Rd: H.Binv.Rd:48-50: Dropping empty section \note
prepare_Rd: V.theta.Rd:28-30: Dropping empty section \details
prepare_Rd: V.theta.Rd:43-45: Dropping empty section \note
prepare_Rd: V.theta.Rd:49-51: Dropping empty section \seealso
prepare_Rd: V.theta.Rd:52-53: Dropping empty section \examples
prepare_Rd: confid.int.theta.Rd:62-64: Dropping empty section \note
prepare_Rd: dd.est.Rd:39-41: Dropping empty section \note
prepare_Rd: dd.est.Rd:45-47: Dropping empty section \seealso
prepare_Rd: ell.theta.Rd:60-62: Dropping empty section \note
prepare_Rd: ell.theta.Rd:69-70: Dropping empty section \examples
prepare_Rd: grad.hessinv.Rd:47-49: Dropping empty section \note
prepare_Rd: ks.sporm.Rd:43-45: Dropping empty section \note
prepare_Rd: ks.stat.Rd:39-41: Dropping empty section \note
prepare_Rd: mrle.sporm.Rd:66-68: Dropping empty section \note
prepare_Rd: mrle.sporm.Rd:72-74: Dropping empty section \seealso
prepare_Rd: newton.theta.Rd:47-49: Dropping empty section \note
prepare_Rd: phi.Rd:32-38: Dropping empty section \value
prepare_Rd: phi.Rd:48-50: Dropping empty section \note
prepare_Rd: plotor.Rd:26-32: Dropping empty section \value
prepare_Rd: plotor.Rd:42-44: Dropping empty section \note
prepare_Rd: plotor.Rd:48-50: Dropping empty section \seealso
prepare_Rd: sporm-package.Rd:53-54: Dropping empty section \seealso
prepare_Rd: sporm-package.Rd:55-56: Dropping empty section \examples
prepare_Rd: test.theta.Rd:54-56: Dropping empty section \note
prepare_Rd: elltheta.rd:53-55: Dropping empty section \note
prepare_Rd: elltheta.rd:62-63: Dropping empty section \examples
fetch_NBAPlayerStatistics: no visible global function definition for
  ‘read.table’
Undefined global functions or variables:
  read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/spp.Rcheck/00install.out’ for details.
Found the following apparent S3 methods exported but not registered:
  coef.Lifedata.MLE coef.deglmx.MLE logLik.Lifedata.MLE plot.MICsplines
  print.Lifedata.MLE print.deglmx print.summary.Lifedata.MLE sqrt.mat
  summary.Lifedata.MLE
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'SlrArd.Rd':
  \usage lines wider than 90 characters:
     SlrArd(T, X, bias = TRUE, method = c("VB", "VBMacKay", "PX-VB"), control = list(), check.lb=TRUE, a0 = 0, b0 = 0, mu0 = 0, xi0 = 1)

These lines will be truncated in the PDF manual.
plot.SPRT: no visible global function definition for ‘par’
plot.SPRT: no visible global function definition for ‘plot’
plot.SPRT: no visible global function definition for ‘abline’
print.SPRT: no visible global function definition for ‘head’
Undefined global functions or variables:
  abline head par plot
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("utils", "head")
to your NAMESPACE file.
fssa20: no visible global function definition for ‘runif’
fssa2d: no visible global function definition for ‘runif’
fssa30: no visible global function definition for ‘runif’
fssa3d: no visible global function definition for ‘runif’
ssa20: no visible global function definition for ‘runif’
ssa2d: no visible global function definition for ‘runif’
ssa30: no visible global function definition for ‘runif’
ssa3d: no visible global function definition for ‘runif’
ssi20: no visible global function definition for ‘runif’
ssi2d: no visible global function definition for ‘runif’
ssi30: no visible global function definition for ‘runif’
ssi3d: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Rd file 'fssa30.Rd':
  \examples lines wider than 100 characters:
     main="Relative frequency distribution in the z=17 slice\n of anisotropic 3D clusters with (1,0)-neighborhood")

Rd file 'fssa3d.Rd':
  \examples lines wider than 100 characters:
     main="Relative frequency distribution in the z=17 slice\n of anisotropic 3D clusters with (1,1)-neighborhood")

Rd file 'fssi30.Rd':
  \examples lines wider than 100 characters:
     main="Relative frequency distribution in the z=17 slice\n of isotropic 3D clusters with (1,0)-neighborhood")

Rd file 'fssi3d.Rd':
  \examples lines wider than 100 characters:
     main="Relative frequency distribution in the z=17 slice\n of isotropic 3D clusters with (1,1)-neighborhood")

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
plotThin: no visible global function definition for ‘par’
plotThin: no visible global function definition for ‘dev.interactive’
plotThin: no visible global function definition for ‘plot’
plotThin: no visible global function definition for ‘hist’
thin: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  dev.interactive hist par plot write.csv
Consider adding
  importFrom("grDevices", "dev.interactive")
  importFrom("graphics", "hist", "par", "plot")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
sGda : <anonymous>: no visible global function definition for ‘cov’
sortgene: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  cov model.matrix
Consider adding
  importFrom("stats", "cov", "model.matrix")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘RJDBC’ ‘RMySQL’ ‘RODBC’ ‘RPostgreSQL’ ‘RSQLite’ ‘tcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
cacheQuery: no visible global function definition for ‘read.csv’
cacheQuery: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  read.csv write.csv
Consider adding
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
SQN: no visible binding for global variable ‘median’
SQN: no visible global function definition for ‘quantile’
SQN.demo.data: no visible global function definition for ‘rnorm’
mix.qn: no visible global function definition for ‘ecdf’
mix.qn: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  ecdf median quantile rnorm
Consider adding
  importFrom("stats", "ecdf", "median", "quantile", "rnorm")
to your NAMESPACE file.
plot.srafit: no visible global function definition for ‘layout’
plot.srafit: no visible global function definition for ‘par’
sraData : vartruncGauss : ff: no visible global function definition for
  ‘dnorm’
sraData : vartruncGauss : ff: no visible global function definition for
  ‘pnorm’
sraData : vartruncGauss: no visible global function definition for
  ‘uniroot’
sraPlotMean: no visible global function definition for ‘axis’
sraPlotMean: no visible global function definition for ‘points’
sraPlotMean: no visible global function definition for ‘lines’
sraPlotMeanResid: no visible global function definition for ‘axis’
sraPlotMeanResid: no visible global function definition for ‘abline’
sraPlotMeanResid: no visible global function definition for ‘points’
sraPlotVar: no visible global function definition for ‘axis’
sraPlotVar: no visible global function definition for ‘points’
sraPlotVar: no visible global function definition for ‘lines’
sraPlotVarResid: no visible global function definition for ‘axis’
sraPlotVarResid: no visible global function definition for ‘abline’
sraPlotVarResid: no visible global function definition for ‘points’
sraPlotlegend: no visible global function definition for ‘legend’
sraStartingvalues : sraStartingvalues.mu0: no visible global function
  definition for ‘rnorm’
sraStartingvalues : sraStartingvalues.logvarA0: no visible global
  function definition for ‘rnorm’
sraStartingvalues : sraStartingvalues.logvarE0: no visible global
  function definition for ‘rnorm’
sraStartingvalues: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline axis dnorm layout legend lines par pnorm points rnorm uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "layout", "legend", "lines",
             "par", "points")
  importFrom("stats", "dnorm", "pnorm", "rnorm", "uniroot")
to your NAMESPACE file.
Found the following hidden files and directories:
  .Rapp.history
  inst/script/.Rapp.history
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
File ‘sROC/R/onload.R’:
  .onLoad calls:
    packageStartupMessage("sROC 0.1-2 loaded")

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
ssd : correction_method_D: no visible global function definition for
  ‘rnorm’
ssd : generate_bootstrap: no visible global function definition for
  ‘rmultinom’
ssd : bootstrap_method: no visible global function definition for
  ‘median’
ssd : bootstrap_method: no visible global function definition for
  ‘quantile’
ssd : unbalanced_generate_bootstrap: no visible global function
  definition for ‘rmultinom’
ssd : unbalanced_bootstrap_method: no visible global function
  definition for ‘median’
ssd : unbalanced_bootstrap_method: no visible global function
  definition for ‘quantile’
ssd: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  median qchisq quantile rmultinom rnorm
Consider adding
  importFrom("stats", "median", "qchisq", "quantile", "rmultinom",
             "rnorm")
to your NAMESPACE file.
L_hNV: no visible global function definition for ‘pnorm’
L_hNV_rho: no visible global function definition for ‘pnorm’
eff.ssfa: no visible global function definition for ‘pnorm’
plot_fitted: no visible global function definition for ‘lines’
plot_moran: no visible global function definition for ‘residuals’
print.summary.ssfa: no visible global function definition for
  ‘printCoefmat’
ssfa: no visible global function definition for ‘model.frame’
ssfa: no visible global function definition for ‘model.response’
ssfa.fit: no visible global function definition for ‘lm’
ssfa.fit: no visible global function definition for ‘var’
ssfa.fit: no visible global function definition for ‘logLik’
summary.ssfa: no visible global function definition for ‘pnorm’
summary.ssfa: no visible global function definition for ‘logLik’
summary.ssfa: no visible global function definition for ‘pchisq’
summary.ssfa: no visible binding for global variable ‘df’
u.ssfa: no visible global function definition for ‘dnorm’
u.ssfa: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  df dnorm lines lm logLik model.frame model.response pchisq pnorm
  printCoefmat residuals var
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "df", "dnorm", "lm", "logLik", "model.frame",
             "model.response", "pchisq", "pnorm", "printCoefmat",
             "residuals", "var")
to your NAMESPACE file.
Package in Depends field not imported from: ‘survey’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fit.model: no visible global function definition for ‘hadamard’
Undefined global functions or variables:
  hadamard
mem.usage: no visible global function definition for ‘read.delim’
Undefined global functions or variables:
  read.delim
Consider adding
  importFrom("utils", "read.delim")
to your NAMESPACE file.
sslCoTrain: no visible global function definition for ‘predict’
sslSelfTrain: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
File ‘SSL/libs/SSL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.heckit5rob coef.heckitrob fitted.heckit5rob fitted.heckitrob
  print.heckit5rob print.heckitrob print.summary.heckit5rob
  print.summary.heckitrob residuals.heckit5rob residuals.heckitrob
  summary.heckit5rob summary.heckitrob vcov.heckit5rob vcov.heckitrob
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
map.world: no visible global function definition for ‘par’
map.world: no visible global function definition for ‘plot.new’
map.world: no visible global function definition for ‘plot.window’
map.world: no visible global function definition for ‘lines’
map.world: no visible global function definition for ‘title’
map.world: no visible global function definition for ‘axis’
map.world: no visible global function definition for ‘box’
plot.smooth.sspline: no visible global function definition for
  ‘predict’
plot.smooth.sspline: no visible global function definition for
  ‘filled.contour’
plot.smooth.sspline: no visible binding for global variable
  ‘terrain.colors’
plot.smooth.sspline: no visible global function definition for ‘title’
plot.smooth.sspline: no visible global function definition for ‘axis’
station: no visible binding for global variable ‘WTdiff’
station: no visible global function definition for ‘points’
Undefined global functions or variables:
  WTdiff axis box filled.contour lines par plot.new plot.window points
  predict terrain.colors title
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "axis", "box", "filled.contour", "lines", "par",
             "plot.new", "plot.window", "points", "title")
  importFrom("stats", "predict")
to your NAMESPACE file.
File ‘sspline/libs/sspline.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
SS.ID: no visible global function definition for ‘var’
SS.sim.chol: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm var
Consider adding
  importFrom("stats", "rnorm", "var")
to your NAMESPACE file.
error.est : <anonymous>: no visible global function definition for
  ‘median’
holm.robust: no visible global function definition for ‘pnorm’
holm.robust: no visible global function definition for ‘median’
holm.robust: no visible global function definition for ‘mad’
huberize: no visible global function definition for ‘quantile’
ssvd.initial: no visible global function definition for ‘mad’
ssvd.iter.thresh: no visible global function definition for ‘mad’
Undefined global functions or variables:
  mad median pnorm quantile
Consider adding
  importFrom("stats", "mad", "median", "pnorm", "quantile")
to your NAMESPACE file.
.ls.objects: no visible binding for global variable ‘object.size’
Undefined global functions or variables:
  object.size
Consider adding
  importFrom("utils", "object.size")
to your NAMESPACE file.
.expandLevels: no visible global function definition for ‘na.omit’
.ffStack: no visible global function definition for ‘na.omit’
.ffffStack: no visible global function definition for ‘na.omit’
Stack : <anonymous>: no visible global function definition for
  ‘na.omit’
ffStack,ffdf-data.frame: no visible global function definition for
  ‘na.omit’
ffStack,ffdf-ffdf: no visible global function definition for ‘na.omit’
ffStack,ffdf-list: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
genericPlot: no visible global function definition for ‘dev.new’
genericPlot: no visible global function definition for ‘par’
genericPlot: no visible global function definition for ‘rainbow’
genericPlot: no visible global function definition for ‘plot’
genericPlot: no visible global function definition for ‘lines’
genericPlot: no visible global function definition for ‘legend’
genericPlot: no visible global function definition for ‘dev.copy2pdf’
genericPlot: no visible global function definition for ‘dev.copy2eps’
genericPlot: no visible global function definition for ‘dev.print’
genericPlot: no visible binding for global variable ‘png’
genericPlot: no visible binding for global variable ‘tiff’
plotStrains: no visible global function definition for ‘rainbow’
plotStrains: no visible global function definition for ‘dev.new’
plotStrains: no visible global function definition for ‘par’
plotStrains: no visible global function definition for ‘plot’
plotStrains: no visible global function definition for ‘lines’
plotStrains: no visible global function definition for ‘legend’
plotStrains: no visible global function definition for ‘dev.copy2pdf’
plotStrains: no visible global function definition for ‘dev.copy2eps’
plotStrains: no visible global function definition for ‘dev.print’
plotStrains: no visible binding for global variable ‘png’
plotStrains: no visible binding for global variable ‘tiff’
Undefined global functions or variables:
  dev.copy2eps dev.copy2pdf dev.new dev.print legend lines par plot png
  rainbow tiff
Consider adding
  importFrom("grDevices", "dev.copy2eps", "dev.copy2pdf", "dev.new",
             "dev.print", "png", "rainbow", "tiff")
  importFrom("graphics", "legend", "lines", "par", "plot")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘Licence’
'library' or 'require' calls to packages already attached by Depends:
  ‘np’ ‘sp’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘np’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
stkde: no visible global function definition for ‘npudensbw’
stkde: no visible global function definition for ‘npudens’
stkde: no visible global function definition for ‘quantile’
stkde: no visible global function definition for ‘heat.colors’
stkde: no visible global function definition for ‘par’
stkde: no visible global function definition for ‘image’
stkde: no visible global function definition for ‘contour’
stkde.base: no visible global function definition for ‘npudensbw’
stkde.base: no visible global function definition for ‘npudens’
stkde.sig: no visible global function definition for ‘SpatialPoints’
stkde.sig: no visible global function definition for ‘spsample’
stkde.sig: no visible global function definition for ‘bbox’
stkde.sig: no visible global function definition for ‘quantile’
stkde.sig: no visible global function definition for ‘heat.colors’
stkde.sig: no visible global function definition for ‘par’
stkde.sig: no visible global function definition for ‘image’
stkde.sig: no visible global function definition for ‘contour’
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.

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

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

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

These lines will be truncated in the PDF manual.
File ‘starma/libs/starma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘codetools’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘codetools’ ‘gss’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘STAR/libs/STAR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  inst/.Renviron.d
  inst/.Rprofile.d
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  print.corsign
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
actvspred: no visible global function definition for ‘quantile’
actvspred: no visible global function definition for ‘aggregate’
actvspred: no visible global function definition for ‘par’
actvspred: no visible global function definition for ‘plot’
actvspred: no visible global function definition for ‘lines’
auc: no visible global function definition for ‘par’
auc: no visible global function definition for ‘plot’
decile: no visible global function definition for ‘quantile’
dqcontinuous : numoutliers: no visible global function definition for
  ‘quantile’
dqcontinuous : <anonymous>: no visible global function definition for
  ‘sd’
dqcontinuous : <anonymous>: no visible global function definition for
  ‘quantile’
gini: no visible global function definition for ‘par’
gini: no visible global function definition for ‘plot’
gini: no visible global function definition for ‘abline’
iv: no visible global function definition for ‘quantile’
iv: no visible global function definition for ‘aggregate’
ks: no visible global function definition for ‘aggregate’
ks: no visible global function definition for ‘par’
ks: no visible global function definition for ‘plot’
ks: no visible global function definition for ‘lines’
outliers: no visible global function definition for ‘quantile’
outliers: no visible global function definition for ‘na.omit’
pentile: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline aggregate lines na.omit par plot quantile sd
Consider adding
  importFrom("graphics", "abline", "lines", "par", "plot")
  importFrom("stats", "aggregate", "na.omit", "quantile", "sd")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘statnet’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘statnet’
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/statnet.Rcheck/00install.out’ for details.
inspect: no visible global function definition for ‘par’
inspect: no visible global function definition for ‘abline’
inspect: no visible global function definition for ‘lines’
inspect: no visible global function definition for ‘points’
plotfit: no visible global function definition for ‘dev.off’
plotfit: no visible global function definition for ‘par’
plotfit: no visible global function definition for ‘lines’
plotfit: no visible global function definition for ‘points’
plotfit: no visible global function definition for ‘legend’
plothill: no visible global function definition for ‘par’
plothill: no visible global function definition for ‘abline’
plothill: no visible global function definition for ‘points’
plotmultifit: no visible global function definition for ‘par’
plotmultifit: no visible global function definition for ‘lines’
plotmultifit: no visible global function definition for ‘points’
plotmultifit: no visible global function definition for ‘pexp’
plotmultifit: no visible global function definition for ‘plnorm’
plotmultifit: no visible global function definition for ‘ppois’
plotmultifit: no visible global function definition for ‘legend’
plotols: no visible global function definition for ‘dev.off’
plotols: no visible global function definition for ‘lm’
plotols: no visible global function definition for ‘par’
plotols: no visible global function definition for ‘abline’
plotols: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline dev.off legend lines lm par pexp plnorm points ppois
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("graphics", "abline", "legend", "lines", "par", "points")
  importFrom("stats", "lm", "pexp", "plnorm", "ppois")
to your NAMESPACE file.
File ‘staTools/libs/staTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
getStp: no visible global function definition for ‘lm’
plot.steeptest: no visible global function definition for ‘plot’
plot.steeptest: no visible global function definition for ‘axis’
plot.steeptest: no visible global function definition for ‘box’
plot.steeptest: no visible global function definition for ‘lm’
plot.steeptest: no visible global function definition for ‘abline’
plot.steeptest: no visible global function definition for ‘legend’
plot.steeptest: no visible global function definition for
  ‘as.graphicsAnnot’
steeptest: no visible global function definition for ‘lm’
summary.steeptest: no visible global function definition for ‘var’
summary.steeptest: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline as.graphicsAnnot axis box legend lm plot quantile var
Consider adding
  importFrom("grDevices", "as.graphicsAnnot")
  importFrom("graphics", "abline", "axis", "box", "legend", "plot")
  importFrom("stats", "lm", "quantile", "var")
to your NAMESPACE file.
File ‘steepness/libs/steepness.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Stem.Bootstrap: no visible global function definition for ‘runif’
filtering: no visible global function definition for ‘is.ts’
filtering: no visible global function definition for ‘ts’
filtering: no visible global function definition for ‘start’
filtering: no visible global function definition for ‘end’
filtering: no visible global function definition for ‘frequency’
kalman: no visible global function definition for ‘ts’
smoothing: no visible global function definition for ‘is.ts’
smoothing: no visible global function definition for ‘ts’
smoothing: no visible global function definition for ‘start’
smoothing: no visible global function definition for ‘end’
smoothing: no visible global function definition for ‘frequency’
Undefined global functions or variables:
  end frequency is.ts runif start ts
Consider adding
  importFrom("stats", "end", "frequency", "is.ts", "runif", "start",
             "ts")
to your NAMESPACE file.
File ‘stepwise/libs/stepwise.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
d1spectrum: no visible global function definition for ‘fft’
d2spectrum: no visible global function definition for ‘fft’
plot.d1nat: no visible global function definition for ‘plot’
plot.d1nat: no visible global function definition for ‘lines’
plot.d1nat: no visible global function definition for ‘legend’
plot.d1nat: no visible global function definition for ‘title’
plot.d1spec: no visible global function definition for ‘plot’
plot.d1spec: no visible global function definition for ‘lines’
plot.d1spec: no visible global function definition for ‘legend’
plot.d1spec: no visible global function definition for ‘title’
plot.d2spec: no visible global function definition for ‘plot’
plot.d2spec: no visible global function definition for ‘lines’
plot.d2spec: no visible global function definition for ‘legend’
plot.d2spec: no visible global function definition for ‘title’
plot.pvalign: no visible global function definition for ‘plot’
plot.pvalign: no visible global function definition for ‘lines’
plot.pvalign: no visible global function definition for ‘legend’
plot.pvalign: no visible global function definition for ‘title’
print.d1nat: no visible global function definition for ‘plot’
print.d1spec: no visible global function definition for ‘plot’
print.d2spec: no visible global function definition for ‘plot’
print.pvalign: no visible global function definition for ‘plot’
utild1bin: no visible global function definition for ‘median’
utild1bin: no visible global function definition for ‘sd’
utild1clean: no visible global function definition for ‘sd’
utild1filt: no visible global function definition for ‘convolve’
Undefined global functions or variables:
  convolve fft legend lines median plot sd title
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "title")
  importFrom("stats", "convolve", "fft", "median", "sd")
to your NAMESPACE file.
File ‘stlplus/libs/stlplus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
myQQNorm: no visible global function definition for ‘mad’
myQQNorm: no visible global function definition for ‘qnorm’
myQQNorm: no visible global function definition for ‘plot’
myQQNorm: no visible global function definition for ‘matlines’
myQQNorm: no visible global function definition for ‘points’
myQQNorm: no visible global function definition for ‘qqline’
myQQNorm: no visible global function definition for ‘box’
qqnormSim,lm: no visible global function definition for ‘resid’
Undefined global functions or variables:
  box mad matlines plot points qnorm qqline resid
Consider adding
  importFrom("graphics", "box", "matlines", "plot", "points")
  importFrom("stats", "mad", "qnorm", "qqline", "resid")
to your NAMESPACE file.
File ‘StMoSim/libs/StMoSim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 'calc.stoich.coef.Rd':
  \usage lines wider than 90 characters:
     calc.stoich.coef(alpha, name, subst, subst.norm, nu.norm = 1, constraints = list(), eps = 1e-5, verbose = TRUE)

These lines will be truncated in the PDF manual.
StratPhyloCongruence: no visible global function definition for ‘runif’
StratPhyloCongruence: no visible global function definition for
  ‘txtProgressBar’
StratPhyloCongruence: no visible global function definition for
  ‘setTxtProgressBar’
StratPhyloCongruence: no visible global function definition for ‘pnorm’
StratPhyloCongruence: no visible global function definition for ‘sd’
geoscalePhylo: no visible global function definition for ‘data’
geoscalePhylo: no visible global function definition for ‘par’
geoscalePhylo: no visible global function definition for ‘text’
geoscalePhylo: no visible global function definition for ‘segments’
geoscalePhylo: no visible global function definition for ‘rect’
geoscalePhylo: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  data par pnorm rect rgb runif sd segments setTxtProgressBar text
  txtProgressBar
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "par", "rect", "segments", "text")
  importFrom("stats", "pnorm", "runif", "sd")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
File ‘strat/libs/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.
Package suggested but not available for checking: ‘samr’
Found the following significant warnings:
  BIRCH/CFTree.cpp:18:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to true [-Wtautological-undefined-compare]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/stream.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘STRaitRazoR’
breakpoints.formula: no visible global function definition for
  ‘%dopar%’
breakpoints.formula: no visible binding for global variable ‘i’
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
sctest.default: no visible global function definition for ‘tail’
Undefined global functions or variables:
  %dopar% i tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
PlotHypTree: no visible global function definition for ‘browseURL’
treePValues: no visible global function definition for ‘lm’
treePValues: no visible global function definition for ‘pf’
plot,GBH-ANY: no visible binding for global variable ‘sorted.hyp’
plot,GBH-ANY: no visible binding for global variable ‘pval’
plot,GBH-ANY: no visible binding for global variable ‘group’
plot,GBH-ANY: no visible binding for global variable ‘type’
Undefined global functions or variables:
  browseURL group lm pf pval sorted.hyp type
Consider adding
  importFrom("stats", "lm", "pf")
  importFrom("utils", "browseURL")
to your NAMESPACE file.
Running examples in ‘structSSI-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EstimatedHFDRControl
> ### Title: Estimate FDR control variations for HFDR procedure
> ### Aliases: EstimatedHFDRControl
> ### Keywords: ~htest
> 
> ### ** Examples
> 
> library('igraph')

Attaching package: ‘igraph’

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

    decompose, spectrum

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

    union

> library('ape')

Attaching package: ‘ape’

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

    edges, mst, ring

> 
> alternative.indices <- sample(1:49, 30)
> unadj.p.values <- vector("numeric", length = 49)
> unadj.p.values[alternative.indices] <- runif(30, 0, 0.01)
> unadj.p.values[-alternative.indices] <- runif(19, 0, 1)
> unadj.p.values[c(1:5)] <- runif(5, 0, 0.01)
> names(unadj.p.values) <- paste("Hyp ", c(1:49))
> 
> tree <- as.igraph(rtree(25))
Error in UseMethod("as.igraph") : 
  no applicable method for 'as.igraph' applied to an object of class "phylo"
Calls: as.igraph
Execution halted
Running ‘testGBHProcedures.R’ [4s/5s]
  Running ‘testHierarchicalMethods.R’ [4s/4s]
Running the tests in ‘tests/testHierarchicalMethods.R’ failed.
Complete output:
  > ## Test the hypothesesTree creation class.
  > 
  > set.seed(130229)
  > library('structSSI')
  > library('ape')
  > library('igraph')
  
  Attaching package: 'igraph'
  
  The following objects are masked from 'package:ape':
  
      edges, mst, ring
  
  The following objects are masked from 'package:stats':
  
      decompose, spectrum
  
  The following object is masked from 'package:base':
  
      union
  
  > tree.1 <- as.igraph(rtree(10))
  Error in UseMethod("as.igraph") : 
    no applicable method for 'as.igraph' applied to an object of class "phylo"
  Calls: as.igraph
  Execution halted
File ‘strum/libs/strum.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘stsm.class’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
stsm.model: no visible global function definition for ‘is.ts’
stsm.model: no visible global function definition for ‘var’
stsm.model: no visible global function definition for ‘frequency’
stsm.model: no visible global function definition for ‘na.omit’
stsm.model: no visible global function definition for ‘fft’
stsm.model: no visible global function definition for ‘new’
stsm.sgf: no visible global function definition for ‘frequency’
char2numeric,stsm: no visible global function definition for
  ‘frequency’
set.cpar,stsm: no visible global function definition for ‘validObject’
set.nopars,stsm: no visible global function definition for
  ‘validObject’
set.pars,stsm: no visible global function definition for ‘validObject’
transPars,stsm: no visible global function definition for ‘var’
Undefined global functions or variables:
  fft frequency is.ts na.omit new validObject var
Consider adding
  importFrom("methods", "new", "validObject")
  importFrom("stats", "fft", "frequency", "is.ts", "na.omit", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘stsm/libs/stsm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.sublasso
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
SubLasso: no visible global function definition for ‘predict’
SubLasso: no visible global function definition for ‘coef’
SubLasso: no visible global function definition for ‘dev.new’
SubLasso: no visible global function definition for ‘cor’
SubLasso: no visible global function definition for ‘boxplot’
predict.sublasso: no visible global function definition for ‘predict’
Undefined global functions or variables:
  boxplot coef cor dev.new predict
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "boxplot")
  importFrom("stats", "coef", "cor", "predict")
to your NAMESPACE file.
identifyGraph: no visible global function definition for ‘phyper’
mytriangle: no visible global function definition for ‘symbols’
plotGraph: no visible global function definition for ‘par’
plotGraph: no visible global function definition for ‘plot’
updateOrgEnvir: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  par phyper plot read.table symbols
Consider adding
  importFrom("graphics", "par", "plot", "symbols")
  importFrom("stats", "phyper")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  predict.subsemble
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
predict.subsemble: no visible global function definition for ‘predict’
predict.subsemble: no visible binding for global variable ‘family’
subsemble: no visible global function definition for ‘gaussian’
subsemble: no visible global function definition for ‘detectCores’
subsemble : .make_Z_l: no visible global function definition for
  ‘parSapply’
subsemble : .make_Z_l: no visible global function definition for
  ‘makeCluster’
subsemble : .make_Z_l: no visible global function definition for
  ‘stopCluster’
subsemble: no visible global function definition for ‘parSapply’
subsemble: no visible global function definition for ‘makeCluster’
subsemble: no visible global function definition for ‘stopCluster’
subsemble: no visible global function definition for ‘predict’
Undefined global functions or variables:
  detectCores family gaussian makeCluster parSapply predict stopCluster
Consider adding
  importFrom("stats", "family", "gaussian", "predict")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘ROCR’ ‘penalized’
  Please remove these calls from your code.
ELF: no visible global function definition for ‘pt’
ELF: no visible global function definition for ‘qnorm’
ELF: no visible global function definition for ‘lm’
ELF: no visible global function definition for ‘lowess’
ELF: no visible global function definition for ‘dnorm’
ELF: no visible global function definition for ‘approx’
subtype: no visible global function definition for ‘runif’
subtype: no visible global function definition for ‘hclust’
subtype: no visible global function definition for ‘dist’
subtype: no visible global function definition for ‘cutree’
subtype: no visible global function definition for ‘pt’
subtype: no visible global function definition for ‘heatmap’
test_subtype_only: no visible global function definition for ‘pt’
test_subtype_only: no visible global function definition for ‘survdiff’
test_subtype_only: no visible global function definition for ‘survfit’
test_subtype_only: no visible global function definition for ‘title’
ufun: no visible global function definition for ‘dnorm’
ufun: no visible global function definition for ‘lowess’
Undefined global functions or variables:
  approx cutree dist dnorm hclust heatmap lm lowess pt qnorm runif
  survdiff survfit title
Consider adding
  importFrom("graphics", "title")
  importFrom("stats", "approx", "cutree", "dist", "dnorm", "hclust",
             "heatmap", "lm", "lowess", "pt", "qnorm", "runif")
to your NAMESPACE file.
Rd file 'subtype.Rd':
  \usage lines wider than 90 characters:
     subtype(GEset, outcomeLabels, treatment=NULL, Npermutes=10, Nchunks = 25, minClusterSizeB = 20, NclustersASet = 100, FDRpermutation = T ... [TRUNCATED]
  \examples lines wider than 100 characters:
     summary(A,f.out=0)  ### f.out can be used for filtering out uninteresting subtypes. e.g. if f.out=2, we ignore subtypes having N01_0<=2 ... [TRUNCATED]

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

These lines will be truncated in the PDF manual.
'library' or 'require' call to ‘tkrplot’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
playSudoku : replot: no visible global function definition for ‘par’
playSudoku : replot: no visible global function definition for ‘plot’
playSudoku : replot: no visible global function definition for
  ‘segments’
playSudoku : replot: no visible global function definition for ‘text’
playSudoku: no visible global function definition for ‘tktoplevel’
playSudoku: no visible global function definition for ‘tkwm.title’
playSudoku: no visible global function definition for ‘tkrplot’
playSudoku: no visible global function definition for ‘tktext’
playSudoku: no visible global function definition for ‘tkscrollbar’
playSudoku : <anonymous>: no visible global function definition for
  ‘tkyview’
playSudoku: no visible global function definition for ‘tkconfigure’
playSudoku : <anonymous>: no visible global function definition for
  ‘tkset’
playSudoku: no visible global function definition for ‘tkpack’
playSudoku: no visible global function definition for ‘tcl’
playSudoku: no visible global function definition for ‘tkcget’
playSudoku : showz: no visible global function definition for
  ‘tkrreplot’
playSudoku : type: no visible global function definition for ‘tkinsert’
playSudoku : type: no visible global function definition for ‘tksee’
playSudoku : kb: no visible global function definition for ‘tkdestroy’
playSudoku: no visible global function definition for
  ‘getGraphicsEvent’
playSudoku: no visible global function definition for ‘tkbind’
playSudoku: no visible global function definition for ‘tkwait.window’
Undefined global functions or variables:
  getGraphicsEvent par plot segments tcl text tkbind tkcget tkconfigure
  tkdestroy tkinsert tkpack tkrplot tkrreplot tkscrollbar tksee tkset
  tktext tktoplevel tkwait.window tkwm.title tkyview
Consider adding
  importFrom("grDevices", "getGraphicsEvent")
  importFrom("graphics", "par", "plot", "segments", "text")
to your NAMESPACE file.
SUE.fitted.values: no visible global function definition for
  ‘model.frame’
SUE.lm: no visible global function definition for ‘model.frame’
SUE.lm: no visible global function definition for ‘lm’
SUE.lm: no visible global function definition for ‘anova’
SUE.plot: no visible global function definition for ‘plot’
SUE.residuals: no visible global function definition for ‘model.frame’
parameters : para2: no visible global function definition for ‘uniroot’
parameters: no visible global function definition for ‘optimize’
parameters: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  anova lm model.frame optimize plot uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "anova", "lm", "model.frame", "optimize",
             "uniroot")
to your NAMESPACE file.
Rd file 'SUE.lm.Rd':
  \examples lines wider than 100 characters:
     ##We analysis the well known stackloss data by using ordinary linear method and the subsampling method. 
     ##proportion of outliers in the data. The subsample size is chosen to be the default size of ns = 11.
     plot(SUE.fitted.values(a2),SUE.residuals(a2),xlab="(b) fitted values",ylab="residuals",ylim=c(-12,12))
     plot(SUE.fitted.values(a3),SUE.residuals(a3),xlab="(c) fitted values",ylab="residuals",ylim=c(-12,12))

These lines will be truncated in the PDF manual.
MCMCCV: no visible global function definition for ‘rnorm’
MLCVGauss: no visible global function definition for ‘runif’
MLCVGauss: no visible global function definition for ‘optim’
SimSunderData: no visible global function definition for ‘runif’
SimSunderData: no visible global function definition for ‘dist’
SimSunderData: no visible global function definition for ‘rnorm’
SimSunderData: no visible global function definition for ‘qgamma’
SimSunderData: no visible global function definition for ‘pnorm’
SimSunderData: no visible global function definition for ‘rmultinom’
Undefined global functions or variables:
  dist optim pnorm qgamma rmultinom rnorm runif
Consider adding
  importFrom("stats", "dist", "optim", "pnorm", "qgamma", "rmultinom",
             "rnorm", "runif")
to your NAMESPACE file.
File ‘Sunder/libs/Sunder.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
sunter: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
supcluster : itgamma: no visible global function definition for
  ‘rgamma’
supcluster : itgamma: no visible global function definition for
  ‘dgamma’
supcluster : itgamma: no visible global function definition for ‘runif’
supcluster : itbeta: no visible global function definition for ‘rnorm’
supcluster : itbeta: no visible global function definition for ‘runif’
supcluster : itj: no visible global function definition for ‘dmultinom’
supcluster: no visible global function definition for ‘kmeans’
tab1: no visible global function definition for ‘image’
tab1: no visible global function definition for ‘gray’
tab1: no visible global function definition for ‘var’
Undefined global functions or variables:
  dgamma dmultinom gray image kmeans rgamma rnorm runif var
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "image")
  importFrom("stats", "dgamma", "dmultinom", "kmeans", "rgamma", "rnorm",
             "runif", "var")
to your NAMESPACE file.
Call with DUP:
   .C(R_clusterer, E = as.double(E), X = as.double(X), W = as.double(W), 
       P = as.double(P), y = as.double(y), prob = as.double(prob), 
       theta = as.double(theta), lambda = as.double(lambda * n), 
       n = as.integer(n), g = as.integer(g), m = as.integer(m), 
       p = as.integer(p), critflag = as.integer(critflag), penflag = as.integer(penflag), 
       blockflag = as.integer(blockflag), valiflag = as.integer(valiflag), 
       traceflag = as.integer(trace), genliste = integer(lSize), 
       kriterium = double(lSize), DUP = FALSE)
DUP is no longer supported and will be ignored.
File ‘supclust/libs/supclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘gputools’
HCLtree: no visible global function definition for ‘hclust’
HCLtree: no visible global function definition for ‘as.dist’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘matplot’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘matlines’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘axis’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘box’
plotProfilesWithinBicluster: no visible global function definition for
  ‘matplot’
plotProfilesWithinBicluster: no visible global function definition for
  ‘title’
plotProfilesWithinBicluster: no visible global function definition for
  ‘axis’
plotProfilesWithinBicluster: no visible global function definition for
  ‘par’
plotProfilesWithinBicluster: no visible global function definition for
  ‘box’
plotProfilesWithinBicluster: no visible global function definition for
  ‘matlines’
plotProfilesWithinBicluster: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  as.dist axis box hclust legend matlines matplot par title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "matlines", "matplot",
             "par", "title")
  importFrom("stats", "as.dist", "hclust")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘boa’ ‘coda’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
superdiag: no visible global function definition for ‘as.mcmc.list’
superdiag: no visible global function definition for ‘as.mcmc’
superdiag: no visible global function definition for ‘runif’
superdiag: no visible global function definition for ‘geweke.diag’
superdiag: no visible global function definition for ‘heidel.diag’
superdiag: no visible global function definition for ‘raftery.diag’
superdiag: no visible global function definition for ‘gelman.diag’
Undefined global functions or variables:
  as.mcmc as.mcmc.list gelman.diag geweke.diag heidel.diag raftery.diag
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
TrainSuperMDS: no visible global function definition for ‘rnorm’
TrainSuperMDSOnce: no visible global function definition for ‘cmdscale’
TrainSuperMDSOnce: no visible global function definition for ‘quantile’
distmat: no visible global function definition for ‘dist’
Undefined global functions or variables:
  cmdscale dist quantile rnorm
Consider adding
  importFrom("stats", "cmdscale", "dist", "quantile", "rnorm")
to your NAMESPACE file.
Found the following significant warnings:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SuppDists.Rcheck/00install.out’ for details.
File ‘SuppDists/libs/SuppDists.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/copulas-concordance.tex’
   ‘vignettes/surrosurv.tex’
(Is a VignetteBuilder field missing?)
Found the following apparent S3 methods exported but not registered:
  print.SurvAM
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Est.Var.CCH.trueweights: no visible binding for global variable ‘var’
getEstimatesSP: no visible global function definition for ‘quantile’
getEstimatesSP: no visible global function definition for ‘resid’
prepareDataNP: no visible global function definition for
  ‘complete.cases’
prepareDataSP: no visible global function definition for
  ‘complete.cases’
processRawOutput: no visible global function definition for ‘qnorm’
survAM.estimate: no visible global function definition for ‘median’
survAM.estimate: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  complete.cases median qnorm quantile resid sd var
Consider adding
  importFrom("stats", "complete.cases", "median", "qnorm", "quantile",
             "resid", "sd", "var")
to your NAMESPACE file.
File ‘survAccuracyMeasures/libs/survAccuracyMeasures.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

plot.survAUC: no visible global function definition for ‘plot’
plot.survAUC: no visible global function definition for ‘lines’
plot.survErr: no visible global function definition for ‘plot’
plot.survErr: no visible global function definition for ‘lines’
schemper: no visible global function definition for ‘predict’
schemper: no visible global function definition for ‘survfit’
schemper: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx lines plot predict survfit
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
File ‘survAUC/libs/survAUC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Est.PH: no visible global function definition for ‘coxph’
Inf.Cval: no visible global function definition for ‘rexp’
Inf.Cval: no visible global function definition for ‘var’
Inf.Cval.Delta: no visible global function definition for ‘rexp’
Inf.Cval.Delta: no visible global function definition for ‘var’
cvC: no visible global function definition for ‘coxph’
cvC: no visible global function definition for ‘weighted.mean’
Undefined global functions or variables:
  coxph rexp var weighted.mean
Consider adding
  importFrom("stats", "rexp", "var", "weighted.mean")
to your NAMESPACE file.
File ‘survC1/libs/survC1.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/survClip.Rnw’
(Is a VignetteBuilder field missing?)
pearson: no visible global function definition for ‘cor’
plot.survcorr: no visible global function definition for ‘pnorm’
plot.survcorr: no visible global function definition for ‘par’
plot.survcorr: no visible global function definition for ‘plot’
plot.survcorr: no visible global function definition for ‘points’
survcorr: no visible global function definition for ‘model.frame’
survcorr: no visible global function definition for ‘qnorm’
survcorr: no visible global function definition for ‘runif’
survcorr: no visible global function definition for ‘pnorm’
survcorr: no visible global function definition for ‘var’
survcorr: no visible global function definition for ‘qt’
Undefined global functions or variables:
  cor model.frame par plot pnorm points qnorm qt runif var
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "cor", "model.frame", "pnorm", "qnorm", "qt",
             "runif", "var")
to your NAMESPACE file.
File ‘surveybootstrap/libs/surveybootstrap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘survival’ which was already attached by Depends.
  Please remove these calls from your code.
Survgini: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘survC1’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Est.HR.FUN: no visible global function definition for ‘coxph’
Est.HR.FUN: no visible global function definition for ‘basehaz’
Est.HR.FUN: no visible global function definition for ‘approx’
Ghat.FUN: no visible global function definition for ‘survfit’
IDI.INF: no visible global function definition for ‘kmcens’
IDI.INF: no visible global function definition for ‘quantile’
IDI.INF.GRAPH: no visible global function definition for ‘plot’
IDI.INF.GRAPH: no visible global function definition for ‘lines’
IDI.INF.GRAPH: no visible global function definition for ‘abline’
IDI.INF.GRAPH: no visible global function definition for ‘points’
IDI.INF.GRAPH: no visible global function definition for ‘title’
PTB.IDI.FUN: no visible global function definition for ‘rexp’
shade: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  abline approx basehaz coxph kmcens lines plot points polygon quantile
  rexp survfit title
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "points", "polygon",
             "title")
  importFrom("stats", "approx", "quantile", "rexp")
to your NAMESPACE file.
Rd file 'IDI.INF.GRAPH.Rd':
  \usage lines wider than 90 characters:
     IDI.INF.GRAPH(x, main = NULL, xlab = NULL, ylab = NULL, cex.main = NULL, cex.lab = NULL, ...)

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
betaEst: no visible global function definition for ‘is’
fullKernel: no visible global function definition for ‘is’
halfKernel: no visible global function definition for ‘is’
kernelAuto: no visible global function definition for ‘quantile’
kernelAuto: no visible global function definition for ‘lm’
kernelAuto: no visible global function definition for ‘pnorm’
kernelFixed: no visible global function definition for ‘pnorm’
lastValue: no visible global function definition for ‘pnorm’
nearValue: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  is lm pnorm quantile
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "lm", "pnorm", "quantile")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘survSNP/libs/survSNP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
fitModel: no visible global function definition for ‘var’
fitModel: no visible global function definition for ‘cov’
svpls: no visible global function definition for ‘pt’
Undefined global functions or variables:
  cov pt var
Consider adding
  importFrom("stats", "cov", "pt", "var")
to your NAMESPACE file.
Calls with DUP:
   .C("myInversion", Senv$diag, Senv$env, Senv$xenv, Senv$N, Senv$Nenv, 
       Senv$Nplus1, DUP = FALSE, PACKAGE = "svcm")
   .C("myTrace", Senv$diag, Senv$env, Senv$xenv, Senv$N, Senv$Nenv, 
       Senv$Nplus1, BBenv$diag, BBenv$env, BBenv$xenv, BBenv$N, 
       BBenv$Nenv, BBenv$Nplus1, ED = ED, DUP = FALSE, PACKAGE = "svcm")
   .C("dsC2env", N, A@x, as.integer(A@i), as.integer(A@p), diagvec = diagvec, 
       env = env, xenv = as.integer(xenv), DUP = FALSE)
DUP is no longer supported and will be ignored.
File ‘svcm/libs/svcm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
dlgMessage.tcltkGUI: no visible global function definition for ‘alarm’
Undefined global functions or variables:
  alarm
Consider adding
  importFrom("utils", "alarm")
to your NAMESPACE file.
Found the following significant warnings:
  trlan/trlcore.c:983:15: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlcore.c:1642:9: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlcore.c:1642:20: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlaux.c:28:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:41:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:62:13: warning: comparison of array 'info->cpfile' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlan.c:171:20: warning: comparison of array 'info->oldcpf' equal to a null pointer is always false [-Wtautological-pointer-compare]
  trlan/ztrlcore.c:1418:12: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/svd.Rcheck/00install.out’ for details.
Running examples in ‘svdvis-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: radviz
> ### Title: Radial Coordinates Plots
> ### Aliases: radviz
> 
> ### ** Examples
> 
> set.seed(1234)
> dat = matrix(rnorm(9*4), 9, 4, dimnames=list(paste(1:9),letters[1:4]))
> radviz(dat, group=c(rep("Group 1",3),rep("Group 2",3),rep("Group 3",3)))
Error: `data` must be uniquely named but has duplicate elements
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 78-80 (svdvis-vignette.Rmd) 
Error: processing vignette ‘svdvis-vignette.Rmd’ failed with diagnostics:
`data` must be uniquely named but has duplicate elements
Execution halted
svd3dplot: no visible global function definition for ‘wireframe’
svd3dplot: no visible global function definition for ‘levelplot’
Undefined global functions or variables:
  levelplot wireframe
startHttpServer : <anonymous> : Rjsonp: no visible global function
  definition for ‘localeToCharset’
Undefined global functions or variables:
  localeToCharset
Consider adding
  importFrom("utils", "localeToCharset")
to your NAMESPACE file.
.onAttach : svBrowser: no visible global function definition for
  ‘browseURL’
.onAttach: no visible global function definition for ‘loadhistory’
Undefined global functions or variables:
  browseURL loadhistory
Consider adding
  importFrom("utils", "browseURL", "loadhistory")
to your NAMESPACE file.
File ‘svmadmm/libs/svmadmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘svmpath/libs/svmpath.so’:
  Found ‘_gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘_gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘_gfortran_st_read’, possibly from ‘read’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi30spec.o’, ‘mi35mps.o’,
      ‘mi36mps.o’, ‘mi40bfil.o’
  Found ‘_gfortran_st_rewind’, possibly from ‘rewind’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi10unix.o’, ‘mi35mps.o’, ‘mi40bfil.o’
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’
File ‘svmpath/libs/svmpath.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 use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
processSocket: no visible global function definition for ‘URLdecode’
Undefined global functions or variables:
  URLdecode
Consider adding
  importFrom("utils", "URLdecode")
to your NAMESPACE file.
.formatResult : capture.str: no visible global function definition for
  ‘str’
createLog: no visible global function definition for ‘sessionInfo’
protocol_junit.svSuiteData: no visible global function definition for
  ‘xmlNode’
protocol_junit.svSuiteData: no visible global function definition for
  ‘addChildren’
protocol_junit.svSuiteData: no visible global function definition for
  ‘saveXML’
protocol_junit.svTestData: no visible global function definition for
  ‘xmlNode’
protocol_junit.svTestData: no visible global function definition for
  ‘addChildren’
Undefined global functions or variables:
  addChildren saveXML sessionInfo str xmlNode
Consider adding
  importFrom("utils", "sessionInfo", "str")
to your NAMESPACE file.
svycox.calibrate: no visible global function definition for ‘quantile’
svycox.calibrate: no visible binding for global variable ‘median’
svycox.calibrate: no visible global function definition for
  ‘as.formula’
svycox.calibrate: no visible global function definition for ‘plot’
svycox.calibrate: no visible global function definition for ‘arrows’
svycox.calibrate: no visible global function definition for ‘abline’
svycox.nomogram: no visible global function definition for ‘predict’
svycox.nomogram: no visible global function definition for ‘as.formula’
svycox.validate : internal.validate.func: no visible global function
  definition for ‘as.formula’
svycox.validate : internal.validate.func: no visible global function
  definition for ‘formula’
Undefined global functions or variables:
  abline arrows as.formula formula median plot predict quantile
Consider adding
  importFrom("graphics", "abline", "arrows", "plot")
  importFrom("stats", "as.formula", "formula", "median", "predict",
             "quantile")
to your NAMESPACE file.
additional_comp: no visible global function definition for ‘aggregate’
additional_compPV : <anonymous>: no visible global function definition
  for ‘aggregate’
cor.aux.func : <anonymous>: no visible global function definition for
  ‘cov.wt’
eta.func : <anonymous>: no visible global function definition for ‘lm’
eta.func : <anonymous>: no visible global function definition for
  ‘anova’
glm.dummy.no.std: no visible global function definition for
  ‘as.formula’
pv_by: no visible binding for global variable ‘var’
pv_perc: no visible binding for global variable ‘var’
pv_quantile: no visible binding for global variable ‘var’
svyPVcor: no visible global function definition for ‘update’
svyPVcor: no visible global function definition for ‘var’
svyPVeta: no visible global function definition for ‘update’
svyPVeta: no visible global function definition for ‘var’
svyPVglm: no visible global function definition for ‘gaussian’
svyPVglm: no visible binding for global variable ‘as.formula’
svyPVglm: no visible binding for global variable ‘var’
svyPVglm: no visible global function definition for ‘pt’
svyPVttest: no visible binding for global variable ‘as.formula’
svyPVttest: no visible global function definition for ‘var’
svyPVttest: no visible global function definition for ‘pt’
svyPVttest: no visible binding for global variable ‘var’
t.test.aux: no visible global function definition for ‘as.formula’
t.test.aux: no visible global function definition for ‘complete.cases’
Undefined global functions or variables:
  aggregate anova as.formula complete.cases cov.wt gaussian lm pt
  update var
Consider adding
  importFrom("stats", "aggregate", "anova", "as.formula",
             "complete.cases", "cov.wt", "gaussian", "lm", "pt",
             "update", "var")
to your NAMESPACE file.
readSWAT: no visible global function definition for ‘read.fortran’
runSWAT2005: no visible global function definition for ‘read.fortran’
runSWAT2009: no visible global function definition for ‘read.fortran’
runSWAT2012: no visible global function definition for ‘read.fortran’
Undefined global functions or variables:
  read.fortran
Consider adding
  importFrom("utils", "read.fortran")
to your NAMESPACE file.
Rd file 'build_swat_basic.Rd':
  \examples lines wider than 100 characters:
     build_swat_basic(dirname="test", iyr="1979", nbyr=13, wsarea=40, elev=200, declat=45, declon=-72, hist_wx=hist_wx) 

Rd file 'readSWAT.Rd':
  \examples lines wider than 100 characters:
       } else { print ("You need to add your file type to this function if it is not output.sub or output.rch")}

These lines will be truncated in the PDF manual.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
  src/SWAT2005/Makefile
  src/SWAT2005/Makefile.win
  src/SWAT2009/Makefile
  src/SWAT2009/Makefile.win
  src/SWAT2012/Makefile
  src/SWAT2012/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
'::' or ':::' import not declared from: ‘fracdiff’
Packages in Depends field not imported from:
  ‘MASS’ ‘fda’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fj_pl: no visible global function definition for ‘getbasismatrix’
fj_pl: no visible global function definition for ‘create.bspline.basis’
fj_pl: no visible global function definition for ‘getbasispenalty’
forward_backward.quantities : <anonymous>: no visible global function
  definition for ‘dnorm’
function_cases1AND2: no visible global function definition for ‘dnorm’
function_cases3AND4: no visible global function definition for ‘dnorm’
pij_iid: no visible global function definition for ‘dnorm’
pilj: no visible global function definition for ‘dnorm’
updateLambda: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  create.bspline.basis dnorm getbasismatrix getbasispenalty optimize
Consider adding
  importFrom("stats", "dnorm", "optimize")
to your NAMESPACE file.
calc_MW: no visible global function definition for ‘read.table’
cfba_moment: no visible global function definition for ‘median’
cfba_moment: no visible global function definition for ‘write.csv’
cfba_moment_mr: no visible global function definition for ‘median’
cfba_moment_mr: no visible global function definition for ‘write.csv’
cfba_moment_pw: no visible global function definition for ‘median’
cfba_moment_pw: no visible global function definition for ‘write.csv’
readmodel: no visible global function definition for ‘as’
Undefined global functions or variables:
  as median read.table write.csv
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "median")
  importFrom("utils", "read.table", "write.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages suggested but not available for checking: ‘sylly.de’ ‘sylly.es’
symbol: no visible global function definition for ‘plot.new’
symbol: no visible global function definition for ‘plot.window’
symbol: no visible global function definition for ‘axis’
symbol: no visible global function definition for ‘box’
symbol: no visible global function definition for ‘title’
symbol: no visible global function definition for ‘rainbow’
symbol: no visible global function definition for ‘hsv’
symbol: no visible global function definition for ‘rect’
symbol: no visible global function definition for ‘polygon’
symbol: no visible global function definition for ‘lines’
symbol: no visible global function definition for ‘text’
Undefined global functions or variables:
  axis box hsv lines plot.new plot.window polygon rainbow rect text
  title
Consider adding
  importFrom("grDevices", "hsv", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "polygon", "rect", "text", "title")
to your NAMESPACE file.
Rd file 'symbol.Rd':
  \usage lines wider than 90 characters:
     symbol(df, type="star", colin=NULL, colout=NULL, colin2=NA, colout2=1, ssize=NULL, labels=0, labelsize=0.6,
            scheme=1, sortby=0, descending=FALSE, coorx=NULL, coory=NULL, lty=1, main=NULL, sub=NULL, xlab=NULL, ylab=NULL,
            add=FALSE, xlim=NULL, ylim=NULL, facew=0.5, faceh=0.5, eyes=0.5, eyed=0.5, mouthw=0.5, mouthc=0.5, brows=0.5,
            browp=0.5, nosel=0.5, nosew=0.5, ears=0.5, pupils=0.5, body=0.5, limb1=0.5, limb2=0.5, limb3=0.5, limb4=0.5, defcol=NA)

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: blockSize
> ### Title: Return the Block Size of a symDMatrix Object.
> ### Aliases: blockSize
> 
> ### ** Examples
> 
> # Load example symDMatrix (G)
> load.symDMatrix(system.file("extdata", "G.RData", package = "symDMatrix"))
opening ff data_1_1.bin readonly
opening ff data_1_2.bin readonly
opening ff data_1_3.bin readonly
Error in ff::open.ff(x) : ff is already open with readonly=TRUE
Calls: load.symDMatrix ... initializeBlock -> initializeBlock.ff_matrix -> <Anonymous>
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(symDMatrix)
  > 
  > test_check("symDMatrix")
  ── 1. Error: (unknown) (@test-symDMatrix.R#15)  ────────────────────────────────
  ff is already open with readonly=TRUE
  1: suppressMessages(load.symDMatrix(system.file("extdata", "G.RData", package = "symDMatrix"))) at testthat/test-symDMatrix.R:15
  2: withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessage"))
  3: load.symDMatrix(system.file("extdata", "G.RData", package = "symDMatrix"))
  4: initializeBlock(object[[i]][[j]], path = dirname(file))
  5: initializeBlock.ff_matrix(object[[i]][[j]], path = dirname(file))
  6: ff::open.ff(x)
  7: stop(paste("ff is already open with readonly=", attr(physical, "readonly"), sep = ""))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-symDMatrix.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
integrate.polynomial : f: no visible global function definition for
  ‘dmvnorm’
Undefined global functions or variables:
  dmvnorm
Package in Depends field not imported from: ‘fields’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cwt_fw: no visible global function definition for ‘fft’
cwt_iw: no visible global function definition for ‘fft’
est_riskshrink_thresh: no visible global function definition for
  ‘median’
Undefined global functions or variables:
  fft median
Consider adding
  importFrom("stats", "fft", "median")
to your NAMESPACE file.
File ‘SynchWave/libs/SynchWave.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘tcltk’ ‘tkrplot’
  Please remove these calls from your code.
Rd file 'SyNet-package.rd':
  \examples lines wider than 100 characters:
       # Run NAM method on the previously inferred sympatry network                                           

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

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

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

These lines will be truncated in the PDF manual.
mainNetFunction: no visible global function definition for ‘png’
mainNetFunction: no visible global function definition for ‘plot’
mainNetFunction: no visible global function definition for ‘lines’
mainNetFunction: no visible global function definition for ‘legend’
mainNetFunction: no visible global function definition for ‘dev.off’
plotPR: no visible global function definition for ‘plot’
plotROC: no visible global function definition for ‘plot’
plotROC: no visible global function definition for ‘lines’
simulatedData: no visible global function definition for ‘rpois’
simulatedData : <anonymous>: no visible global function definition for
  ‘rpois’
simulatedData : rlognormpois: no visible global function definition for
  ‘rnorm’
simulatedData : rlognormpois: no visible global function definition for
  ‘rpois’
Undefined global functions or variables:
  dev.off legend lines plot png rnorm rpois
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "rnorm", "rpois")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘LowRankQP’ ‘rgenoud’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
fn.V: no visible global function definition for ‘LowRankQP’
gaps.plot: no visible global function definition for ‘abline’
path.plot: no visible global function definition for ‘lines’
path.plot: no visible global function definition for ‘abline’
path.plot: no visible global function definition for ‘legend’
synth: no visible binding for global variable ‘sd’
synth: no visible binding for global variable ‘var’
synth: no visible global function definition for ‘LowRankQP’
Undefined global functions or variables:
  LowRankQP abline legend lines sd var
Consider adding
  importFrom("graphics", "abline", "legend", "lines")
  importFrom("stats", "sd", "var")
to your NAMESPACE file.
Found the following significant warnings:
  lib_FeasibleMatrix.cpp:53:7: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  lib_FeasibleMatrix.cpp:168:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  lib_FeasibleMatrix.cpp:176:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  lib_sample_kcycle.cpp:141:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/systemicrisk.Rcheck/00install.out’ for details.
.checkDimAndTest: no visible global function definition for
  ‘chisq.test’
.checkDimAndTest: no visible global function definition for
  ‘fisher.test’
plotTable1Heatmap: no visible global function definition for ‘par’
plotTable1Heatmap: no visible global function definition for ‘image’
plotTable1Heatmap: no visible global function definition for ‘abline’
plotTable1Heatmap: no visible global function definition for ‘axis’
plotTable1Heatmap: no visible global function definition for ‘text’
plotTable1Heatmap: no visible global function definition for ‘legend’
plotTable1Heatmap: no visible global function definition for ‘box’
Undefined global functions or variables:
  abline axis box chisq.test fisher.test image legend par text
Consider adding
  importFrom("graphics", "abline", "axis", "box", "image", "legend",
             "par", "text")
  importFrom("stats", "chisq.test", "fisher.test")
to your NAMESPACE file.
'library' or 'require' call to ‘grid’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘perturb’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘grid’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cellgram: no visible global function definition for ‘grid.rect’
cellgram: no visible global function definition for ‘gpar’
cellgram: no visible global function definition for ‘grid.segments’
cellgram: no visible global function definition for ‘grid.circle’
cellgram: no visible global function definition for ‘grid.polygon’
cellgram: no visible global function definition for ‘grid.text’
cellgram: no visible global function definition for ‘unit’
compare: no visible global function definition for ‘sd’
tableplot.colldiag: no visible global function definition for
  ‘colldiag’
tableplot.colldiag: no visible global function definition for ‘xtabs’
tableplot.default: no visible global function definition for
  ‘grid.newpage’
tableplot.default: no visible global function definition for
  ‘grid.layout’
tableplot.default: no visible global function definition for ‘unit’
tableplot.default: no visible global function definition for
  ‘pushViewport’
tableplot.default: no visible global function definition for ‘viewport’
tableplot.default: no visible global function definition for
  ‘grid.text’
tableplot.default: no visible global function definition for
  ‘upViewport’
tableplot.default: no visible global function definition for ‘gpar’
tableplot.default: no visible global function definition for
  ‘grid.rect’
tableplot.default: no visible global function definition for
  ‘popViewport’
Undefined global functions or variables:
  colldiag gpar grid.circle grid.layout grid.newpage grid.polygon
  grid.rect grid.segments grid.text popViewport pushViewport sd unit
  upViewport viewport xtabs
Consider adding
  importFrom("stats", "sd", "xtabs")
to your NAMESPACE file.
Rd file 'Linehan.Rd':
  \examples lines wider than 100 characters:
             cell.specs=list(list(0,"grey50",1,1,"red",1,"white","grey90",2,.7,"black",FALSE,"black",99)),
             cell.specs=list(list(0,c("black","blue"),1,1,c("black","blue"),1,"white","grey80",2,.7,"black",FALSE,"black",99))

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

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

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

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

These lines will be truncated in the PDF manual.
Found the following apparent S3 methods exported but not registered:
  print.plist
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
TCRsink: no visible global function definition for ‘head’
Undefined global functions or variables:
  head
Consider adding
  importFrom("utils", "head")
to your NAMESPACE file.
itabplot : <anonymous>: no visible global function definition for
  ‘capture.output’
itabplot: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL capture.output
Consider adding
  importFrom("utils", "browseURL", "capture.output")
to your NAMESPACE file.
File ‘tagcloud/libs/tagcloud.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tailDepFun/libs/tailDepFun.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  proj.data proj.dir proj.dir2
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
NANOVA.test: no visible global function definition for ‘ecdf’
NANOVA.test2: no visible global function definition for ‘ecdf’
NANOVA.test3: no visible global function definition for ‘ecdf’
fdr.table: no visible global function definition for ‘median’
fdr.table: no visible global function definition for ‘quantile’
gene.classifier1: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  ecdf median quantile write.table
Consider adding
  importFrom("stats", "ecdf", "median", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Rd file 'NANOVA.test.Rd':
  \usage lines wider than 90 characters:
     NANOVA.test2(data,f1,f2,type,time.course,equal.size=FALSE,B=100,robustify=FALSE,eb=FALSE,df=0)

Rd file 'tanova.Rd':
  \usage lines wider than 90 characters:
     tanova(data, f1, f2, tp, B=100, FDR=0.05,robustify=FALSE, equal.size=FALSE, qt=-1, longitudinal=TRUE, test.type=0,eb=FALSE,df=0)
     gene.classifier1(data, f1, f2, B=100,FDR=0.05, robustify=FALSE, equal.size=FALSE, eb=FALSE,qt=-1)
     gene.classifier2(data, f1, f2, B=100,FDR=0.05, robustify=FALSE, equal.size=FALSE, time.course, qt=-1,eb=FALSE,df=1)

These lines will be truncated in the PDF manual.
'library' or 'require' calls in package code:
  ‘gdata’ ‘ggplot2’ ‘grid’ ‘lattice’ ‘xtable’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
AnalyzeLVZ: no visible global function definition for ‘approx’
ConvP2Vdepthinv: no visible global function definition for ‘approx’
DistSummary: no visible global function definition for ‘heat.colors’
Earthplot: no visible global function definition for ‘heat.colors’
Earthplot: no visible global function definition for ‘par’
Earthplot: no visible global function definition for ‘plot’
Earthplot: no visible global function definition for ‘approx’
Earthplot: no visible global function definition for ‘image’
Earthplot: no visible binding for global variable ‘lines’
FindRoots: no visible global function definition for ‘uniroot’
InterpModel: no visible global function definition for ‘approx’
LinInterp: no visible global function definition for ‘approx’
PolarPlot: no visible binding for global variable ‘plot’
Rayfan: no visible binding for global variable ‘lines’
polaraxis: no visible global function definition for ‘text’
Undefined global functions or variables:
  approx heat.colors image lines par plot text uniroot
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "image", "lines", "par", "plot", "text")
  importFrom("stats", "approx", "uniroot")
to your NAMESPACE file.
Rd file 'DistSummary.Rd':
  \usage lines wider than 90 characters:
     DistSummary(delta, h, model, phaselist = 'default', prop = "vp", image.col = heat.colors(500), n = 200, ...)

Rd file 'Rayfan.Rd':
  \usage lines wider than 90 characters:
     Rayfan(phaselist, h, model, deltalist = 1:17 * 20, minp = 0.5, plot = TRUE, add = TRUE, col = rep("black", length(phaselist)), verbose  ... [TRUNCATED]

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
BootTree: no visible global function definition for ‘hclust’
BootTree: no visible global function definition for ‘dist’
BootTree: no visible global function definition for ‘as.dist’
BootTree: no visible global function definition for ‘cor’
BootTree: no visible binding for global variable ‘var’
Pgpd: no visible global function definition for ‘optim’
Pgpd : <anonymous>: no visible global function definition for ‘optim’
Pgpd: no visible global function definition for ‘var’
Pgpd: no visible global function definition for ‘rnorm’
Pgpd: no visible global function definition for ‘quantile’
Pvalue: no visible global function definition for ‘rnorm’
SigTree: no visible global function definition for ‘data’
TreeStat: no visible global function definition for ‘hclust’
TreeStat: no visible global function definition for ‘as.dist’
TreeStat: no visible global function definition for ‘dist’
TreeStat: no visible global function definition for ‘cor’
plot.best: no visible global function definition for ‘hclust’
plot.best: no visible global function definition for ‘as.dist’
plot.best: no visible global function definition for ‘dist’
plot.best: no visible global function definition for ‘cor’
plot.best: no visible global function definition for ‘plot’
treetext: no visible global function definition for ‘par’
treetext: no visible global function definition for ‘text’
Undefined global functions or variables:
  as.dist cor data dist hclust optim par plot quantile rnorm text var
Consider adding
  importFrom("graphics", "par", "plot", "text")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "optim",
             "quantile", "rnorm", "var")
  importFrom("utils", "data")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  slice.fun
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
cluster_cutoff_at_first_empty_bin: no visible global function
  definition for ‘hist’
mapper1D: no visible global function definition for ‘dist’
mapper1D: no visible global function definition for ‘as.dist’
mapper1D: no visible global function definition for ‘hclust’
mapper1D: no visible global function definition for ‘cutree’
mapper2D: no visible global function definition for ‘dist’
mapper2D: no visible global function definition for ‘as.dist’
mapper2D: no visible global function definition for ‘hclust’
mapper2D: no visible global function definition for ‘cutree’
Undefined global functions or variables:
  as.dist cutree dist hclust hist
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "as.dist", "cutree", "dist", "hclust")
to your NAMESPACE file.
File ‘TDboost/libs/TDboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘RSEIS’ ‘pracma’ ‘signal’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  predict.Weights predict.Weights2
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
TeachNet: no visible global function definition for ‘predict’
createWeights1: no visible global function definition for ‘rnorm’
createWeights2: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  predict rnorm
Consider adding
  importFrom("stats", "predict", "rnorm")
to your NAMESPACE file.
aniplotevents: no visible global function definition for ‘plot’
aniplotevents: no visible global function definition for ‘lines’
cbfs: no visible global function definition for ‘rnorm’
cbfs: no visible global function definition for ‘runif’
cbfs_red: no visible global function definition for ‘arima.sim’
cbfs_red: no visible global function definition for ‘runif’
eventCluster: no visible global function definition for ‘princomp’
eventCluster: no visible global function definition for ‘kmeans’
measures: no visible global function definition for ‘sd’
measures: no visible global function definition for ‘var’
measures: no visible global function definition for ‘PP.test’
noiseTests: no visible global function definition for ‘Box.test’
noiseTests: no visible global function definition for ‘PP.test’
noiseTests: no visible global function definition for ‘ar’
plotevents: no visible global function definition for ‘plot’
plotevents: no visible global function definition for ‘lines’
ur.za.fast : roll: no visible global function definition for ‘coef’
ur.za.fast : roll: no visible global function definition for ‘lm’
Undefined global functions or variables:
  Box.test PP.test ar arima.sim coef kmeans lines lm plot princomp
  rnorm runif sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "Box.test", "PP.test", "ar", "arima.sim", "coef",
             "kmeans", "lm", "princomp", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
Running examples in ‘temperatureresponse-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: equ10
> ### Title: Equation 10
> ### Aliases: equ10
> 
> ### ** Examples
> 
> output <- with(Emiliania_huxleyi, equ10(temp=temp, rate=rate))
Warning in nls.lm(par = start, fn = FCT, jac = jac, control = control, lower = lower,  :
  NAs introduced by coercion to integer range
Error in if (class(try_test) == "try-error" | class(try_test_2) == "try-error") { : 
  the condition has length > 1
Calls: with ... with.default -> eval -> eval -> equ10 -> <Anonymous>
Execution halted
Calls with DUP:
   .C(tensoraCmulhelper, dimx = as.integer(c(outerx, inner, para)), 
       as.integer(c(inner, outery, para)), as.integer(c(outerx, 
           outery, para)), as.complex(X[xtidx]), as.complex(Y[ytidx]), 
       erg = complex(outerx * outery * para), NAOK = TRUE, DUP = FALSE)
   .C(tensoramulhelper, dimx = as.integer(c(outerx, inner, para)), 
       as.integer(c(inner, outery, para)), as.integer(c(outerx, 
           outery, para)), as.numeric(X[xtidx]), as.numeric(Y[ytidx]), 
       erg = numeric(outerx * outery * para), NAOK = TRUE, DUP = FALSE)
DUP is no longer supported and will be ignored.
S3 methods shown with full name in documentation object 'mean.tensor':
  ‘mean.tensor’

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘tensorA/libs/tensorA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
TER.deesc.1.B : A1.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.1.B : A1.f: no visible binding for global variable ‘ID’
TER.deesc.1.B : A2.n.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.1.B : A2.n.f: no visible binding for global variable ‘ID’
TER.deesc.1.B: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.1.B: no visible binding for global variable ‘ID’
TER.deesc.A.B : A1.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : A1.f: no visible binding for global variable ‘ID’
TER.deesc.A.B : A3.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : A3.f: no visible binding for global variable ‘ID’
TER.deesc.A.B : A2.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : A2.f: no visible binding for global variable ‘ID’
TER.deesc.A.B : B1.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : B1.f: no visible binding for global variable ‘ID’
TER.deesc.A.B: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B: no visible binding for global variable ‘ID’
Undefined global functions or variables:
  ID
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘tergm’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘tergm’
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/tergm.Rcheck/00install.out’ for details.
Problems with news in ‘inst/NEWS.Rd’:
  Malformed NEWS.Rd file:
  Chunk starting
    \itemize{
        By request from Sam Jennes,
        \code{\lin
  contains no \item.
File ‘TESS/libs/TESS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File which contains pragma(s) suppressing diagnostics:
  ‘inst/include/testthat/vendor/catch.h’
Found the following apparent S3 methods exported but not registered:
  print.tepAssign print.tepBADA print.tepDICA print.tepGPLS
  print.tepGraphs print.tepPLS print.tepPLSCA print.texpoOutput
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
phyper_right: no visible global function definition for ‘dhyper’
progression: no visible global function definition for ‘density’
progression: no visible global function definition for ‘plot’
progression: no visible global function definition for ‘points’
progression: no visible global function definition for ‘legend’
progression: no visible global function definition for ‘text’
specificities.distribution.plot: no visible global function definition
  for ‘dhyper’
specificities.distribution.plot: no visible global function definition
  for ‘plot’
specificities.distribution.plot: no visible global function definition
  for ‘Axis’
specificities.distribution.plot: no visible global function definition
  for ‘arrows’
specificities.distribution.plot: no visible global function definition
  for ‘text’
specificities.distribution.plot: no visible global function definition
  for ‘title’
specificities.probabilities.vector: no visible global function
  definition for ‘phyper’
Undefined global functions or variables:
  Axis arrows density dhyper legend phyper plot points text title
Consider adding
  importFrom("graphics", "Axis", "arrows", "legend", "plot", "points",
             "text", "title")
  importFrom("stats", "density", "dhyper", "phyper")
to your NAMESPACE file.
File ‘textreg/libs/textreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
transfer: no visible global function definition for ‘rgamma’
transfer: no visible global function definition for ‘rnorm’
transfer: no visible global function definition for ‘rnbinom’
transfer: no visible global function definition for ‘rpois’
transfer: no visible global function definition for ‘rbinom’
transfer: no visible global function definition for ‘runif’
plot,transfer: no visible global function definition for ‘barplot’
plot,transfer: no visible global function definition for ‘axis’
plot,transfer: no visible global function definition for ‘par’
plot,transfer: no visible global function definition for ‘hist’
Undefined global functions or variables:
  axis barplot hist par rbinom rgamma rnbinom rnorm rpois runif
Consider adding
  importFrom("graphics", "axis", "barplot", "hist", "par")
  importFrom("stats", "rbinom", "rgamma", "rnbinom", "rnorm", "rpois",
             "runif")
to your NAMESPACE file.
ParseTrueFX: no visible global function definition for ‘read.csv’
TrueFXRef: no visible global function definition for ‘download.file’
TrueFXRef: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL download.file read.csv
Consider adding
  importFrom("utils", "browseURL", "download.file", "read.csv")
to your NAMESPACE file.
File ‘tgcd/libs/tgcd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tgp/libs/tgp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘dada2’
Thinknum: no visible global function definition for ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
File ‘ThreeArmedTrials/libs/ThreeArmedTrials.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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_traceplot: no visible global function definition for ‘rainbow’
coef_traceplot: no visible global function definition for ‘plot’
coef_traceplot: no visible global function definition for ‘abline’
coef_traceplot : <anonymous>: no visible global function definition for
  ‘lines’
coef_traceplot: no visible global function definition for ‘text’
ee.GEE.aux : <anonymous>: no visible global function definition for
  ‘combn’
Undefined global functions or variables:
  abline combn lines plot rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "plot", "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
summary.tsls: no visible global function definition for ‘printCoefmat’
threesls: no visible global function definition for ‘cor’
threesls: no visible global function definition for ‘pt’
tsls.formula: no visible global function definition for ‘model.matrix’
tsls.formula: no visible global function definition for
  ‘model.response’
Undefined global functions or variables:
  cor model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.matrix", "model.response",
             "printCoefmat", "pt")
to your NAMESPACE file.
.LoadTickDataHK: no visible global function definition for ‘read.csv’
.LoadTickDataSHSZ: no visible global function definition for ‘read.csv’
DrawDown: no visible global function definition for ‘na.omit’
PerformanceReport: no visible global function definition for
  ‘aggregate’
PerformanceReport: no visible global function definition for ‘sd’
Undefined global functions or variables:
  aggregate na.omit read.csv sd
Consider adding
  importFrom("stats", "aggregate", "na.omit", "sd")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
newTiddler: no visible global function definition for ‘new’
twImage: no visible global function definition for ‘new’
twLink: no visible global function definition for ‘new’
twList: no visible global function definition for ‘new’
twTable: no visible global function definition for ‘new’
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package suggested but not available for checking: ‘Rblpapi’
File ‘tidyxl/libs/tidyxl.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
    Object: ‘xlex.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tiff/libs/tiff.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘shiny’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘ggplot2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
timeline: no visible global function definition for ‘ggplot’
timeline: no visible global function definition for ‘geom_segment’
timeline: no visible global function definition for ‘aes_string’
timeline: no visible global function definition for ‘geom_rect’
timeline: no visible global function definition for ‘geom_text’
timeline: no visible global function definition for ‘theme’
timeline: no visible global function definition for ‘element_blank’
timeline: no visible global function definition for ‘xlab’
timeline: no visible global function definition for ‘ylab’
timeline: no visible global function definition for ‘xlim’
timeline: no visible global function definition for
  ‘scale_y_continuous’
timeline: no visible global function definition for ‘geom_point’
timeline: no visible global function definition for ‘scale_color_grey’
timeline: no visible global function definition for ‘geom_hline’
Undefined global functions or variables:
  aes_string element_blank geom_hline geom_point geom_rect geom_segment
  geom_text ggplot scale_color_grey scale_y_continuous theme xlab xlim
  ylab
Found the following significant warnings:
  tm.c:184:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  tm.c:185:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TimeMachine.Rcheck/00install.out’ for details.
Found the following apparent S3 methods exported but not registered:
  density.tm mean.tm print.tm quantile.tm summary.tm
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
density.tm: no visible global function definition for ‘density’
mu.mle: no visible global function definition for ‘optimize’
pophistory.tm: no visible binding for global variable ‘quantile’
quantile.tm: no visible global function definition for ‘quantile’
sample.pop: no visible global function definition for ‘runif’
summary.tm: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  density optimize quantile runif
Consider adding
  importFrom("stats", "density", "optimize", "quantile", "runif")
to your NAMESPACE file.
File ‘TimeMachine/libs/TimeMachine.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘TimeMachine-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pophistory
> ### Title: History of Population Size
> ### Aliases: pophistory pophistory.tm
> 
> ### ** Examples
> 
> # Load example dataset
> data(pdm)
> 
> transitions <- full.transitions(pdm$unitary.transitions, pdm$loci)
> pi <- stationary.dist(transitions)
> n <- 10
> mu <- 1
> samples <- 10
> est.res <- tm(transitions, pi, pdm$population, n, mu, samples)
> 
> # Plot minimum, median and maximum SEN as a function of population size
> h <- pophistory(est.res, probs=c(0, 0.5, 1))
Error in UseMethod("pophistory") : 
  no applicable method for 'pophistory' applied to an object of class "tm"
Calls: pophistory -> pophistory
Execution halted
'library' or 'require' calls in package code:
  ‘ggplot2’ ‘plyr’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Matrix’ ‘lubridate’ ‘timeDate’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
is.Bizday: no visible global function definition for ‘isWeekday’
plotCalendarHeatmap: no visible global function definition for ‘ddply’
plotCalendarHeatmap: no visible global function definition for ‘.’
plotCalendarHeatmap: no visible binding for global variable ‘year’
plotCalendarHeatmap: no visible binding for global variable ‘month’
plotCalendarHeatmap: no visible binding for global variable ‘week’
plotCalendarHeatmap: no visible global function definition for ‘ggplot’
plotCalendarHeatmap: no visible global function definition for ‘aes’
plotCalendarHeatmap: no visible binding for global variable ‘monthweek’
plotCalendarHeatmap: no visible binding for global variable ‘weekday’
plotCalendarHeatmap: no visible global function definition for
  ‘geom_tile’
plotCalendarHeatmap: no visible global function definition for
  ‘facet_grid’
plotCalendarHeatmap: no visible global function definition for
  ‘scale_fill_gradientn’
projectDate: no visible global function definition for ‘holidayNYSE’
projectDate: no visible global function definition for
  ‘sparse.model.matrix’
Undefined global functions or variables:
  . aes ddply facet_grid geom_tile ggplot holidayNYSE isWeekday month
  monthweek scale_fill_gradientn sparse.model.matrix week weekday year
boot_autocov: no visible global function definition for ‘is.ts’
boot_autocov: no visible global function definition for ‘tsboot’
boot_autocov: no visible global function definition for ‘quantile’
boot_autocov: no visible global function definition for ‘par’
boot_autocov: no visible global function definition for ‘frequency’
boot_autocov: no visible global function definition for ‘polygon’
boot_autocov: no visible global function definition for ‘lines’
boot_autocov: no visible global function definition for ‘abline’
boot_autocov: no visible global function definition for ‘acf’
boot_spec: no visible global function definition for ‘is.ts’
boot_spec: no visible global function definition for ‘tsboot’
boot_spec: no visible global function definition for ‘spec.pgram’
boot_spec: no visible global function definition for ‘quantile’
boot_spec: no visible global function definition for ‘polygon’
boot_spec: no visible global function definition for ‘lines’
redraw: no visible global function definition for ‘spec.pgram’
statistic: no visible global function definition for ‘acf’
Undefined global functions or variables:
  abline acf frequency is.ts lines par polygon quantile spec.pgram
  tsboot
Consider adding
  importFrom("graphics", "abline", "lines", "par", "polygon")
  importFrom("stats", "acf", "frequency", "is.ts", "quantile",
             "spec.pgram")
to your NAMESPACE file.
'::' or ':::' imports not declared from:
  ‘fracdiff’ ‘timeDate’ ‘tseries’
author.search: no visible binding for global variable ‘na.omit’
reference.list: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
drawGraph: no visible global function definition for ‘pdf’
drawGraph: no visible global function definition for ‘par’
drawGraph: no visible global function definition for ‘plot’
drawGraph: no visible global function definition for ‘segments’
drawGraph: no visible global function definition for ‘lines’
drawGraph: no visible global function definition for ‘text’
drawGraph: no visible global function definition for ‘dev.off’
drugRank: no visible global function definition for ‘aggregate’
floating2: no visible global function definition for ‘cor’
timma: no visible global function definition for ‘median’
timma: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  aggregate cor dev.off lines median par pdf plot segments text
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot", "segments", "text")
  importFrom("stats", "aggregate", "cor", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
File ‘timma/libs/timma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘TIMP/libs/TIMP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘ExPosition’ ‘InPosition’ ‘TExPosition’ ‘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.tepBADA.inference.battery print.tepDICA.inference.battery
  print.tinpoAllBoots print.tinpoBoot print.tinpoBootTests
  print.tinpoComponents print.tinpoLOO print.tinpoOmni
  print.tinpoOutput print.tinpoR2
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Non-standard files/directories found at top level:
  ‘DESCRIPTION.orig’ ‘README.rst’
tipom.car: no visible global function definition for ‘abline’
tipom.car: no visible global function definition for ‘axis’
tipom.heat: no visible global function definition for ‘image’
tipom.heat: no visible global function definition for ‘gray’
tipom.lw: no visible global function definition for ‘plot’
tipom.lw: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline axis gray image plot
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "image", "plot")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘boot’ ‘lattice’ ‘splines’ ‘tcltk’
  Please remove these calls from your code.
ls.tree: no visible global function definition for ‘lm’
ls.tree: no visible global function definition for ‘coef’
Undefined global functions or variables:
  coef lm
Consider adding
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
File ‘TKF/libs/TKF.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 an obsolete/platform-specific call in the following function:
  ‘.my.tkdev’
Found the platform-specific device:
  ‘X11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
File ‘tkrplot/libs/tkrplot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
FLXmclust.Density: no visible global function definition for ‘dmvnorm’
FLXmclust.Estimate: no visible global function definition for ‘flexmix’
FLXmclust.Estimate: no visible global function definition for
  ‘FLXmclust’
coefmclust: no visible global function definition for ‘parameters’
flexmix.Density: no visible global function definition for
  ‘model.matrix’
flexmix.Density: no visible global function definition for
  ‘model.response’
flexmix.Density: no visible global function definition for
  ‘model.frame’
flexmix.Density: no visible global function definition for ‘dnorm’
flexmix.Density: no visible global function definition for ‘dpois’
flexmix.Density: no visible global function definition for ‘dbinom’
flexmix.Estimate: no visible global function definition for ‘flexmix’
flexmix.Estimate: no visible global function definition for ‘FLXglm’
tleplot,TLE-data.frame: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  FLXglm FLXmclust dbinom dmvnorm dnorm dpois flexmix legend
  model.frame model.matrix model.response parameters
Consider adding
  importFrom("graphics", "legend")
  importFrom("stats", "dbinom", "dnorm", "dpois", "model.frame",
             "model.matrix", "model.response")
to your NAMESPACE file.
'library' or 'require' call to ‘mvtnorm’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
EMN: no visible global function definition for ‘dmvnorm’
EMN: no visible global function definition for ‘pmvnorm’
EMT: no visible global function definition for ‘GenzBretz’
EMT: no visible global function definition for ‘dmvt’
EMT: no visible global function definition for ‘pmvt’
MomemNT: no visible global function definition for ‘pnorm’
MomemNT: no visible global function definition for ‘dnorm’
MomemNT: no visible global function definition for ‘pmvnorm’
MomemNT: no visible global function definition for ‘dmvnorm’
TT.moment: no visible global function definition for ‘GenzBretz’
TT.moment: no visible global function definition for ‘pmvt’
TT.moment: no visible global function definition for ‘dt’
TT.moment: no visible global function definition for ‘pt’
TT.moment: no visible global function definition for ‘dmvt’
cdfNI: no visible global function definition for ‘pnorm’
cdfNI: no visible global function definition for ‘pt’
inits: no visible global function definition for ‘lm’
Undefined global functions or variables:
  GenzBretz dmvnorm dmvt dnorm dt lm pmvnorm pmvt pnorm pt
Consider adding
  importFrom("stats", "dnorm", "dt", "lm", "pnorm", "pt")
to your NAMESPACE file.
Rd file 'UTIdata.Rd':
  \examples lines wider than 100 characters:
     x = cbind((UTIdata$Fup==0)+0, (UTIdata$Fup==1)+0, (UTIdata$Fup==3)+0, (UTIdata$Fup==6)+0, (UTIdata$Fup==9)+0, (UTIdata$Fup==12)+0, (UTI ... [TRUNCATED]

These lines will be truncated in the PDF manual.
search_collection: no visible global function definition for
  ‘URLencode’
search_company: no visible global function definition for ‘URLencode’
search_keyword: no visible global function definition for ‘URLencode’
search_list: no visible global function definition for ‘URLencode’
search_movie: no visible global function definition for ‘URLencode’
search_multi: no visible global function definition for ‘URLencode’
search_person: no visible global function definition for ‘URLencode’
search_tv: no visible global function definition for ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
File ‘tmg/libs/tmg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
extractContentDOM: no visible global function definition for
  ‘capture.output’
extractHTMLStrip: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  capture.output
Consider adding
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Packages suggested but not available for checking:
  ‘Rcampdf’ ‘tm.lexicon.GeneralInquirer’
File ‘tmvnsim/libs/tmvnsim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tmvtnorm/libs/tmvtnorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("toaster")
  Loading required package: RODBC
  > 
  > test_check("toaster")
  ── 1. Failure: format 'boxplot' works (@test-showData.R#12)  ───────────────────
  setdiff(p$layout$panel_ranges[[1]]$x.labels, getNumericColumns(notNullNumData)) not equal to character(0).
  target is NULL, current is character
  
  ── 2. Failure: format 'boxplot' with facets works (@test-showData.R#21)  ───────
  nrow(p$layout$panel_layout) not equal to length(cols).
  target is NULL, current is numeric
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 496 SKIPPED: 0 FAILED: 2
  1. Failure: format 'boxplot' works (@test-showData.R#12) 
  2. Failure: format 'boxplot' with facets works (@test-showData.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘corpus.JSS.papers’
File ‘TopKLists/libs/TopKLists.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Tosls.formula: no visible global function definition for ‘model.matrix’
Tosls.formula: no visible global function definition for
  ‘model.response’
summary: no visible global function definition for ‘coef’
summary: no visible global function definition for ‘pt’
Undefined global functions or variables:
  coef model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.matrix", "model.response", "pt")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘Cairo’ ‘RGtk2’ ‘colorspace’ ‘gWidgets’ ‘tourr’
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘TeachingDemos’ ‘ash’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Cairo’ ‘RGtk2’ ‘colorspace’ ‘gWidgets’ ‘tourr’
  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: ‘rmongodb’
ConfA: no visible global function definition for ‘qf’
EstM2Sn: no visible global function definition for ‘nlm’
EstM2Sn: no visible global function definition for ‘qnorm’
TV.model: no visible global function definition for ‘dev.new’
TV.model: no visible global function definition for ‘points’
betaBino: no visible global function definition for ‘pbinom’
doseD: no visible global function definition for ‘lm’
doseD: no visible global function definition for ‘dev.new’
doseD: no visible global function definition for ‘par’
doseD: no visible global function definition for ‘plot’
doseD: no visible global function definition for ‘axTicks’
doseD: no visible global function definition for ‘axis’
doseD: no visible global function definition for ‘lines’
doseD: no visible global function definition for ‘abline’
doseD: no visible global function definition for ‘legend’
setD: no visible global function definition for ‘dev.new’
setD: no visible global function definition for ‘par’
setD: no visible global function definition for ‘pbinom’
setD: no visible global function definition for ‘abline’
setD: no visible global function definition for ‘axis’
setD: no visible global function definition for ‘rect’
setD: no visible global function definition for ‘lines’
setD: no visible global function definition for ‘text’
setD: no visible global function definition for ‘axTicks’
setD: no visible global function definition for ‘legend’
spoD : spoD_A: no visible global function definition for ‘chisq.test’
Undefined global functions or variables:
  abline axTicks axis chisq.test dev.new legend lines lm nlm par pbinom
  plot points qf qnorm rect text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axTicks", "axis", "legend", "lines",
             "par", "plot", "points", "rect", "text")
  importFrom("stats", "chisq.test", "lm", "nlm", "pbinom", "qf", "qnorm")
to your NAMESPACE file.
align1d : obj: no visible global function definition for ‘dist’
align2d : obj: no visible global function definition for ‘dist’
align2d : pen: no visible global function definition for ‘dist’
align2d: no visible global function definition for ‘dist’
sumt: no visible global function definition for ‘optim’
tpe1d: no visible global function definition for ‘hclust’
tpe2d: no visible global function definition for ‘hclust’
tpe2d: no visible global function definition for ‘cmdscale’
Undefined global functions or variables:
  cmdscale dist hclust optim
Consider adding
  importFrom("stats", "cmdscale", "dist", "hclust", "optim")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/tpr.Rcheck/00install.out’ for details.
Found the following calls to attach():
File ‘track/R/track.attach.R’:
  attach(what = NULL, pos = pos, name = name)
See section ‘Good practice’ in ‘?attach’.
DeadReckoning: no visible global function definition for ‘filter’
DeadReckoning: no visible global function definition for ‘approx’
DeadReckoning: no visible global function definition for ‘lm’
Mapper: no visible global function definition for ‘colorRampPalette’
Mapper: no visible global function definition for ‘terrain.colors’
Mapper: no visible global function definition for ‘points’
Mapper: no visible global function definition for ‘axis’
Standardize: no visible global function definition for ‘lm’
Undefined global functions or variables:
  approx axis colorRampPalette filter lm points terrain.colors
Consider adding
  importFrom("grDevices", "colorRampPalette", "terrain.colors")
  importFrom("graphics", "axis", "points")
  importFrom("stats", "approx", "filter", "lm")
to your NAMESPACE file.
Running ‘ggplot_extraction.R’ [9s/10s]
  Running ‘trackr-tests.R’ [7s/9s]
Running the tests in ‘tests/trackr-tests.R’ failed.
Complete output:
  > library(trackr)
  Loading required package: histry
  > library(knitr)
  > be = JSONBackend(tempfile())
  > tdb = TrackrDB(backend=be, img_dir = tempdir())
  > defaultTDB(tdb)
  An object of class "TrackrDB"
  Slot "opts":
  An object of class "TrackrOptions"
  Slot "insert_delay":
  [1] 0
  
  Slot "img_dir":
  [1] "/tmp/Rtmpbpud06"
  
  Slot "img_ext":
  [1] "png"
  
  Slot "backend_opts":
  list()
  
  
  Slot "backend":
  Reference class object of class "JSONBackend"
  Field "docs":
  DocList (0x0)
  Field ".file":
  [1] "/tmp/Rtmpbpud06/file6dfa5ed406d1"
  Field "file":
  [1] "/tmp/Rtmpbpud06/file6dfa5ed406d1"
  
  > 
  > rmdfil = system.file("test_docs/knitr_test.Rmd", package = "trackr")
  > knit_and_record(rmdfil, verbose = TRUE)
  
  
  processing file: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/trackr/test_docs/knitr_test.Rmd
  
  
  processing file: knitr_test.Rmd
    ordinary text without R code
  
  label: plot
  Error in file(file, ifelse(append, "a", "w")) : 
    cannot open the connection
  Calls: knit_and_record ... <Anonymous> -> .handleSimpleError -> h -> cat -> file
  In addition: Warning messages:
  1: In dir.create(dirname(name), recursive = TRUE) :
    cannot create dir 'knitr_test_files/figure-html', reason 'No such file or directory'
  2: In file(file, ifelse(append, "a", "w")) :
    cannot open file 'knitr_test.knit.md': Read-only file system
  Execution halted
microsoftTranslate: no visible global function definition for
  ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
rtrapezoid: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
File ‘trapezoid/libs/trapezoid.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘treeclim/libs/treeclim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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_JTree: no visible global function definition for ‘flush.console’
Run_JTree: no visible global function definition for ‘cov2cor’
Undefined global functions or variables:
  cov2cor flush.console
Consider adding
  importFrom("stats", "cov2cor")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
LikAge: no visible global function definition for ‘read.table’
bd.ME.optim: no visible global function definition for ‘optim’
bd.ME.optim.rho: no visible global function definition for ‘optim’
bd.ME.optim.rho.all: no visible global function definition for ‘optim’
bd.MEyule.optim: no visible global function definition for ‘optimize’
bd.MEyule.optim: no visible global function definition for ‘optim’
bd.age.optim.matlab: no visible global function definition for
  ‘read.table’
bd.groups.conf: no visible global function definition for ‘uniroot’
bd.shifts.plot: no visible global function definition for ‘plot’
bd.shifts.plot: no visible global function definition for ‘lines’
bdsky.stt.optim: no visible global function definition for ‘optim’
create.mat: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  lines optim optimize plot read.table uniroot write.table
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "optim", "optimize", "uniroot")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
plot.treeperm: no visible global function definition for ‘hist’
plot.treeperm: no visible global function definition for ‘points’
plot.treeperm: no visible global function definition for ‘text’
treeperm.formula: no visible global function definition for
  ‘model.frame’
treeperm.formula: no visible global function definition for
  ‘model.response’
Undefined global functions or variables:
  hist model.frame model.response points text
Consider adding
  importFrom("graphics", "hist", "points", "text")
  importFrom("stats", "model.frame", "model.response")
to your NAMESPACE file.
File ‘treeperm/libs/treeperm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘TrialSize/libs/TrialSize.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘tricolore-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ColorKey
> ### Title: Ternary Balance Scheme Legend
> ### Aliases: ColorKey
> ### Keywords: internal
> 
> ### ** Examples
> 
> tricolore:::ColorKey(breaks = 5, h_ = 0, c_ = 140, l_ = 70, contrast = 0.5,
+                      center = rep(1/3, 3), spread = 1)
Error in f(..., self = self) : unused argument (plot$coordinates)
Calls: <Anonymous> -> print.ggplot -> ggplot_build -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 82-89 (european_education.Rmd) 
Error: processing vignette ‘european_education.Rmd’ failed with diagnostics:
unused argument (plot$coordinates)
Execution halted
File ‘triebeard/libs/triebeard.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.trifield
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.trifield: no visible global function definition for ‘topo.colors’
plot.trifield: no visible global function definition for ‘plot’
plot.trifield: no visible global function definition for ‘image’
plot.trifield: no visible global function definition for ‘contour’
plot.trifield: no visible global function definition for ‘text’
ternary.legend: no visible global function definition for ‘arrows’
ternary.legend: no visible global function definition for ‘text’
triaxes: no visible global function definition for ‘lines’
tribox: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  arrows contour image lines plot polygon text topo.colors
Consider adding
  importFrom("grDevices", "topo.colors")
  importFrom("graphics", "arrows", "contour", "image", "lines", "plot",
             "polygon", "text")
to your NAMESPACE file.
Rd file 'plot.trifield.Rd':
  \usage lines wider than 90 characters:
     plot(x, contours = TRUE, col = topo.colors(256), lab1 = "A = 0", lab2 = "B = 0", lab3 = "C = 0", tribox = TRUE, axis.lines = TRUE, ...)

Rd file 'ternary.legend.Rd':
  \usage lines wider than 90 characters:
     ternary.legend(x0 = 0.2, y0 = 0.8, radius = 0.1, lab1 = "A", lab2 = "B", lab3 = "C", infl = 1.5, cex = 0.75, length = 0.05, ...)

These lines will be truncated in the PDF manual.
cinbag: no visible global function definition for ‘var’
trimTrees: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict var
Consider adding
  importFrom("stats", "predict", "var")
to your NAMESPACE file.
File ‘trimTrees/libs/trimTrees.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘gtools’ ‘mgcv’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘gtools’ ‘mgcv’ ‘msm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HtoGp: no visible global function definition for ‘odd’
HtoGp: no visible global function definition for ‘even’
plot.pirls.gam: no visible global function definition for ‘par’
plot.pirls.gam: no visible global function definition for ‘plot’
plot.pirls.gam: no visible global function definition for ‘title’
plot.pirls.gam: no visible global function definition for ‘lines’
plot.pirls.gam: no visible global function definition for ‘rug’
plot.pirls.gam: no visible global function definition for ‘mtext’
test.trioGxE: no visible global function definition for ‘write.table’
trioGxE: no visible global function definition for ‘quantile’
trioGxE: no visible global function definition for ‘qtnorm’
trioplot: no visible global function definition for ‘quantile’
trioplot: no visible global function definition for ‘formula’
trioplot: no visible global function definition for ‘gam’
trioplot: no visible global function definition for ‘binomial’
Undefined global functions or variables:
  binomial even formula gam lines mtext odd par plot qtnorm quantile
  rug title write.table
Consider adding
  importFrom("graphics", "lines", "mtext", "par", "plot", "rug", "title")
  importFrom("stats", "binomial", "formula", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
File ‘tripack/libs/tripack.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.
DrawMargin: no visible global function definition for ‘qnorm’
DrawProbability: no visible global function definition for ‘pnorm’
Factor: no visible global function definition for ‘new’
Gaussian: no visible global function definition for ‘new’
LikelihoodFactor: no visible global function definition for ‘new’
Parameters: no visible global function definition for ‘new’
Player: no visible global function definition for ‘new’
PriorFactor: no visible global function definition for ‘new’
SumFactor: no visible global function definition for ‘new’
TruncateFactor: no visible global function definition for ‘new’
Variable: no visible global function definition for ‘new’
Vdraw: no visible global function definition for ‘dnorm’
Vdraw: no visible global function definition for ‘pnorm’
Vwin: no visible global function definition for ‘dnorm’
Vwin: no visible global function definition for ‘pnorm’
Wdraw: no visible global function definition for ‘dnorm’
Wdraw: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dnorm new pnorm qnorm
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dnorm", "pnorm", "qnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
cdens: no visible global function definition for ‘head’
dplot: no visible global function definition for ‘knots’
dplot: no visible global function definition for ‘median’
dplot: no visible global function definition for ‘par’
dplot: no visible global function definition for ‘plot.stepfun’
dplot: no visible global function definition for ‘abline’
edf: no visible global function definition for ‘approxfun’
mctest : rdist: no visible global function definition for ‘runif’
mctest : S: no visible global function definition for ‘optim’
qplot: no visible global function definition for ‘plot’
qplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline approxfun head knots median optim par plot plot.stepfun runif
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "approxfun", "knots", "median", "optim",
             "plot.stepfun", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
File ‘truncgof/libs/truncgof.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
dmvnb: no visible global function definition for ‘dbinom’
drvts: no visible global function definition for ‘dnorm’
drvts: no visible global function definition for ‘dbinom’
dsvts: no visible global function definition for ‘dnorm’
rescale: no visible global function definition for ‘qlogis’
rescale: no visible global function definition for ‘plogis’
tslogl: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dbinom dnorm plogis qlogis
Consider adding
  importFrom("stats", "dbinom", "dnorm", "plogis", "qlogis")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  print.tsbugs
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'ar.bugs.Rd':
  \examples lines wider than 100 characters:
     ar2 <- ar.bugs(y = diff(LH), ar.order = 2, ar.prior = "dunif(-1,1)", var.prior = "dgamma(0.001,0.001)")

Rd file 'rv.bugs.Rd':
  \usage lines wider than 90 characters:
                     rv.tol0.prior = "dgamma(0.000001,0.000001)", rv.eps.prior = "dbeta(1, 100)", 
  \examples lines wider than 100 characters:
       plot(NULL, type = "n", xlim = tsp(sigma.pn)[1:2], ylim = range(sigma.pn[, 1:95]), main = "sigma_t")

Rd file 'sv.bugs.Rd':
  \examples lines wider than 100 characters:
       plot(NULL, type = "n", xlim = tsp(sigma.pn)[1:2], ylim = range(sigma.pn[, 1:95]), main = "sigma_t")

These lines will be truncated in the PDF manual.
tfDetails: no visible global function definition for ‘start’
tfDetails: no visible global function definition for ‘end’
Undefined global functions or variables:
  end start
Consider adding
  importFrom("stats", "end", "start")
to your NAMESPACE file.
Qhat: no visible global function definition for ‘pnorm’
plrt: no visible global function definition for ‘uniroot’
plrt: no visible global function definition for ‘optimize’
simulatedata: no visible global function definition for ‘rnorm’
tsc.test: no visible global function definition for ‘shapiro.test’
tsc.test: no visible global function definition for ‘p.adjust’
tsc.test: no visible global function definition for ‘glm’
tsc.test : f: no visible global function definition for ‘pnorm’
tsc.test: no visible global function definition for ‘uniroot’
tsc.test: no visible global function definition for ‘optimize’
variance: no visible global function definition for ‘density’
variance: no visible global function definition for ‘ecdf’
Undefined global functions or variables:
  density ecdf glm optimize p.adjust pnorm rnorm shapiro.test uniroot
Consider adding
  importFrom("stats", "density", "ecdf", "glm", "optimize", "p.adjust",
             "pnorm", "rnorm", "shapiro.test", "uniroot")
to your NAMESPACE file.
File ‘tsc/libs/tsc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘deSolve’
  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.ami plot.d2 plot.false.nearest print.d2 print.false.nearest
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'sim.cont.Rd':
  \examples lines wider than 100 characters:
     rossler.ts <- sim.cont(rossler.syst, start=0, end=650, dt=0.1, start.x=c(0,0,0), parms=c(0.15, 0.2, 10))

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
vintageMap: no visible global function definition for ‘read.table’
TSget,character-TSfameLocalConnection: no visible global function
  definition for ‘as.ts’
TSget,character-TSfameLocalConnection: no visible global function
  definition for ‘zoo’
TSget,character-TSfameLocalConnection: no visible global function
  definition for ‘frequency’
TSget,character-TSfameServerConnection: no visible global function
  definition for ‘as.ts’
TSget,character-TSfameServerConnection: no visible global function
  definition for ‘zoo’
TSget,character-TSfameServerConnection: no visible global function
  definition for ‘frequency’
Undefined global functions or variables:
  as.ts frequency read.table zoo
Consider adding
  importFrom("stats", "as.ts", "frequency")
  importFrom("utils", "read.table")
to your NAMESPACE file.
DstandardizedLoadings.TSFmodel: no visible global function definition
  for ‘cov’
FAfitStats.TSFmodel: no visible global function definition for ‘cov’
FAfitStats.default: no visible global function definition for ‘cor’
FAfitStats.default: no visible global function definition for
  ‘factanal’
FAfitStats.default: no visible global function definition for ‘pchisq’
FAmodelFitStats: no visible global function definition for ‘pchisq’
checkResiduals.TSFmodel: no visible global function definition for
  ‘cov’
distribution.factorsEstEval: no visible global function definition for
  ‘par’
distribution.factorsEstEval: no visible binding for global variable
  ‘par’
distribution.factorsEstEval: no visible global function definition for
  ‘density’
distribution.factorsEstEval: no visible global function definition for
  ‘matplot’
distribution.factorsEstEval: no visible global function definition for
  ‘title’
summary.TSFmodel: no visible global function definition for ‘start’
summary.TSFmodel: no visible global function definition for ‘end’
Undefined global functions or variables:
  cor cov density end factanal matplot par pchisq start title
Consider adding
  importFrom("graphics", "matplot", "par", "title")
  importFrom("stats", "cor", "cov", "density", "end", "factanal",
             "pchisq", "start")
to your NAMESPACE file.
Func.SAX: no visible global function definition for ‘sd’
Func.SAX: no visible global function definition for ‘qnorm’
Func.matrix: no visible global function definition for ‘qnorm’
Func.motif: no visible global function definition for ‘sd’
Func.motif: no visible global function definition for ‘na.omit’
Func.motif: no visible global function definition for ‘combn’
Func.motif.multivariate: no visible global function definition for
  ‘txtProgressBar’
Func.motif.multivariate: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  combn na.omit qnorm sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit", "qnorm", "sd")
  importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
dLag : dlag.f: no visible global function definition for
  ‘complete.cases’
distmat: no visible global function definition for ‘dist’
fitCity: no visible global function definition for ‘glm.control’
fitCity: no visible global function definition for ‘terms’
ldmvnorm: no visible global function definition for ‘mahalanobis’
lspline: no visible global function definition for ‘quantile’
plot.tsdecomp: no visible global function definition for ‘par’
plot.tsdecomp: no visible global function definition for ‘plot’
setupFormula: no visible global function definition for ‘as.formula’
spatialgibbs: no visible global function definition for ‘rnorm’
spatialgibbs: no visible global function definition for ‘rgamma’
spatialgibbs: no visible global function definition for ‘runif’
tsdecomp: no visible global function definition for ‘fft’
Undefined global functions or variables:
  as.formula complete.cases dist fft glm.control mahalanobis par plot
  quantile rgamma rnorm runif terms
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.formula", "complete.cases", "dist", "fft",
             "glm.control", "mahalanobis", "quantile", "rgamma", "rnorm",
             "runif", "terms")
to your NAMESPACE file.
covTranspose11: warning in glasso(sc, 2 * rhoc/n, wi.init = gc$wi,
  w.init = gc$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of ‘penalize.diag’ to
  ‘penalize.diagonal’
covTranspose11: warning in glasso(sr, 2 * rhor/p, wi.init = gr$wi,
  w.init = gr$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of ‘penalize.diag’ to
  ‘penalize.diagonal’
.help.ESS: no visible global function definition for ‘index.search’
TransSphere : ttin: no visible global function definition for ‘t.test’
TransSphere: no visible global function definition for ‘sd’
TransSphere: no visible global function definition for ‘quantile’
TransSphere: no visible global function definition for ‘pt’
Undefined global functions or variables:
  index.search pt quantile sd t.test
Consider adding
  importFrom("stats", "pt", "quantile", "sd", "t.test")
to your NAMESPACE file.
File ‘tspmeta/libs/tspmeta.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
TT.GS : TT.GS.sp: no visible global function definition for ‘qt’
TT.GS : TT.GS.sp: no visible global function definition for ‘runif’
TT.GS : TT.GS.sp: no visible global function definition for ‘pt’
TT.moment: no visible global function definition for ‘dt’
TT.moment: no visible global function definition for ‘pt’
Undefined global functions or variables:
  dt pt qt runif
Consider adding
  importFrom("stats", "dt", "pt", "qt", "runif")
to your NAMESPACE file.
ttScreening: no visible global function definition for ‘gaussian’
ttScreening: no visible global function definition for ‘glm.control’
ttScreening: no visible global function definition for ‘model.response’
ttScreening: no visible global function definition for ‘is.empty.model’
ttScreening: no visible global function definition for ‘model.matrix’
ttScreening: no visible global function definition for ‘na.omit’
ttScreening: no visible global function definition for ‘terms’
ttScreening: no visible global function definition for ‘capture.output’
ttScreening: no visible global function definition for ‘glm’
ttScreening: no visible binding for global variable ‘gaussian’
ttScreening: no visible global function definition for ‘pt’
ttScreening: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  capture.output gaussian glm glm.control is.empty.model model.matrix
  model.response na.omit p.adjust pt terms
Consider adding
  importFrom("stats", "gaussian", "glm", "glm.control", "is.empty.model",
             "model.matrix", "model.response", "na.omit", "p.adjust",
             "pt", "terms")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
.saveDevice: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off
Consider adding
  importFrom("grDevices", "dev.off")
to your NAMESPACE file.
ttwa: no visible global function definition for ‘aggregate’
ttwa: no visible global function definition for ‘txtProgressBar’
ttwa: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  aggregate setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "aggregate")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
http.connection: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
turf: no visible global function definition for ‘read.table’
turf: no visible global function definition for ‘flush.console’
turf.combos: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn flush.console read.table
Consider adding
  importFrom("utils", "combn", "flush.console", "read.table")
to your NAMESPACE file.
File ‘tvd/libs/tvd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘TwoPhaseInd/libs/TwoPhaseInd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.twoStageGwasPower print.twoStageNull
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
condnorm: no visible global function definition for ‘pnorm’
condnorm: no visible global function definition for ‘dnorm’
find.p.joint: no visible global function definition for ‘integrate’
find.p.joint.alt: no visible global function definition for ‘integrate’
termsInt: no visible global function definition for ‘pnorm’
termsInt.alt: no visible global function definition for ‘pnorm’
twoStageNull: no visible global function definition for ‘qnorm’
twoStageNull: no visible global function definition for ‘optimize’
twoStagePower: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dnorm integrate optimize pnorm qnorm
Consider adding
  importFrom("stats", "dnorm", "integrate", "optimize", "pnorm", "qnorm")
to your NAMESPACE file.
Rd file 'twoStageGwasPower.Rd':
  \usage lines wider than 90 characters:
     twoStageGwasPower(pD, pG, grr, inheritance = "multiplicative", pi.samples, pi.markers, alpha.marker, n.cases, n.controls)

These lines will be truncated in the PDF manual.
txtacf: no visible binding for global variable ‘na.fail’
txtacf: no visible global function definition for ‘acf’
txtboxplot : <anonymous>: no visible global function definition for
  ‘boxplot.stats’
txtboxplot: no visible global function definition for ‘boxplot.stats’
txtdensity: no visible global function definition for ‘density’
Undefined global functions or variables:
  acf boxplot.stats density na.fail
Consider adding
  importFrom("grDevices", "boxplot.stats")
  importFrom("stats", "acf", "density", "na.fail")
to your NAMESPACE file.
Crm: no visible global function definition for ‘integrate’
Crm : <anonymous>: no visible global function definition for
  ‘integrate’
Crm: no visible global function definition for ‘optimize’
ail1: no visible global function definition for ‘uniroot’
ail2 : fu : <anonymous>: no visible global function definition for
  ‘integrate’
ail2: no visible global function definition for ‘uniroot’
aip : fu : <anonymous>: no visible global function definition for
  ‘integrate’
aip: no visible global function definition for ‘uniroot’
ait1: no visible global function definition for ‘uniroot’
ait2 : fu : <anonymous>: no visible global function definition for
  ‘integrate’
ait2: no visible global function definition for ‘uniroot’
sim3p3: no visible global function definition for ‘rbinom’
simCrm: no visible global function definition for ‘rbinom’
simCrm: no visible global function definition for ‘palette’
simCrm: no visible global function definition for ‘gray’
simCrm: no visible global function definition for ‘plot’
simCrm: no visible global function definition for ‘abline’
simCrm: no visible global function definition for ‘lines’
ssim3p3: no visible global function definition for ‘txtProgressBar’
ssim3p3: no visible global function definition for ‘setTxtProgressBar’
ssimCrm: no visible global function definition for ‘txtProgressBar’
ssimCrm: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  abline gray integrate lines optimize palette plot rbinom
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("grDevices", "gray", "palette")
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "integrate", "optimize", "rbinom", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
rmd2pdf: no visible global function definition for ‘tail’
rnw2pdf: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
File ‘ucminf/libs/ucminf.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(udapi)
  > 
  > test_check("udapi")
  ── 1. Failure: specific content can be retrieved (@test_udapi.R#5)  ────────────
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 11 - 10 == 1
  
  ── 2. Failure: random content can be retrieved (@test_udapi.R#10)  ─────────────
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 11 - 10 == 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 9 SKIPPED: 0 FAILED: 2
  1. Failure: specific content can be retrieved (@test_udapi.R#5) 
  2. Failure: random content can be retrieved (@test_udapi.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘udunits2/libs/udunits2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
ubRacing : predCandidate: no visible global function definition for
  ‘predict’
ubRacing : aux2.friedman.edit: no visible global function definition
  for ‘pchisq’
ubRacing : aux2.friedman.edit: no visible global function definition
  for ‘qt’
ubRacing : aux.friedman.edit: no visible global function definition for
  ‘wilcox.test’
ubRacing : aux.ttest.edit: no visible global function definition for
  ‘t.test’
ubRacing : aux.ttest.edit: no visible global function definition for
  ‘p.adjust’
ubRacing : idFolds: no visible global function definition for
  ‘quantile’
ubRacing: no visible binding for global variable ‘sd’
ubSmoteExs: no visible global function definition for ‘runif’
Undefined global functions or variables:
  p.adjust pchisq predict qt quantile runif sd t.test wilcox.test
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "predict", "qt", "quantile",
             "runif", "sd", "t.test", "wilcox.test")
to your NAMESPACE file.
med: no visible global function definition for ‘quantile’
uh: no visible global function definition for ‘mad’
uh.bu: no visible global function definition for ‘mad’
Undefined global functions or variables:
  mad quantile
Consider adding
  importFrom("stats", "mad", "quantile")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  predict.uniCox print.uniCoxCVFit print.uniCoxFit
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
permute.rows: no visible global function definition for ‘runif’
uniCox: no visible global function definition for ‘quantile’
uniCoxCV: no visible global function definition for ‘quantile’
uniCoxCV: no visible global function definition for ‘coxph’
uniCoxCV: no visible binding for global variable ‘var’
Undefined global functions or variables:
  coxph quantile runif var
Consider adding
  importFrom("stats", "quantile", "runif", "var")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'predict.uniCox':
  ‘predict.uniCox’

S3 methods shown with full name in documentation object 'uniCox-internal':
  ‘print.uniCoxCVFit’ ‘print.uniCoxFit’

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
dudewicz.unif.test: no visible global function definition for ‘runif’
frosini.unif.test: no visible global function definition for ‘runif’
hegazy.unif.test: no visible global function definition for ‘runif’
kolmogorov.unif.test: no visible global function definition for ‘runif’
kuiper.unif.test: no visible global function definition for ‘runif’
neyman.unif.test: no visible global function definition for ‘runif’
quesenberry.unif.test: no visible global function definition for
  ‘runif’
sarkadi.unif.test: no visible global function definition for ‘runif’
sherman.unif.test: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
cumcount: no visible global function definition for ‘setNames’
uniqtag: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
File ‘urca/libs/urca.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘uroot/libs/uroot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘USAboundariesData’
readSEER: no visible global function definition for ‘read.fwf’
Undefined global functions or variables:
  read.fwf
Consider adding
  importFrom("utils", "read.fwf")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘UScensus2000cdp/R/zzz.R’:
  .First.lib calls:
    cat(paste("'", ehelp[4], "'\n", "Version ", ehelp[2], " created on ",     ehelp[3], ".\n", sep = ""))
    cat(paste(substring(ehelp[3], first = 16), "\n", "Version ",     substring(ehelp[4], first = 16), " created on ", substring(ehelp[5],         first = 16), ".\n", sep = ""))
    cat(paste("copyright (c) 2009, Zack W. Almquist, University of California-Irvine\n",     sep = ""))
    cat("For citation information, type citation(\"UScensus2000cdp\").\n")
    cat("Type help(package=\"UScensus2000cdp\") to get started.\n")

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

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

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

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

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

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

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

These lines will be truncated in the PDF manual.
File ‘utf8latex/libs/utf8latex.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘uuid/libs/uuid.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘gen_uuid.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘gen_uuid.o’
File ‘uuid/libs/uuid.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 use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
histw: no visible global function definition for ‘plot.new’
histw: no visible global function definition for ‘plot.window’
histw: no visible global function definition for ‘axis’
histw: no visible global function definition for ‘rect’
histw: no visible global function definition for ‘lines’
uwham.boot: no visible binding for global variable ‘var’
Undefined global functions or variables:
  axis lines plot.new plot.window rect var
Consider adding
  importFrom("graphics", "axis", "lines", "plot.new", "plot.window",
             "rect")
  importFrom("stats", "var")
to your NAMESPACE file.
Packages suggested but not available for checking: ‘vaers’ ‘vaersND’
File ‘validatejsonr/libs/validatejsonr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Mammen: no visible global function definition for ‘runif’
PR2: no visible global function definition for ‘ar.burg’
PR2: no visible global function definition for ‘pt’
PR2: no visible global function definition for ‘pf’
PR3: no visible global function definition for ‘ar.burg’
PR3: no visible global function definition for ‘pt’
PR3: no visible global function definition for ‘pf’
VAR.FOR: no visible global function definition for ‘qnorm’
VAR.ForeB: no visible global function definition for ‘runif’
VAR.LRtest: no visible global function definition for ‘pchisq’
VAR.LRtest: no visible global function definition for ‘pf’
VAR.PI: no visible global function definition for ‘quantile’
VAR.Waldtest: no visible global function definition for ‘pf’
VAR.irf: no visible global function definition for ‘par’
VAR.irf: no visible global function definition for ‘plot’
VAR.irf: no visible global function definition for ‘abline’
VAR1.sim: no visible global function definition for ‘rnorm’
resamp: no visible global function definition for ‘runif’
Undefined global functions or variables:
  abline ar.burg par pchisq pf plot pt qnorm quantile rnorm runif
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "ar.burg", "pchisq", "pf", "pt", "qnorm",
             "quantile", "rnorm", "runif")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘Todo’
black_scholes: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
burdenPlot: no visible global function definition for ‘density’
burdenPlot: no visible global function definition for ‘axis’
burdenPlot: no visible global function definition for ‘points’
burdenPlot: no visible global function definition for ‘lines’
burdenPlot: no visible global function definition for ‘abline’
burdenPlot: no visible global function definition for ‘text’
burdenPlot: no visible global function definition for ‘sd’
burdenPlot: no visible global function definition for ‘segments’
vbdm: no visible global function definition for ‘var’
vbdm: no visible global function definition for ‘pchisq’
vbdmR : run_discrete_mixture_vanilla: no visible global function
  definition for ‘var’
vbdmR: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  abline axis density lines pchisq points sd segments text var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "points", "segments",
             "text")
  importFrom("stats", "density", "pchisq", "sd", "var")
to your NAMESPACE file.
File ‘vbdm/libs/vbdm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘VBLPCM/libs/VBLPCM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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_KL : rtnorm: no visible global function definition for ‘runif’
compute_KL : rtnorm: no visible global function definition for ‘dnorm’
compute_KL: no visible global function definition for ‘qnorm’
compute_KL: no visible global function definition for ‘dnorm’
compute_KL: no visible global function definition for ‘pnorm’
compute_KL: no visible global function definition for ‘var’
compute_KL: no visible global function definition for ‘rbinom’
compute_KL: no visible global function definition for ‘rnorm’
compute_KL: no visible global function definition for ‘sd’
vbsr: no visible global function definition for ‘qchisq’
vbsr: no visible global function definition for ‘var’
vbsr: no visible global function definition for ‘pchisq’
vbsr: no visible global function definition for ‘sd’
vbsr: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  dnorm pchisq pnorm qchisq qnorm rbinom rnorm runif sd var
Consider adding
  importFrom("stats", "dnorm", "pchisq", "pnorm", "qchisq", "qnorm",
             "rbinom", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
File ‘vbsr/libs/vbsr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.vda.le.default: no visible global function definition for ‘predict’
cv.vda.r.default: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
File ‘VDA/libs/VDA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Compare2FDS: no visible global function definition for ‘runif’
Compare2FDS: no visible global function definition for ‘lm’
Compare2FDS: no visible global function definition for ‘model.matrix’
Compare2FDS: no visible global function definition for ‘plot’
Compare2FDS: no visible global function definition for ‘abline’
Compare2FDS: no visible global function definition for ‘lines’
Compare2FDS: no visible global function definition for ‘text’
Compare2Vdg: no visible global function definition for ‘par’
Compare2Vdg: no visible global function definition for ‘plot’
Compare2Vdg: no visible global function definition for ‘lines’
Compare2Vdg: no visible global function definition for ‘legend’
FDSPlot: no visible global function definition for ‘runif’
FDSPlot: no visible global function definition for ‘lm’
FDSPlot: no visible global function definition for ‘model.matrix’
FDSPlot: no visible global function definition for ‘plot’
FDSPlot: no visible global function definition for ‘abline’
Vdgraph: no visible global function definition for ‘par’
Vdgraph: no visible global function definition for ‘plot’
Vdgraph: no visible global function definition for ‘lines’
Vdgraph: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline legend lines lm model.matrix par plot runif text
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "plot",
             "text")
  importFrom("stats", "lm", "model.matrix", "runif")
to your NAMESPACE file.
File ‘Vdgraph/libs/Vdgraph.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
calculateParameters,AffineTransformation: no visible global function
  definition for ‘lm’
calculateParameters,AffineTransformation: no visible global function
  definition for ‘coef’
calculateParameters,SimilarityTransformation: no visible global
  function definition for ‘lm’
calculateParameters,SimilarityTransformation: no visible global
  function definition for ‘coef’
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for ‘points’
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for ‘legend’
Undefined global functions or variables:
  coef legend lm points
Consider adding
  importFrom("graphics", "legend", "points")
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
DrawDensity3D: no visible global function definition for ‘colorRamp’
DrawDensity3D: no visible global function definition for ‘rgb’
ReadFromFile3D: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  colorRamp read.table rgb
Consider adding
  importFrom("grDevices", "colorRamp", "rgb")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'library' or 'require' call to ‘stats’ which was already attached by Depends.
  Please remove these calls from your code.
H: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = H, func.arg = list(func.arg), boot.arg)):
  partial argument match of ‘arg’ to ‘args’
M.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = M.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
Rel.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = Rel.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
bootstrap: warning in do.call(what = func, arg = list(boots[, , i])):
  partial argument match of ‘arg’ to ‘args’
bootstrap: warning in do.call(what = func, arg = c(abundances =
  list(boots[, , i]), func.arg)): partial argument match of ‘arg’ to
  ‘args’
d: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = d, func.arg = list(func.arg), boot.arg)):
  partial argument match of ‘arg’ to ‘args’
sim.groups: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of ‘arg’ to ‘args’
sim.table: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of ‘arg’ to ‘args’
similarity: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = similarity, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
turnover: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = turnover, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
prepare_Rd: H.Rd:41-42: Dropping empty section \note
prepare_Rd: M.homog.Rd:19-21: Dropping empty section \details
prepare_Rd: M.homog.Rd:35-36: Dropping empty section \note
prepare_Rd: Rel.homog.Rd:24-25: Dropping empty section \note
prepare_Rd: bootstrap.Rd:34: Dropping empty section \note
prepare_Rd: d.Rd:35-36: Dropping empty section \note
prepare_Rd: normalize.rows.Rd:26-27: Dropping empty section \note
prepare_Rd: p.q.sum.Rd:23-24: Dropping empty section \note
prepare_Rd: p.q.sum.Rd:26: Dropping empty section \examples
prepare_Rd: sim.groups.Rd:27-28: Dropping empty section \note
prepare_Rd: sim.table.Rd:25-26: Dropping empty section \note
prepare_Rd: similarity.Rd:25-26: Dropping empty section \note
prepare_Rd: turnover.Rd:17-18: Dropping empty section \details
prepare_Rd: turnover.Rd:29-30: Dropping empty section \note
plot.VennDiagram : <anonymous>: no visible global function definition
  for ‘hcl’
plot.VennDiagram: no visible global function definition for ‘plot.new’
plot.VennDiagram: no visible global function definition for
  ‘plot.window’
plot.VennDiagram: no visible global function definition for ‘col2rgb’
plot.VennDiagram: no visible global function definition for ‘rgb’
plot.VennDiagram: no visible global function definition for ‘polygon’
plot.VennDiagram: no visible global function definition for ‘text’
plot.VennDiagram: no visible global function definition for ‘title’
Undefined global functions or variables:
  col2rgb hcl plot.new plot.window polygon rgb text title
Consider adding
  importFrom("grDevices", "col2rgb", "hcl", "rgb")
  importFrom("graphics", "plot.new", "plot.window", "polygon", "text",
             "title")
to your NAMESPACE file.
File ‘VIFCP/libs/VIFCP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
vif: no visible global function definition for ‘sd’
vif: no visible global function definition for ‘lm’
vif: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  lm pnorm sd
Consider adding
  importFrom("stats", "lm", "pnorm", "sd")
to your NAMESPACE file.
Rd file 'vif.Rd':
  \usage lines wider than 90 characters:
             vif(y, x, w0 = 0.05, dw = 0.05, subsize = 200, trace = TRUE, mode = c("dense", "sparse"))
  \examples lines wider than 100 characters:
             vif.sel <- vif(housingexp$y, housingexp$x, w0 = 0.0005, dw = 0.005, subsize = 300, trace = FALSE);

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘vines/libs/vines.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.
panel.meansdplot : meansdplot.stats: no visible global function
  definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
prepare_Rd: panel.meansdplot.Rd:42-45: Dropping empty section \value
prepare_Rd: panel.meansdplot.Rd:49-51: Dropping empty section \note
prepare_Rd: panel.violinm.Rd:40-42: Dropping empty section \details
prepare_Rd: panel.violinm.Rd:43-49: Dropping empty section \value
prepare_Rd: panel.violinm.Rd:53-55: Dropping empty section \note
prepare_Rd: panel.violinm.Rd:50-52: Dropping empty section \author
prepare_Rd: violinmplot.Rd:34-36: Dropping empty section \details
prepare_Rd: violinmplot.Rd:48-50: Dropping empty section \note
Package in Depends field not imported from: ‘sm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
vioplot: no visible global function definition for ‘quantile’
vioplot: no visible global function definition for ‘median’
vioplot: no visible global function definition for ‘plot.new’
vioplot: no visible global function definition for ‘plot.window’
vioplot: no visible global function definition for ‘axis’
vioplot: no visible global function definition for ‘box’
vioplot: no visible global function definition for ‘polygon’
vioplot: no visible global function definition for ‘lines’
vioplot: no visible global function definition for ‘rect’
vioplot: no visible global function definition for ‘points’
Undefined global functions or variables:
  axis box lines median plot.new plot.window points polygon quantile
  rect
Consider adding
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "points", "polygon", "rect")
  importFrom("stats", "median", "quantile")
to your NAMESPACE file.
viopoints.default: no visible global function definition for ‘par’
viopoints.default: no visible global function definition for ‘plot.new’
viopoints.default: no visible global function definition for
  ‘plot.window’
viopoints.default: no visible global function definition for ‘axis’
viopoints.default: no visible global function definition for ‘arrows’
viopoints.default: no visible global function definition for
  ‘getFromNamespace’
viopoints.default: no visible global function definition for ‘title’
viopoints.default: no visible global function definition for ‘box’
Undefined global functions or variables:
  arrows axis box getFromNamespace par plot.new plot.window title
Consider adding
  importFrom("graphics", "arrows", "axis", "box", "par", "plot.new",
             "plot.window", "title")
  importFrom("utils", "getFromNamespace")
to your NAMESPACE file.
File ‘vita/libs/vita.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Decile.Plot: no visible global function definition for ‘barplot’
Decile.Plot: no visible global function definition for ‘axis’
Sliding.Window: no visible global function definition for ‘plot’
Sliding.Window: no visible global function definition for ‘lines’
Sliding.Window: no visible global function definition for ‘legend’
Undefined global functions or variables:
  axis barplot legend lines plot
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines", "plot")
to your NAMESPACE file.
RCplot: no visible global function definition for ‘residuals’
RCplot: no visible global function definition for ‘predict’
RCplot: no visible global function definition for ‘par’
RCplot: no visible global function definition for ‘plot.new’
RCplot: no visible global function definition for ‘plot.window’
RCplot: no visible global function definition for ‘strwidth’
RCplot: no visible global function definition for ‘plot’
RCplot: no visible global function definition for ‘abline’
RCplot: no visible global function definition for ‘text’
RCplot: no visible global function definition for ‘mtext’
fitted.vlmc: no visible global function definition for ‘predict’
print.vlmc: no visible global function definition for ‘AIC’
residuals.vlmc: no visible global function definition for ‘predict’
simulate.vlmc: no visible global function definition for ‘runif’
summary.vlmc: no visible global function definition for ‘predict’
vlmc: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  AIC abline mtext par plot plot.new plot.window predict qchisq
  residuals runif strwidth text
Consider adding
  importFrom("graphics", "abline", "mtext", "par", "plot", "plot.new",
             "plot.window", "strwidth", "text")
  importFrom("stats", "AIC", "predict", "qchisq", "residuals", "runif")
to your NAMESPACE file.
File ‘VLMC/libs/VLMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
voss1d: no visible global function definition for ‘approx’
voss1d: no visible global function definition for ‘rnorm’
voss1g: no visible global function definition for ‘dchisq’
voss1g: no visible global function definition for ‘approx’
voss1g: no visible global function definition for ‘rnorm’
voss2d: no visible global function definition for ‘rnorm’
voss2g: no visible global function definition for ‘dchisq’
voss2g: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  approx dchisq rnorm
Consider adding
  importFrom("stats", "approx", "dchisq", "rnorm")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Quitting from lines 43-46 (intro_to_voteogram.Rmd) 
Error: processing vignette ‘intro_to_voteogram.Rmd’ failed with diagnostics:
non-numeric argument to mathematical function
Execution halted
'library' or 'require' call to ‘raster’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
level: no visible global function definition for ‘quantile’
obj.rec: no visible global function definition for ‘txtProgressBar’
obj.rec: no visible global function definition for ‘setTxtProgressBar’
project: no visible global function definition for ‘aggregate’
raster.proj: no visible global function definition for ‘quantile’
raster.proj: no visible global function definition for ‘rasterFromXYZ’
raster.proj: no visible global function definition for ‘plot.new’
raster.proj: no visible global function definition for ‘plot’
raster.proj: no visible global function definition for ‘legend’
sub.obj: no visible global function definition for ‘aggregate’
sub.obj: no visible global function definition for ‘txtProgressBar’
sub.obj: no visible global function definition for ‘setTxtProgressBar’
surface: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  aggregate legend plot plot.new quantile rasterFromXYZ
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "plot", "plot.new")
  importFrom("stats", "aggregate", "quantile")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Package suggested but not available for checking: ‘hglm’
'library' or 'require' call to ‘misc3d’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.vscc: no visible global function definition for ‘rainbow’
plot.vscc: no visible global function definition for ‘pairs’
Undefined global functions or variables:
  pairs rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "pairs")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘vwr-Ex.R’
Packages in Depends field not imported from:
  ‘lattice’ ‘latticeExtra’ ‘stringdist’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ald: no visible global function definition for ‘detectCores’
ald: no visible global function definition for ‘mclapply’
coltheart.N: no visible global function definition for ‘detectCores’
coltheart.N: no visible global function definition for ‘mclapply’
hamming.distance: no visible global function definition for
  ‘stringdist’
ldknn: no visible global function definition for ‘detectCores’
ldknn: no visible global function definition for ‘mclapply’
ldknn.odds: no visible global function definition for ‘glm’
ldknn.odds: no visible binding for global variable ‘binomial’
ldknn.odds: no visible global function definition for ‘coefficients’
levenshtein.damerau.distance: no visible global function definition for
  ‘stringdist’
levenshtein.distance: no visible global function definition for
  ‘stringdist’
plot.ldknn.run: no visible global function definition for ‘histogram’
plot.ldknn.run: no visible global function definition for
  ‘theEconomist.theme’
plot.ldknn.run: no visible global function definition for ‘xyplot’
plot.ldknn.run: no visible global function definition for ‘as.layer’
Undefined global functions or variables:
  as.layer binomial coefficients detectCores glm histogram mclapply
  stringdist theEconomist.theme xyplot
Consider adding
  importFrom("stats", "binomial", "coefficients", "glm")
to your NAMESPACE file.
Package in Depends field not imported from: ‘Rcpp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'waffect-package.Rd':
  \examples lines wider than 100 characters:
     ## Not run: Typical usage to simulate case/control phenotypes under H1 (in this example: 5 individuals, 2 cases, 3 controls, the probab ... [TRUNCATED]
     ## Not run: Simulation of phenotypes in the multiclass case (in this example: 4 individuals and  3 classes, 1 individual in class 1, 2  ... [TRUNCATED]

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

These lines will be truncated in the PDF manual.
File ‘waffect/libs/waffect.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘waffect.o’
File ‘waffect/libs/waffect.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 use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

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

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

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

These lines will be truncated in the PDF manual.
Foreign function call to a different package:
  .C("comwr", ..., PACKAGE = "wavethresh")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.dwt plot.dwt.multiple plot.modwt print.dwt print.modwt
  print.wt.filter summary.dwt summary.modwt summary.wt.filter
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘wavelets/libs/wavelets.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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.dwt.2d
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘waveslim/libs/waveslim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
changepoints.sbs: no visible global function definition for ‘mad’
changepoints.wbs: no visible global function definition for ‘var’
changepoints.wbs: no visible global function definition for ‘quantile’
plot.sbs: no visible global function definition for ‘ts.plot’
plot.sbs: no visible global function definition for ‘lines’
plot.sbs: no visible global function definition for ‘title’
random.intervals: no visible global function definition for ‘runif’
sbs.default: no visible global function definition for ‘var’
wbs.default: no visible global function definition for ‘var’
Undefined global functions or variables:
  lines mad quantile runif title ts.plot var
Consider adding
  importFrom("graphics", "lines", "title")
  importFrom("stats", "mad", "quantile", "runif", "ts.plot", "var")
to your NAMESPACE file.
File ‘wbs/libs/wbs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
onesamplemeantest: no visible global function definition for ‘pnorm’
twosamplemeantest: no visible global function definition for ‘pnorm’
wcq: no visible global function definition for ‘var’
wcq: no visible global function definition for ‘pnorm’
wcq.fdrc: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  p.adjust pnorm var
Consider adding
  importFrom("stats", "p.adjust", "pnorm", "var")
to your NAMESPACE file.
File ‘webreadr/libs/webreadr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Weighted.Box.test: no visible global function definition for ‘acf’
Weighted.Box.test: no visible binding for global variable ‘na.pass’
Weighted.Box.test: no visible global function definition for ‘pgamma’
Weighted.Box.test: no visible global function definition for ‘pchisq’
Weighted.LM.test: no visible global function definition for ‘acf’
Weighted.LM.test: no visible binding for global variable ‘na.pass’
Weighted.LM.test: no visible global function definition for ‘pgamma’
Undefined global functions or variables:
  acf na.pass pchisq pgamma
Consider adding
  importFrom("stats", "acf", "na.pass", "pchisq", "pgamma")
to your NAMESPACE file.
File ‘weightedScores/libs/weightedScores.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ...
! LaTeX Error: Missing \begin{document}.

Error: processing vignette ‘WeightedMixedModels.Rmd’ failed with diagnostics:
Failed to compile WeightedMixedModels.tex. See WeightedMixedModels.log for more info.
Execution halted
'library' or 'require' call to ‘markdown’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  t_region.cpp:78:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:115:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:120:7: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/WhopGenome.Rcheck/00install.out’ for details.
dlog.norm: no visible global function definition for ‘rnorm’
fun.load.hals.a: no visible global function definition for ‘sfExport’
fun.load.hals.a: no visible global function definition for ‘sfLibrary’
fun.load.hals.fill: no visible global function definition for
  ‘sfExport’
fun.load.hals.fill: no visible global function definition for
  ‘sfLibrary’
fun.load.widals.a: no visible global function definition for ‘sfExport’
fun.load.widals.a: no visible global function definition for
  ‘sfLibrary’
fun.load.widals.fill: no visible global function definition for
  ‘sfExport’
fun.load.widals.fill: no visible global function definition for
  ‘sfLibrary’
unif.mh: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rnorm runif sfExport sfLibrary
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
File ‘widals/libs/widals.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘genefilter’ ‘parallel’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.onAttach: no visible global function definition for
  ‘packageDescription’
.relax.cvcompute: no visible binding for global variable
  ‘weighted.mean’
.relax.widenet.cv.elnet: no visible global function definition for
  ‘predict’
.relax.widenet.cv.elnet: no visible binding for global variable
  ‘weighted.mean’
.relax.widenet.cv.lognet: no visible global function definition for
  ‘predict’
.relax.widenet.cv.lognet: no visible binding for global variable
  ‘weighted.mean’
.widenet.cv.elnet: no visible global function definition for ‘predict’
.widenet.cv.elnet: no visible binding for global variable
  ‘weighted.mean’
.widenet.cv.lognet: no visible global function definition for ‘predict’
.widenet.cv.lognet: no visible binding for global variable
  ‘weighted.mean’
predict.widenet: no visible global function definition for ‘predict’
screen.cor : <anonymous>: no visible global function definition for
  ‘var’
screen.cor : <anonymous>: no visible global function definition for
  ‘cor.test’
screen.ttest: no visible global function definition for ‘colttests’
widenet: no visible global function definition for ‘mc.reset.stream’
widenet: no visible global function definition for ‘mclapply’
widenet: no visible global function definition for ‘predict’
Undefined global functions or variables:
  colttests cor.test mc.reset.stream mclapply packageDescription
  predict var weighted.mean
Consider adding
  importFrom("stats", "cor.test", "predict", "var", "weighted.mean")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
File ‘widenet/libs/widenet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Bundesliga.Mannschaft: no visible global function definition for ‘data’
Bundesliga.Mannschaft: no visible binding for global variable
  ‘Bundesliga’
Bundesliga.Tabelle: no visible global function definition for ‘data’
Bundesliga.Tabelle: no visible binding for global variable ‘Bundesliga’
Bundesliga.XML: no visible global function definition for ‘data’
Bundesliga.XML: no visible binding for global variable ‘Bundesliga’
sens.spec: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘wikibooks/R/Bundesliga.Mannschaft.R’:
  data(Bundesliga)
File ‘wikibooks/R/Bundesliga.Tabelle.R’:
  data(Bundesliga)
File ‘wikibooks/R/Bundesliga.XML.R’:
  data(Bundesliga)
See section ‘Good practice’ in ‘?data’.
wilcox.selection.split: no visible global function definition for
  ‘pnorm’
wilcox.test2: no visible global function definition for ‘wilcox.test’
Undefined global functions or variables:
  pnorm wilcox.test
Consider adding
  importFrom("stats", "pnorm", "wilcox.test")
to your NAMESPACE file.
Cs: no visible global function definition for ‘wilcox.test’
Don: no visible global function definition for ‘points’
Don: no visible global function definition for ‘chisq.test’
Lixn: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  chisq.test pchisq points wilcox.test
Consider adding
  importFrom("graphics", "points")
  importFrom("stats", "chisq.test", "pchisq", "wilcox.test")
to your NAMESPACE file.
plotTrait: no visible global function definition for ‘plot’
plotTrait: no visible global function definition for ‘points’
plotTrait: no visible global function definition for ‘legend’
test.windex: no visible global function definition for ‘hist’
test.windex: no visible global function definition for ‘abline’
test.windex: no visible global function definition for ‘legend’
windex: no visible global function definition for ‘sd’
windex: no visible global function definition for ‘var’
windex: no visible global function definition for ‘dist’
windex: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline dist hist legend plot points quantile sd var
Consider adding
  importFrom("graphics", "abline", "hist", "legend", "plot", "points")
  importFrom("stats", "dist", "quantile", "sd", "var")
to your NAMESPACE file.
File ‘wingui/libs/wingui.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
dbayes: no visible global function definition for ‘mahalanobis’
dbayes: no visible global function definition for ‘var’
wmd: no visible global function definition for ‘cor’
wmd: no visible global function definition for ‘var’
Undefined global functions or variables:
  cor mahalanobis var
Consider adding
  importFrom("stats", "cor", "mahalanobis", "var")
to your NAMESPACE file.
fit,Leader: no visible global function definition for ‘lm’
plotfit,Leader: no visible global function definition for ‘par’
plotfit,Leader: no visible global function definition for ‘plot’
Undefined global functions or variables:
  lm par plot
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
'library' or 'require' call to ‘tm’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
File ‘wordcloud/libs/wordcloud.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
  ‘plyr’ ‘reshape2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
wordmatch: no visible global function definition for ‘llply’
wordmatch : <anonymous>: no visible global function definition for
  ‘llply’
wordmatch: no visible global function definition for ‘melt’
wordmatch: no visible global function definition for ‘count’
Undefined global functions or variables:
  count llply melt
pickList : <anonymous>: 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 ‘wordspace/libs/wordspace.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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.
simul.wsvm: no visible binding for global variable ‘mixture.example’
wsvm.boost: no visible global function definition for ‘plot’
Undefined global functions or variables:
  mixture.example plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Rd file 'simul.wsvm.Rd':
  \usage lines wider than 90 characters:
         simul.wsvm(set.seeds = 123, obs.num = 1000, mu = c(0,0), cov.mat = 0.2*diag(2), X = NULL, Y = NULL)

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

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

These lines will be truncated in the PDF manual.
quadplot: no visible global function definition for ‘median’
xgobi: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  median write.table
Consider adding
  importFrom("stats", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
XHWE: no visible global function definition for ‘read.table’
result: no visible global function definition for ‘pchisq’
result: no visible global function definition for ‘rbinom’
result: no visible global function definition for ‘rmultinom’
Undefined global functions or variables:
  pchisq rbinom read.table rmultinom
Consider adding
  importFrom("stats", "pchisq", "rbinom", "rmultinom")
  importFrom("utils", "read.table")
to your NAMESPACE file.
R5.value.default: no visible binding for global variable ‘data.table’
R5.value.default: no visible global function definition for
  ‘as.data.table’
R5.value.parse: no visible binding for global variable ‘data.table’
R5.value.parse: no visible global function definition for
  ‘is.data.table’
R5.value.parse: no visible global function definition for
  ‘as.data.table’
stampme: no visible global function definition for ‘flush.console’
stampmsg: no visible global function definition for ‘flush.console’
write.data.table: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  as.data.table data.table flush.console is.data.table write.table
Consider adding
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
File ‘xml2/libs/xml2.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_WriteConnection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard files/directories found at top level:
  ‘Bug.R’ ‘Bugs.html’ ‘Check’ ‘CodeDetails’ ‘DESCRIPTION.in’ ‘Docs’
  ‘FAQ.html’ ‘FIXME_NOW’ ‘GNUmakefile’ ‘GNUmakefile.admin’
  ‘Makevars.in’ ‘MemoryBug.R’ ‘NAMESPACE.in’ ‘NodeFuns’ ‘Notes’
  ‘QuestionSolutions’ ‘README.windows’ ‘Rsamples’ ‘TAGS’
  ‘Todo-orig.html’ ‘Todo.xml’ ‘VersionInfo’ ‘addFinalizer’ ‘checkLinks’
  ‘dotCalls’ ‘expat’ ‘index.html’ ‘index.html.in’ ‘libxml’
  ‘libxml2.9.R’ ‘scrapingData.xml’ ‘testRemoveFinalizers.R’
  ‘testRemoveFinalizers.c’ ‘xpathPointer.xml’
newXMLDoc: no visible binding for global variable ‘doc’
source: no visible binding for global variable ‘use_file’
xmlFlatListTree : f: no visible binding for global variable ‘nodeNames’
xmlFlatListTree : f: no visible binding for global variable ‘idx’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘nodeSet’
xmlFlatListTree : addNode: no visible binding for global variable
  ‘nodeSet’
xmlFlatListTree : addNode: no visible binding for global variable ‘idx’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘nodeNames’
xmlFlatListTree : addNode: no visible binding for global variable
  ‘nodeNames’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘idx’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘parentCount’
xmlFlatListTree : addNode: no visible binding for global variable
  ‘parentCount’
xmlFlatListTree : <anonymous>: no visible binding for global variable
  ‘e’
xmlFlatTree : <anonymous>: no visible binding for global variable ‘e’
Undefined global functions or variables:
  doc e idx nodeNames nodeSet parentCount use_file
Rd file 'makeClassTemplate.Rd':
  \examples lines wider than 100 characters:
     "<doc><part><name>ABC</name><type>XYZ</type><cost>3.54</cost><status>available</status></part></doc>"

Rd file 'xmlClone.Rd':
  \examples lines wider than 100 characters:
     xmlParse('<doc><author id="dtl"><firstname>Duncan</firstname><surname>Temple Lang</surname></author></doc>')

Rd file 'xmlToS4.Rd':
  \examples lines wider than 100 characters:
      "<doc><part><name>ABC</name><type>XYZ</type><cost>3.54</cost><status>available</status></part></doc>"

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
LPGM: no visible global function definition for ‘flush.console’
PGM: no visible global function definition for ‘flush.console’
PGM.path.neighborhood: no visible global function definition for
  ‘runif’
PGMSim: no visible global function definition for ‘rpois’
PGMSim: no visible global function definition for ‘par’
WPGMSim: no visible global function definition for ‘rpois’
XMRF.Sim: no visible global function definition for ‘cov2cor’
XMRF.Sim: no visible global function definition for ‘rbinom’
XMRF.Sim: no visible global function definition for ‘rnorm’
glm.generic: no visible global function definition for ‘flush.console’
mymult: no visible global function definition for ‘rmultinom’
plot.GMS: no visible global function definition for ‘pdf’
plot.GMS: no visible global function definition for ‘dev.off’
plotNet: no visible global function definition for ‘pdf’
plotNet: no visible global function definition for ‘dev.off’
print.GMS: no visible global function definition for ‘str’
processSeq: no visible binding for global variable ‘quantile’
processSeq: no visible binding for global variable ‘var’
processSeq: no visible global function definition for ‘ks.test’
rmpois : <anonymous>: no visible global function definition for ‘rpois’
Undefined global functions or variables:
  cov2cor dev.off flush.console ks.test par pdf quantile rbinom
  rmultinom rnorm rpois runif str var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par")
  importFrom("stats", "cov2cor", "ks.test", "quantile", "rbinom",
             "rmultinom", "rnorm", "rpois", "runif", "var")
  importFrom("utils", "flush.console", "str")
to your NAMESPACE file.
File ‘XMRF/libs/XMRF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘xseq/libs/xseq.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.
Non-standard file/directory found at top level:
  ‘CONTRIBUTORS’
Found the following apparent S3 methods exported but not registered:
  plot.cca print.F.test.cca print.cca print.summary.cca summary.cca
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘yakmoR/libs/yakmoR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
big.read.table: no visible global function definition for ‘read.table’
big.read.table: no visible global function definition for ‘object.size’
sparkline: no visible global function definition for ‘is.ts’
sparkline: no visible global function definition for ‘time’
sparkline: no visible global function definition for ‘boxplot’
Undefined global functions or variables:
  boxplot is.ts object.size read.table time
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "is.ts", "time")
  importFrom("utils", "object.size", "read.table")
to your NAMESPACE file.
bootstrapswapcurve: no visible global function definition for ‘ts’
fitted: no visible global function definition for ‘ts’
forwardrates: no visible global function definition for ‘ts’
residuals: no visible global function definition for ‘ts’
tZC_NS: no visible global function definition for ‘cmpfun’
tZC_NS_extra: no visible global function definition for ‘cmpfun’
tZC_SV: no visible global function definition for ‘cmpfun’
tZC_SV_extra: no visible global function definition for ‘cmpfun’
ycextra: no visible global function definition for ‘new’
ycinter: no visible global function definition for ‘new’
ycplot: no visible global function definition for ‘par’
ycplot: no visible global function definition for ‘points’
ycplot: no visible global function definition for ‘abline’
ycplot: no visible global function definition for ‘hist’
ycplot: no visible global function definition for ‘lines’
ycplot: no visible global function definition for ‘density’
ycplot: no visible global function definition for ‘qqnorm’
ycplot: no visible global function definition for ‘qqline’
ycsummary: no visible global function definition for ‘shapiro.test’
ycsummary: no visible global function definition for ‘pf’
Undefined global functions or variables:
  abline cmpfun density hist lines new par pf points qqline qqnorm
  shapiro.test ts
Consider adding
  importFrom("graphics", "abline", "hist", "lines", "par", "points")
  importFrom("methods", "new")
  importFrom("stats", "density", "pf", "qqline", "qqnorm",
             "shapiro.test", "ts")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.NS.estimator: no visible global function definition for ‘lm’
.NS.estimator: no visible global function definition for ‘coef’
.NS.estimator: no visible global function definition for ‘na.omit’
.NS.estimator: no visible global function definition for ‘resid’
.NSS.estimator: no visible global function definition for ‘lm’
.NSS.estimator: no visible global function definition for ‘coef’
.NSS.estimator: no visible global function definition for ‘na.omit’
.NSS.estimator: no visible global function definition for ‘resid’
NSrates: no visible global function definition for ‘time’
Nelson.Siegel: no visible global function definition for ‘optimize’
Srates: no visible global function definition for ‘time’
Svensson: no visible global function definition for ‘median’
Svensson: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  coef lm median na.omit optimize resid time
Consider adding
  importFrom("stats", "coef", "lm", "median", "na.omit", "optimize",
             "resid", "time")
to your NAMESPACE file.
Rd file 'ECBYieldCurve.Rd':
  \examples lines wider than 100 characters:
     plot(mat.ECB, ECBYieldCurve[i,], type="o", xlab="Maturities structure in years", ylab="Interest rates values")

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

These lines will be truncated in the PDF manual.
kmeansN: no visible global function definition for ‘kmeans’
kmeansN: no visible global function definition for ‘aggregate’
kmeansN2: no visible global function definition for ‘aggregate’
kmeansN2: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  aggregate kmeans sd
Consider adding
  importFrom("stats", "aggregate", "kmeans", "sd")
to your NAMESPACE file.
Deprecated license: CC BY-SA 2.0 + file LICENSE
Package suggested but not available for checking: ‘zdat’
Found the following apparent S3 methods exported but not registered:
  cbind.zoocat
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'merge':
  ‘cbind.zoocat’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Error in re-building vignettes:
  ...
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: reshape2

Attaching package: 'zoocat'

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

    cor

Quitting from lines 69-74 (my-vignette.Rmd) 
Error: processing vignette ‘my-vignette.Rmd’ failed with diagnostics:
no applicable method for ‘cattr’ applied to an object of class "zoo"
Execution halted
File which contains pragma(s) suppressing diagnostics:
  ‘src/third_party/zstd-1.2.0/lib/dictBuilder/divsufsort.c’
Found the following apparent S3 methods exported but not registered:
  confint.zyp
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
confint.zyp: no visible global function definition for ‘qnorm’
confint.zyp: no visible global function definition for ‘var’
zyp.sen: no visible global function definition for ‘terms’
zyp.sen: no visible global function definition for ‘median’
zyp.trend.csv: no visible global function definition for ‘read.csv’
zyp.trend.csv: no visible global function definition for ‘write.csv’
zyp.yuepilon: no visible global function definition for ‘acf’
zyp.yuepilon: no visible binding for global variable ‘na.pass’
zyp.yuepilon: no visible global function definition for ‘confint’
zyp.yuepilon: no visible global function definition for ‘lm’
zyp.zhang: no visible global function definition for ‘acf’
zyp.zhang: no visible binding for global variable ‘na.pass’
zyp.zhang: no visible global function definition for ‘confint’
zyp.zhang: no visible global function definition for ‘lm’
Undefined global functions or variables:
  acf confint lm median na.pass qnorm read.csv terms var write.csv
Consider adding
  importFrom("stats", "acf", "confint", "lm", "median", "na.pass",
             "qnorm", "terms", "var")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
Running ‘testthat.R’ [2s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(alphavantager)
  > 
  > test_check("alphavantager")
  ── 1. Error: call Technical Indicators (@test_av_get.R#69)  ────────────────────
  Thank you for using Alpha Vantage! Please visit https://www.alphavantage.co/premium/ if you would like to have a higher API call volume.. API parameters used: symbol=MSFT, function=RSI, interval=monthly, time_period=60, series_type=close, apikey=HIDDEN_FOR_YOUR_SAFETY
  1: av_get(symbol, av_fun, interval = interval, time_period = time_period, series_type = series_type) at testthat/test_av_get.R:69
  2: stop(content, call. = F)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 12 SKIPPED: 0 FAILED: 1
  1. Error: call Technical Indicators (@test_av_get.R#69) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  analyzeFMRI.c:948:3: warning: ‘strncat’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  analyzeFMRI.c:975:5: warning: ‘strncat’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/AnalyzeFMRI.Rcheck/00install.out’ for details.
Found the following significant warnings:
  libantiword/summary.c:732:24: warning: ‘%02d’ directive writing between 2 and 11 bytes into a region of size between 0 and 7 [-Wformat-overflow=]
  libantiword/summary.c:753:25: warning: ‘%02d’ directive writing between 2 and 11 bytes into a region of size between 7 and 14 [-Wformat-overflow=]
  libantiword/summary.c:775:25: warning: ‘%02d’ directive writing between 2 and 11 bytes into a region of size between 7 and 14 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/antiword.Rcheck/00install.out’ for details.
Found the following significant warnings:
  me.c:226:3: warning: ‘strncpy’ specified bound 30 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ape.Rcheck/00install.out’ for details.
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  pa.c:247:2: warning: initialization of ‘struct audio_instance * (*)(struct SEXPREC *, float,  int)’ from incompatible pointer type ‘void * (*)(struct SEXPREC *, float,  int)’ [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/audio.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Blasso.cpp:451:53: warning: ‘*<unknown>.Blasso::icept’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bayesCL.Rcheck/00install.out’ for details.
Found the following significant warnings:
  mcmc.c:337:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BayHap.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘ggplot2::sym’ by ‘relations::sym’ when loading ‘benchmark’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/benchmark.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [6s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BGData)
  Loading required package: BEDMatrix
  Loading required package: LinkedMatrix
  Loading required package: symDMatrix
  > 
  > test_check("BGData")
  ── 1. Error: getG_symDMatrix on 1 cores (@test-utils.R#98)  ────────────────────
  blocks need to be of type ColumnLinkedMatrix
  1: getG_symDMatrix(X = W, blockSize = ceiling(nrow(W)/3), folder = paste0(testPath, 
         "test-", randomString()), nTasks = nTasks, nCores = nCores) at testthat/test-utils.R:98
  2: symDMatrix::symDMatrix(blocks, center, scale)
  3: new(structure("symDMatrix", package = "symDMatrix"), ...)
  4: initialize(value, ...)
  5: initialize(value, ...)
  6: stop("blocks need to be of type ColumnLinkedMatrix")
  
  ── 2. Error: getG_symDMatrix on 2 cores (@test-utils.R#98)  ────────────────────
  blocks need to be of type ColumnLinkedMatrix
  1: getG_symDMatrix(X = W, blockSize = ceiling(nrow(W)/3), folder = paste0(testPath, 
         "test-", randomString()), nTasks = nTasks, nCores = nCores) at testthat/test-utils.R:98
  2: symDMatrix::symDMatrix(blocks, center, scale)
  3: new(structure("symDMatrix", package = "symDMatrix"), ...)
  4: initialize(value, ...)
  5: initialize(value, ...)
  6: stop("blocks need to be of type ColumnLinkedMatrix")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 304 SKIPPED: 0 FAILED: 2
  1. Error: getG_symDMatrix on 1 cores (@test-utils.R#98) 
  2. Error: getG_symDMatrix on 2 cores (@test-utils.R#98) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rapidjsonr/include/rapidjson/document.h:2030:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<> >::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::MemoryPoolAllocator<> >’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rapidjsonr/include/rapidjson/document.h:2017:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<> >’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bigrquery.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘blkergm’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘blkergm’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/blkergm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘btergm’
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘btergm’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/btergm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  hash.c:144:5: warning: ‘strncpy’ specified bound 2048 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/C50.Rcheck/00install.out’ for details.
Found the following significant warnings:
  catnet_rexport.cpp:202:17: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:206:15: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:213:16: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 0 and 1023 [-Wformat-overflow=]
  catnet_rexport.cpp:216:18: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:217:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:232:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:231:18: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/catnet.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘BMisc::lhs.vars’ by ‘formula.tools::lhs.vars’ when loading ‘ccfa’
  Warning: replacing previous import ‘BMisc::rhs.vars’ by ‘formula.tools::rhs.vars’ when loading ‘ccfa’
  Warning: replacing previous import ‘BMisc::rhs’ by ‘formula.tools::rhs’ when loading ‘ccfa’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ccfa.Rcheck/00install.out’ for details.
Running examples in ‘censusapi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: listCensusApis
> ### Title: Get dataset metadata on all available APIs as a data frame
> ### Aliases: listCensusApis
> ### Keywords: metadata
> 
> ### ** Examples
> 
> apis <- listCensusApis()
Error in open.connection(con, "rb") : 
  Timeout was reached: Connection timed out after 10001 milliseconds
Calls: listCensusApis ... fromJSON_string -> parseJSON -> parse_con -> open -> open.connection
Execution halted
Found the following significant warnings:
  guess_type.c:14:9: warning: ‘strncpy’ specified bound 512 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/checkmate.Rcheck/00install.out’ for details.
Running ‘test-all.R’ [0m/12m]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(cli)
  > library(testthat)
  > old.env <- Sys.getenv("checkpoint.mock.install")
  > Sys.setenv("checkpoint.mock.install" = TRUE)
  > test_check("checkpoint")
  Loading required package: checkpoint
  
  checkpoint: Part of the Reproducible R Toolkit from Microsoft
  https://mran.microsoft.com/documents/rro/reproducibility/
  ── 1. Failure: is.404 (@test-0-is-404.R#14)  ───────────────────────────────────
  is.404("http://mran.microsoft.com/snapshot/2015-05-01") isn't false.
  
  ── 2. Failure: is.404 works with https (@test-0-is-404.R#25)  ──────────────────
  is.404("https://mran.microsoft.com/snapshot") isn't false.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 52 SKIPPED: 6 FAILED: 2
  1. Failure: is.404 (@test-0-is-404.R#14) 
  2. Failure: is.404 works with https (@test-0-is-404.R#25) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  lprintf.c:336:17: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/creditr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  hash.c:144:5: warning: ‘strncpy’ specified bound 2048 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Cubist.Rcheck/00install.out’ for details.
Found the following significant warnings:
  GetData.c:342:15: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 3 [-Wformat-overflow=]
  GetData.c:355:15: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 3 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DetSel.Rcheck/00install.out’ for details.
Found the following significant warnings:
  clipper.cpp:721:34: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct ClipperLib::TEdge’; use assignment or value-initialization instead [-Wclass-memaccess]
  dbfopen.c:1346:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopen.c:1328:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopen.c:879:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  dbfopen.c:1693:9: warning: ‘strncpy’ output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
  dbfopen.c:2065:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dggridR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘BMisc::lhs.vars’ by ‘formula.tools::lhs.vars’ when loading ‘did’
  Warning: replacing previous import ‘BMisc::rhs.vars’ by ‘formula.tools::rhs.vars’ when loading ‘did’
  Warning: replacing previous import ‘BMisc::rhs’ by ‘formula.tools::rhs’ when loading ‘did’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/did.Rcheck/00install.out’ for details.
Found the following significant warnings:
  dcm2niix/nii_dicom.cpp:637:29: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 80 [-Wformat-truncation=]
  dcm2niix/nii_dicom_batch.cpp:3583:34: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound 1 equals source length [-Wstringop-overflow=]
  dcm2niix/nii_dicom_batch.cpp:3576:10: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/divest.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dpglasso.Rcheck/00install.out’ for details.
Found the following significant warnings:
  mainR.c:204:62: warning: ‘strncat’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  mainR.c:225:65: warning: ‘strncat’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dynr.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=36.094994,-111.837962&zoom=12&size=640x640&scale=2&maptype=satellite&language=en-EN&sensor=false
Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=24.2,-77.88&zoom=11&size=640x640&scale=2&maptype=satellite&language=en-EN&sensor=false
Quitting from lines 43-44 (earthtones.rmd) 
Error: processing vignette ‘earthtones.rmd’ failed with diagnostics:
cannot open URL ‘http://maps.googleapis.com/maps/api/staticmap?center=37.89,-122.28&zoom=11&size=640x640&scale=2&maptype=satellite&language=en-EN&sensor=false’
Execution halted
Found the following significant warnings:
  main.c:334:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:575:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:518:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:805:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:755:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1034:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:983:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1377:7: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1279:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1678:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1962:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1912:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:2316:7: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:2212:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/enviPat.Rcheck/00install.out’ for details.
Found the following significant warnings:
  epanet.c:999:5: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:1000:5: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:1492:3: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:2308:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:2309:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input1.c:454:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input1.c:455:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input3.c:604:2: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/epanet2toolkit.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘ergm.count’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘ergm.count’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ergm.count.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘ergm::colMeans.mcmc.list’ by ‘statnet.common::colMeans.mcmc.list’ when loading ‘ergm.ego’
  Warning: replacing previous import ‘ergm::sweep.mcmc.list’ by ‘statnet.common::sweep.mcmc.list’ when loading ‘ergm.ego’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ergm.ego.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘ergm.graphlets’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘ergm.graphlets’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ergm.graphlets.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘ergm.rank’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘ergm.rank’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ergm.rank.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘ergm.userterms’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘ergm.userterms’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ergm.userterms.Rcheck/00install.out’ for details.
Found the following significant warnings:
  RngStream.c:352:6: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/excursions.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [22s/36s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(exifr)
  Using ExifTool version 11.08
  > 
  > test_check("exifr")
  ── 1. Failure: read_exif reads images in the inst directory (@test_read_exif.R#1
  ncol(df) not equal to 267.
  1/1 mismatches
  [1] 268 - 267 == 1
  
    % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                   Dload  Upload   Total   Spent    Left  Speed
  
    0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
    0 2838k    0  6645    0     0   6002      0  0:08:04  0:00:01  0:08:03  6002
  100 2838k  100 2838k    0     0  2040k      0  0:00:01  0:00:01 --:--:-- 2040k
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 39 SKIPPED: 0 FAILED: 1
  1. Failure: read_exif reads images in the inst directory (@test_read_exif.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
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-gcc/Work/PKGS/FastRWeb.Rcheck/00install.out’ for details.
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
  Warning: 'cBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
     user system elapsed
fcr 7.498  0.074   8.899
Found the following significant warnings:
  FLAN_Clone.h:131:11: warning: ‘*<unknown>.FLAN_SimClone::mDist’ is used uninitialized in this function [-Wuninitialized]
  FLAN_Clone.h:204:11: warning: ‘*<unknown>.FLAN_SimInhomogeneousClone::mMU’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/flan.Rcheck/00install.out’ for details.
Found the following significant warnings:
  RngStream.c:275:7: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/freeknotsplines.Rcheck/00install.out’ for details.
Found the following significant warnings:
  hap_c.c:380:28: warning: ‘%03d’ directive writing between 3 and 10 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  hap_c.c:392:28: warning: ‘%03d’ directive writing between 3 and 10 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gap.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Gdmlib.cpp:2352:19: warning: ‘%lf’ directive writing between 3 and 317 bytes into a region of size between 0 and 1023 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gdm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rapidjsonr/include/rapidjson/document.h:2030:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<> >::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::MemoryPoolAllocator<> >’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rapidjsonr/include/rapidjson/document.h:2017:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<> >’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/geojsonsf.Rcheck/00install.out’ for details.
Found the following significant warnings:
  rboxlib.c:351:5: warning: ‘strncat’ output may be truncated copying between 0 and 199 bytes from a string of length 199 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/geometry.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_41_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gglasso.Rcheck/00install.out’ for details.
Running examples in ‘ggmap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: theme_nothing
> ### Title: Make a blank ggplot2 theme.
> ### Aliases: theme_nothing
> 
> ### ** Examples
> 
> 
> 
> # no legend example
> n <- 50
> df <- expand.grid(x = 1:n,y = 1:n)[sample(n^2,.5*n^2),]
> p <- qplot(x, y, data = df, geom = 'tile')
> p
> p + theme_nothing()
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
> p + theme_nothing(legend = TRUE) # no difference
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Theme element panel.border missing
Theme element axis.line.x.bottom missing
Theme element axis.ticks.x.bottom missing
Theme element axis.line.y.left missing
Theme element axis.ticks.y.left missing
Theme element plot.title missing
Theme element plot.subtitle missing
Theme element plot.tag missing
Theme element plot.caption missing
> p +
+   scale_x_continuous(expand = c(0,0)) +
+   scale_y_continuous(expand = c(0,0)) +
+   theme_nothing()
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
> 
> 
> 
> # legend example
> df$class <- factor(sample(0:1, .5*n^2,  replace = TRUE))
> p <- qplot(x, y, data = df, geom = "tile", fill = class)
> p
> p + theme_nothing()
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
> p + theme_nothing(legend = TRUE)
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Theme element panel.border missing
Theme element axis.line.x.bottom missing
Theme element axis.ticks.x.bottom missing
Theme element axis.line.y.left missing
Theme element axis.ticks.y.left missing
Error in UseMethod("element_grob") : 
  no applicable method for 'element_grob' applied to an object of class "NULL"
Calls: <Anonymous> ... guide_gengrob.legend -> ggname -> grobName -> element_grob
Execution halted
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ggvis)
  > 
  > test_check("ggvis")
  ── 1. Error: (unknown) (@test-specs.r#5)  ──────────────────────────────────────
  no applicable method for 'group_by_' applied to an object of class "ggvis"
  1: suppressMessages(sys.source(spec, envir = new.env(), chdir = TRUE)) at testthat/test-specs.r:5
  2: withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessage"))
  3: sys.source(spec, envir = new.env(), chdir = TRUE)
  4: eval(exprs[i], envir)
  5: eval(exprs[i], envir)
  6: mtcars %>% ggvis(x = ~wt, stroke = ~cyl) %>% group_by(cyl) %>% layer_freqpolys(width = 1) %>% 
         save_spec("layer/freqpoly-grouped.json")
  7: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  8: eval(quote(`_fseq`(`_lhs`)), env, env)
  9: eval(quote(`_fseq`(`_lhs`)), env, env)
  10: `_fseq`(`_lhs`)
  11: freduce(value, `_function_list`)
  12: function_list[[i]](value)
  13: group_by(., cyl)
  14: group_by.default(., cyl)
  15: group_by_(.data, .dots = compat_as_lazy_dots(...), add = add)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 447 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-specs.r#5) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  dump_json_ast.cpp:21:12: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 1000 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/graphql.Rcheck/00install.out’ for details.
Running ‘run-tests.R’ [2s/3s]
Running the tests in ‘tests/run-tests.R’ failed.
Complete output:
  > library(testthat)
  > library(gWidgets2)
  Loading required package: digest
  > options(guiToolkit="tcltk")
  > 
  > 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)
  > ## issues
  > f <- Filter(function(x) !grepl("df.R", x), f)
  > f <- Filter(function(x) !grepl("text.R", x), f)
  > f <- Filter(function(x) !grepl("tree.R", x), f)
  > 
  > sapply(f, function(i) {
  +   message("testing ", i)
  +   source(i)
  + })
  testing /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/gWidgets2/tests/button.R
  Loading required package: gWidgets2tcltk
  Loading required package: memoise
  Loading required package: tcltk
  testing /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/gWidgets2/tests/calendar.R
  testing /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/gWidgets2/tests/checkbox.R
  testing /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/gWidgets2/tests/combobox.R
  testing /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/gWidgets2/tests/containers.R
  Error: svalue(cards) not equal to 1.
  Modes: logical, numeric
  target is logical, current is numeric
  Execution halted
Running examples in ‘happybiRthday-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: celebrate
> ### Title: Celebrating software birthdays
> ### Aliases: celebrate
> 
> ### ** Examples
> 
> celebrate("Bohdan-Khomtchouk")
Error in gh::gh("/users/:username/repos", username = github_username,  : 
  GitHub API error (403): 403 Forbidden
  API rate limit exceeded for 137.208.57.142. (But here's the good news: Authenticated requests get a higher rate limit. Check out the documentation for more details.)
Calls: celebrate -> <Anonymous> -> gh_process_response
Execution halted
Found the following significant warnings:
  readstat/readstat_writer.c:82:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  readstat/readstat_writer.c:261:5: warning: ‘strncpy’ specified bound 256 equals destination size [-Wstringop-truncation]
  readstat/readstat_writer.c:316:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  readstat/sas/readstat_sas7bcat_write.c:108:5: warning: ‘strncpy’ output may be truncated copying 64 bytes from a string of length 99 [-Wstringop-truncation]
  readstat/sas/readstat_sas.c:284:5: warning: ‘strncpy’ output may be truncated copying 64 bytes from a string of length 99 [-Wstringop-truncation]
  readstat/sas/readstat_sas.c:337:5: warning: ‘strncpy’ output may be truncated copying 8 bytes from a string of length 31 [-Wstringop-truncation]
  readstat/spss/readstat_sav_write.c:150:5: warning: ‘strncpy’ output may be truncated copying 9 bytes from a string of length 9 [-Wstringop-truncation]
  readstat/spss/readstat_sav_write.c:158:5: warning: ‘strncpy’ output may be truncated copying 8 bytes from a string of length 8 [-Wstringop-truncation]
  readstat/spss/readstat_por_write.c:194:5: warning: ‘strncpy’ output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/haven.Rcheck/00install.out’ for details.
Found the following significant warnings:
  gener.c:39:26: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hier.part.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(stringr)
  > library(io)
  Loading required package: filenamer
  > 
  > test_check("io")
  ── 1. Error: (unknown) (@test_read-write-read.R#8)  ────────────────────────────
  no applicable method for 'h5write' applied to an object of class "character"
  1: test_read_write_read(f) at testthat/test_read-write-read.R:8
  2: qwrite(x, outfile) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/io.Rcheck/tests/testthat/helper.R:48
  3: .qwrite(x, if (is.filename(file)) as.character(file) else file, if (is.null(type)) .infer_file_type(file) else type, 
         ...)
  4: qwrite.hdf5(x, if (is.filename(file)) as.character(file) else file, if (is.null(type)) .infer_file_type(file) else type, 
         ...)
  5: .write_hdf5_array(x, file)
  6: rhdf5::h5write("array", file, "type")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_read-write-read.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  asio_bindings.cpp:234:10: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 24 equals destination size [-Wstringop-truncation]
  asio_bindings.cpp:268:10: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 24 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/iptools.Rcheck/00install.out’ for details.
Found the following significant warnings:
  jqr.c:11:3: warning: ‘strncpy’ specified bound 1000 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/jqr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  push_parser.c:75:5: warning: ‘strncpy’ specified bound 1024 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/jsonlite.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘ergm::colMeans.mcmc.list’ by ‘statnet.common::colMeans.mcmc.list’ when loading ‘latentnet’
  Warning: replacing previous import ‘ergm::sweep.mcmc.list’ by ‘statnet.common::sweep.mcmc.list’ when loading ‘latentnet’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/latentnet.Rcheck/00install.out’ for details.
Found the following significant warnings:
  demean.c:282:35: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=]
  kaczmarz.c:220:36: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lfe.Rcheck/00install.out’ for details.
Found the following significant warnings:
  liblwgeom/lwutil.c:317:5: warning: ‘strncat’ specified bound 3 equals source length [-Wstringop-overflow=]
  liblwgeom/lwutil.c:323:5: warning: ‘strncat’ specified bound 3 equals source length [-Wstringop-overflow=]
  liblwgeom/lwutil.c:344:5: warning: ‘strncat’ specified bound 3 equals source length [-Wstringop-overflow=]
  liblwgeom/lwutil.c:349:5: warning: ‘strncat’ specified bound 3 equals source length [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lwgeom.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [40s/60s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > suppressPackageStartupMessages(library(metacoder))
  Warning message:
  In stri_count_regex(string, pattern, opts_regex = opts(pattern)) :
    argument is not an atomic vector; coercing
  > 
  > test_check("metacoder")
  ── 1. Failure: Mothur classify.seqs *.tax.summary  detailed parsing (@test--pars
  `result <- parse_mothur_tax_summary(text = raw_data)` did not produce any warnings.
  
  ── 2. Failure: Mothur classify.seqs *.tax.summary  detailed parsing (@test--pars
  `result_from_file <- parse_mothur_tax_summary(file = "example_data/mothur_summary.txt")` did not produce any warnings.
  
  ── 3. Failure: Mothur classify.seqs *.tax.summary simple parsing (@test--parsers
  `result <- parse_mothur_tax_summary(text = raw_data)` did not produce any warnings.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 96 SKIPPED: 1 FAILED: 3
  1. Failure: Mothur classify.seqs *.tax.summary  detailed parsing (@test--parsers_and_writers.R#78) 
  2. Failure: Mothur classify.seqs *.tax.summary  detailed parsing (@test--parsers_and_writers.R#79) 
  3. Failure: Mothur classify.seqs *.tax.summary simple parsing (@test--parsers_and_writers.R#97) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:

  Warning: 'getArgvals' is deprecated.
  Warning: 'getArgvals' is deprecated.
  Warning: 'getArgvals' is deprecated.
  Warning: 'getArgvals' is deprecated.
  Warning: 'getArgvals' is deprecated.
  Warning: 'getArgvals' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
            user system elapsed
univDecomp 4.601  0.051   6.455
Found the following significant warnings:
  migrate.c:179:30: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:186:26: warning: ‘.asc’ directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:199:28: warning: ‘.asc’ directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:286:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:312:29: warning: ‘%d’ directive writing between 1 and 8 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:559:31: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:595:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:603:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MigClim.Rcheck/00install.out’ for details.
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sparsepp/include/sparsepp/spp.h:2111:23: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘spp::sparsetable<std::pair<const long unsigned int, double>, spp::libc_allocator<std::pair<const long unsigned int, double> > >::group_type’ {aka ‘class spp::sparsegroup<std::pair<const long unsigned int, double>, spp::libc_allocator<std::pair<const long unsigned int, double> > >’} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sparsepp/include/sparsepp/spp.h:2111:23: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘spp::sparsetable<std::pair<const std::__cxx11::basic_string<char>, long unsigned int>, spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, long unsigned int> > >::group_type’ {aka ‘class spp::sparsegroup<std::pair<const std::__cxx11::basic_string<char>, long unsigned int>, spp::libc_allocator<std::pair<const std::__cxx11::basic_string<char>, long unsigned int> > >’} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sparsepp/include/sparsepp/spp.h:1389:19: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘spp::sparsegroup<std::pair<const long unsigned int, double>, spp::libc_allocator<std::pair<const long unsigned int, double> > >::value_type’ {aka ‘struct std::pair<const long unsigned int, double>’} with no trivial copy-assignment; use copy-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mlvocab.Rcheck/00install.out’ for details.
Found the following significant warnings:
  monetdblite/src/gdk/gdk_heap.c:189:3: warning: ‘strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
  monetdblite/src/gdk/gdk_heap.c:260:30: warning: ‘%s’ directive writing likely 3 or more bytes into a region of size between 0 and 99 [-Wformat-overflow=]
  monetdblite/src/mal/sqlbackend/rel_bin.c:2949:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/rel_bin.c:1083:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/sql_statement.c:3193:3: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/sql_statement.c:3196:3: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/sql_statement.c:3186:3: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/sql/server/rel_planner.c:82:4: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/sql/server/rel_semantic.c:54:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/sql/server/rel_updates.c:1729:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MonetDBLite.Rcheck/00install.out’ for details.
Running examples in ‘mopa-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: OCSVMprofiling
> ### Title: Environmental profiling with One-Classification Support Vector
> ###   Machine
> ### Aliases: OCSVMprofiling
> 
> ### ** Examples
> 
> ## Load presence data
> data(Oak_phylo2)
> 
> ## Load climate data
> destfile <- tempfile()
> data.url <- "https://raw.githubusercontent.com/SantanderMetGroup/mopa/master/data/biostack.rda"
> download.file(data.url, destfile)
trying URL 'https://raw.githubusercontent.com/SantanderMetGroup/mopa/master/data/biostack.rda'
Warning in download.file(data.url, destfile) :
  cannot open URL 'https://raw.githubusercontent.com/SantanderMetGroup/mopa/master/data/biostack.rda': HTTP status was '502 Bad Gateway'
Error in download.file(data.url, destfile) : 
  cannot open URL 'https://raw.githubusercontent.com/SantanderMetGroup/mopa/master/data/biostack.rda'
Execution halted
Error in re-building vignettes:
  ...
Warning in file(file, "rt") :
  cannot open URL 'https://raw.githubusercontent.com/thomaspernet/data_csv_r/master/data/Computers.csv': HTTP status was '502 Bad Gateway'
Quitting from lines 217-220 (muHVT.Rmd) 
Error: processing vignette ‘muHVT.Rmd’ failed with diagnostics:
cannot open the connection to 'https://raw.githubusercontent.com/thomaspernet/data_csv_r/master/data/Computers.csv'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 189-219 (nifti_basics.Rmd) 
Error: processing vignette ‘nifti_basics.Rmd’ failed with diagnostics:
Bad Gateway (HTTP 502).
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(nlstimedist)
  > 
  > test_check("nlstimedist")
  ── 1. Failure: Ensure the glance method is returning expected values (@test-glan
  `out` not equal to `expect`.
  Rows in x but not y: 1. Rows in y but not x: 1. 
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 6 SKIPPED: 0 FAILED: 1
  1. Failure: Ensure the glance method is returning expected values (@test-glance.timedist.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  medusa.long2text.cpp:16:21: warning: ‘%ld’ directive writing between 1 and 20 bytes into a region of size 16 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Numero.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ba81quad.cpp:305:28: warning: ‘%d’ directive output may be truncated writing between 1 and 11 bytes into a region of size 9 [-Wformat-truncation=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/OpenMx.Rcheck/00install.out’ for details.
Found the following significant warnings:
  compile.c:243:13: warning: ‘strncpy’ output truncated before terminating nul copying 1 byte from a string of the same length [-Wstringop-truncation]
  compile.c:250:13: warning: ‘strncpy’ output truncated before terminating nul copying 1 byte from a string of the same length [-Wstringop-truncation]
  compile.c:246:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  print.c:97:9: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
  print.c:133:9: warning: ‘strncpy’ output truncated before terminating nul copying 5 bytes from a string of the same length [-Wstringop-truncation]
  print.c:196:13: warning: ‘strncpy’ output truncated before terminating nul copying 5 bytes from a string of the same length [-Wstringop-truncation]
  print.c:215:13: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ore.Rcheck/00install.out’ for details.
Found the following significant warnings:
  fdouble_metaphone.c:268:5: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PGRdup.Rcheck/00install.out’ for details.
Found the following significant warnings:
  phreeqcpp/transport.cpp:2090:10: warning: ‘%s’ directive writing up to 255 bytes into a region of size 170 [-Wformat-overflow=]
  phreeqcpp/transport.cpp:2132:10: warning: ‘%s’ directive writing up to 255 bytes into a region of size 170 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/phreeqc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  zhegv.c:216:27: warning: ‘strncpy’ specified bound 2 equals destination size [-Wstringop-truncation]
  zhegv.c:216:27: warning: ‘strncpy’ specified bound 3 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PRIMME.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_28_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PropClust.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
trying URL ‘http://github.com/dobriban/pweight/raw/master/vignettes/iGWAS.cad.example.RData’
Quitting from lines 34-38 (iGWAS-DataExample.Rmd) 
Error: processing vignette ‘iGWAS-DataExample.Rmd’ failed with diagnostics:
cannot open URL ‘http://github.com/dobriban/pweight/raw/master/vignettes/iGWAS.cad.example.RData’
Execution halted
Found the following significant warnings:
  R4dfp-object.c:253:3: warning: ‘strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
  R4dfp-object.c:260:3: warning: ‘strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/R4dfp.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in roc.default(response, m[[predictors]], ...) :
  'response' has more than two levels. Consider setting 'levels' explicitly or using 'multiclass.roc' instead
Quitting from lines 411-412 (Vignette.Rmd) 
Error: processing vignette ‘Vignette.Rmd’ failed with diagnostics:
Failed to download https://raw.githubusercontent.com/tmnaylor/malpass_foils/master/malp1.jpg (HTTP 502)
Execution halted
Found the following significant warnings:

  Warning: 'glue::collapse' is deprecated.
  Warning: 'glue::collapse' is deprecated.
  Warning: 'glue::collapse' is deprecated.
  Warning: 'glue::collapse' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
           user system elapsed
visualize 5.163  0.059   8.185
Found the following significant warnings:
  kleinkram.cc:1018:18: warning: ‘ '’ directive writing 2 bytes into a region of size between 1 and 1000 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RandomFieldsUtils.Rcheck/00install.out’ for details.
Found the following significant warnings:
  avc_binwr.c:166:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:173:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:180:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:187:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:1453:29: warning: ‘%4.4d’ directive writing between 4 and 10 bytes into a region of size 5 [-Wformat-overflow=]
  avc_binwr.c:1553:28: warning: ‘%s’ directive writing up to 39 bytes into a region of size between 38 and 77 [-Wformat-overflow=]
  avc_e00write.c:386:30: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  avc_e00write.c:387:30: warning: ‘-ID’ directive writing 3 bytes into a region of size between 1 and 40 [-Wformat-overflow=]
  avc_e00write.c:401:61: warning: ‘%s’ directive writing up to 39 bytes into a region of size 17 [-Wformat-overflow=]
  avc_e00write.c:397:61: warning: ‘%s’ directive writing up to 39 bytes into a region of size 17 [-Wformat-overflow=]
  avc_e00write.c:409:39: warning: ‘%s’ directive writing up to 39 bytes into a region of size 33 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RArcInfo.Rcheck/00install.out’ for details.
Found the following significant warnings:
  samtools/bam.c:118:2: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
  samtools/razf.c:178:2: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
  rbamtools.cpp:126:10: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rbamtools.Rcheck/00install.out’ for details.
Running examples in ‘Rchoice-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: estfun.Rchoice
> ### Title: Gradient for observations
> ### Aliases: estfun.Rchoice
> 
> ### ** Examples
> 
> ## Probit model
> data("Workmroz")
> probit <- Rchoice(lfp ~ k5 + k618 + age + wc + hc + lwg + inc,  
+                   data = Workmroz , family = binomial('probit'))
> summary(probit)

Model: binomial
Model estimated on: Sun Aug 12 05:40:57 PM 2018 

Call:
Rchoice(formula = lfp ~ k5 + k618 + age + wc + hc + lwg + inc, 
    data = Workmroz, family = binomial("probit"), method = "nr")


Frequencies of categories:
y
     0      1 
0.4316 0.5684 
The estimation took: 0h:0m:0s 

Coefficients:
          Estimate Std. Error z-value Pr(>|z|)    
constant  1.918422   0.380654   5.040 4.66e-07 ***
k5       -0.874711   0.113558  -7.703 1.33e-14 ***
k618     -0.038594   0.040489  -0.953 0.340488    
age      -0.037824   0.007609  -4.971 6.67e-07 ***
wc        0.488314   0.135487   3.604 0.000313 ***
hc        0.057170   0.124005   0.461 0.644776    
lwg       0.365629   0.087779   4.165 3.11e-05 ***
inc      -0.020525   0.004777  -4.297 1.73e-05 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Optimization of log-likelihood by Newton-Raphson maximisation
Log Likelihood: -452.7
Number of observations: 753
Number of iterations: 4
Exit of MLE: gradient close to zero> 
> library(sandwich)
> estfun(probit) 
Error in UseMethod("estfun") : 
  no applicable method for 'estfun' applied to an object of class "Rchoice"
Calls: estfun
Execution halted
Found the following significant warnings:
  Rreadsdpa.c:608:15: warning: ‘strncpy’ output may be truncated copying 3999 bytes from a string of length 3999 [-Wstringop-truncation]
  Rreadsdpa.c:1041:13: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  Rreadsdpa.c:1042:13: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:164:4: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:165:4: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rdsdp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  compile.cc:292:69: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class re2::Prog::Inst’; use assignment or value-initialization instead [-Wclass-memaccess]
  regexp.cc:343:33: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
  regexp.cc:344:32: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/re2r.Rcheck/00install.out’ for details.
Found the following significant warnings:
  localtime.c:1817:5: warning: ‘strncpy’ specified bound 1000 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/readr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  phonet.c:1207:34: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  phonet.c:1208:34: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RecordLinkage.Rcheck/00install.out’ for details.
Running ‘testCases.R’ [1s/2s]
Running the tests in ‘tests/testCases.R’ failed.
Complete output:
  > ## test constrained lm, rlm, glm
  > # mixing weights
  > # bootstrap standard errors
  > # models with and without intercept
  > # case weights
  > # constraints on factors and interactions
  > 
  > library(restriktor)
  This is restriktor 0.1-80.711
  restriktor is BETA software! Please report any bugs.
  > n <- 100
  > p <- 4
  > betas = c(0.1,0.2,0.3,0.4,0.5)
  > set.seed(3013073)
  > X <- cbind(mvtnorm:::rmvnorm(n, mean=rep(0,p), sigma=diag(p)), rbinom(n,1,0.5))
  > colnames(X) <- c("x1","x2","x3","x4","f1")
  > z <- X %*% betas        
  > y <- z + rnorm(n)
  > DATA <- data.frame(y, X)
  > 
  > # intercept model
  > model1 <- y ~  1 + x1 + x2 + x3 + x4
  > # no intercept model
  > model2 <- y ~ -1 + x1 + x2 + x3 + x4
  > # intercept model with interaction
  > model3 <- y ~ 1 + x1*f1 + x2*f1 + x3*f1 + x4*f1
  > # intercept model with interaction
  > model4 <- y ~ -1 + x1*f1 + x2*f1 + x3*f1 + x4*f1
  > 
  > ############################ lm #################################
  > linmod1 <- lm(model1, data = DATA)
  > linmod2 <- lm(model2, data = DATA)
  > linmod3 <- lm(model3, data = DATA)
  > linmod1wt <- lm(model1, data = DATA, weights = abs(rnorm(n)))
  > linmod2wt <- lm(model2, data = DATA, weights = abs(rnorm(n)))
  > linmod1fac <- lm(model3, data = DATA)
  > linmod2fac <- lm(model4, data = DATA)
  > 
  > constraints1 <- 'x1 > 0; x2 > 0; x3 > 0'
  > fit.restr1 <- restriktor(linmod1, constraints1)
  Error in UseMethod("conLM") : 
    no applicable method for 'conLM' applied to an object of class "lm"
  Calls: restriktor
  Execution halted
Found the following significant warnings:
  RhpcMPI.c:301:5: warning: ‘strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rhpc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  cornellout.cpp:99:20: warning: ‘%2d’ directive writing between 2 and 11 bytes into a region of size between 0 and 931 [-Wformat-overflow=]
  cornellout.cpp:137:26: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  cornellout.cpp:129:26: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 988 and 995 [-Wformat-overflow=]
  mat.cpp:315:4: warning: ‘*<unknown>.dataMat::p’ is used uninitialized in this function [-Wuninitialized]
  tilia.cpp:179:14: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 61 bytes from a string of length 199 [-Wstringop-truncation]
  tilia.cpp:180:10: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 19 bytes from a string of length 19 [-Wstringop-truncation]
  tilia.cpp:225:14: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 8 bytes from a string of length 199 [-Wstringop-truncation]
  tilia.cpp:228:17: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 8 bytes from a string of length 29 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rioja.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’
File ‘rJava/libs/rJava.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 use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
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:
  libjson/Source/JSONSharedString.h:297:17: warning: ‘json_shared_string::len’ will be initialized after [-Wreorder]
  libjson/Source/JSONSharedString.h:295:40: warning:   ‘json_shared_string::json_shared_string_internal* json_shared_string::_str’ [-Wreorder]
  libjson/Source/JSONSharedString.h:180:9: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONSharedString.h:182:9: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONDefs/GNU_C.h:58:28: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  libjson/Source/JSONStream.h:79:7: warning: ‘JSONStream::state’ will be initialized after [-Wreorder]
  libjson/Source/JSONStream.h:76:28: warning:   ‘void (* JSONStream::call)(void*, void*)’ [-Wreorder]
  JSONStream.cpp:8:1: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONStream.h:77:27: warning: ‘JSONStream::err_call’ will be initialized after [-Wreorder]
  libjson/Source/JSONStream.h:75:17: warning:   ‘json_string JSONStream::buffer’ [-Wreorder]
  JSONStream.cpp:12:1: warning:   when initialized here [-Wreorder]
  libjson/Source/internalJSONNode.h:257:18: warning: ‘internalJSONNode::_name_encoded’ will be initialized after [-Wreorder]
  libjson/Source/internalJSONNode.h:256:17: warning:   ‘json_string internalJSONNode::_name’ [-Wreorder]
  internalJSONNode.cpp:78:1: warning:   when initialized here [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RJSONIO.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ../inst/include/lasattributer.hpp:81:29: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying 31 bytes from a string of the same length [-Wstringop-truncation]
  LASlib/laswriter.cpp:1040:14: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rlas.Rcheck/00install.out’ for details.
Found the following significant warnings:
  RngStream.c:347:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rlecuyer.Rcheck/00install.out’ for details.
Found the following significant warnings:
  origcmaes.cc:2852:13: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  origcmaes.cc:2855:12: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  origcmaes.cc:2858:12: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rmalschains.Rcheck/00install.out’ for details.
Found the following significant warnings:
  bgc_hmm.c:241:31: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
  rph_tfbs.c:371:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:351:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:819:5: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rphast.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [4s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Copyright (c) 2015-present, Facebook, Inc.
  > # All rights reserved.
  > #
  > # This source code is licensed under the BSD-style license found in the
  > # LICENSE file in the root directory of this source tree. An additional grant
  > # of patent rights can be found in the PATENTS file in the same directory.
  > 
  > library("testthat")
  > library("DBI")
  > library("RPresto")
  > 
  > test_check("RPresto")
  -- 1. Failure: as() works (@test-src_translate_env.R#52)  ----------------------
  translate_sql(as(x, 0), con = conn[["con"]]) not equal to dplyr::sql("CAST(\"x\" AS \"DOUBLE\")").
  1/1 mismatches
  x[1]: "AS(\"x\", 0.0)"
  y[1]: "CAST(\"x\" AS \"DOUBLE\")"
  
  -- 2. Failure: as() works (@test-src_translate_env.R#56)  ----------------------
  translate_sql(pmax(x), con = conn[["con"]]) not equal to dplyr::sql("GREATEST(\"x\")").
  1/1 mismatches
  x[1]: "MAX(\"x\")"
  y[1]: "GREATEST(\"x\")"
  
  -- 3. Failure: as() works (@test-src_translate_env.R#60)  ----------------------
  translate_sql_(...) not equal to dplyr::sql("CAST(\"x\" AS \"ARRAY<VARCHAR>\")").
  1/1 mismatches
  x[1]: "AS(\"x\", ())"
  y[1]: "CAST(\"x\" AS \"ARRAY<VARCHAR>\")"
  
  -- 4. Failure: as() works (@test-src_translate_env.R#69)  ----------------------
  translate_sql_(list(substituted.expression), con = conn[["con"]]) not equal to dplyr::sql("CAST(\"x\" AS \"DATE\")").
  1/1 mismatches
  x[1]: "AS(\"x\", '2018-08-12')"
  y[1]: "CAST(\"x\" AS \"DATE\")"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 223 SKIPPED: 28 FAILED: 4
  1. Failure: as() works (@test-src_translate_env.R#52) 
  2. Failure: as() works (@test-src_translate_env.R#56) 
  3. Failure: as() works (@test-src_translate_env.R#60) 
  4. Failure: as() works (@test-src_translate_env.R#69) 
  
  Error: testthat unit tests failed
  Execution halted
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’
File ‘Rserve/libs/Rserve.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 use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
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:
  RngStreams.c:332:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rstream.Rcheck/00install.out’ for details.
Found the following significant warnings:
  bgc_hmm.c:241:31: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
  rph_tfbs.c:371:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:351:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:819:5: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rtfbs.Rcheck/00install.out’ for details.
Found the following significant warnings:
  vcglib/wrap/io_trimesh/export_stl.h:99:18: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated copying 80 bytes from a string of length 101 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rvcg.Rcheck/00install.out’ for details.
Found the following significant warnings:
  geometry/s2loop.cc:85:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2loop.cc:247:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2polyline.cc:52:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2polyline.cc:94:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2regioncoverer.cc:119:28: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct S2RegionCoverer::Candidate’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/s2.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/scio.Rcheck/00install.out’ for details.
Found the following significant warnings:
  catnet_rexport.cpp:221:17: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:229:15: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:237:16: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 0 and 1023 [-Wformat-overflow=]
  catnet_rexport.cpp:240:18: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:241:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:258:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:257:18: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sdnet.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_1_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sdwd.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: Array reference at (1) out of bounds (43 > 42) in loop beginning at (2)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sequoia.Rcheck/00install.out’ for details.
Found the following apparent S3 methods exported but not registered:
  points.within
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'points.within':
  ‘points.within’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  command.c:6:5: warning: ‘strncpy’ specified bound 1024 equals destination size [-Wstringop-truncation]
  scp.c:14:5: warning: ‘strncpy’ specified bound 1024 equals destination size [-Wstringop-truncation]
  scp.c:23:3: warning: ‘strncpy’ specified bound 4000 equals destination size [-Wstringop-truncation]
  scp.c:74:3: warning: ‘strncpy’ specified bound 4000 equals destination size [-Wstringop-truncation]
  scp.c:75:3: warning: ‘strncpy’ specified bound 4000 equals destination size [-Wstringop-truncation]
  session.c:30:5: warning: ‘strncpy’ specified bound 1024 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ssh.Rcheck/00install.out’ for details.
Found the following significant warnings:
  dbfopenSSN.c:1119:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopenSSN.c:1100:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopenSSN.c:663:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  dbfopenSSN.c:1511:2: warning: ‘strncpy’ output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SSN.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘statnet’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘statnet’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/statnet.Rcheck/00install.out’ for details.
Running ‘testGBHProcedures.R’ [3s/5s]
  Running ‘testHierarchicalMethods.R’ [3s/6s]
Running the tests in ‘tests/testHierarchicalMethods.R’ failed.
Complete output:
  > ## Test the hypothesesTree creation class.
  > 
  > set.seed(130229)
  > library('structSSI')
  > library('ape')
  > library('igraph')
  
  Attaching package: 'igraph'
  
  The following objects are masked from 'package:ape':
  
      edges, mst, ring
  
  The following objects are masked from 'package:stats':
  
      decompose, spectrum
  
  The following object is masked from 'package:base':
  
      union
  
  > tree.1 <- as.igraph(rtree(10))
  Error in UseMethod("as.igraph") : 
    no applicable method for 'as.igraph' applied to an object of class "phylo"
  Calls: as.igraph
  Execution halted
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘tergm’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘tergm’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tergm.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [3s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("toaster")
  Loading required package: RODBC
  > 
  > test_check("toaster")
  ── 1. Failure: format 'boxplot' works (@test-showData.R#12)  ───────────────────
  setdiff(p$layout$panel_ranges[[1]]$x.labels, getNumericColumns(notNullNumData)) not equal to character(0).
  target is NULL, current is character
  
  ── 2. Failure: format 'boxplot' with facets works (@test-showData.R#21)  ───────
  nrow(p$layout$panel_layout) not equal to length(cols).
  target is NULL, current is numeric
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 496 SKIPPED: 0 FAILED: 2
  1. Failure: format 'boxplot' works (@test-showData.R#12) 
  2. Failure: format 'boxplot' with facets works (@test-showData.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  RngStream.c:347:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TPmsm.Rcheck/00install.out’ for details.
Package in Depends field not imported from: ‘lgtdl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ci.plot: no visible global function definition for ‘gaussian’
ci.plot: no visible global function definition for ‘qnorm’
ci.plot: no visible global function definition for ‘plot’
ci.plot: no visible global function definition for ‘lines’
cst.fit.ff: no visible global function definition for ‘pnorm’
cstfit.1: no visible global function definition for ‘var’
gof.test.boots.pf: no visible binding for global variable ‘sd’
gof.test.int.1.ff: no visible global function definition for ‘quantile’
gof.test.int.1.ff: no visible global function definition for ‘var’
gof.test.int.ff: no visible global function definition for ‘pnorm’
gofTest: no visible binding for global variable ‘sd’
plotGof: no visible global function definition for ‘plot’
plotGof : <anonymous>: no visible global function definition for
  ‘lines’
plotGof: no visible global function definition for ‘lines’
sig.test.int.1.ff: no visible global function definition for ‘quantile’
sig.test.int.1.ff: no visible global function definition for ‘var’
sig.test.int.ff: no visible global function definition for ‘pnorm’
test.boots.1: no visible binding for global variable ‘sd’
tpr: no visible global function definition for ‘poisson’
tpr: no visible global function definition for ‘glm.fit’
tpr: no visible global function definition for ‘coef’
tpr: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx coef gaussian glm.fit lines plot pnorm poisson qnorm quantile
  sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "approx", "coef", "gaussian", "glm.fit", "pnorm",
             "poisson", "qnorm", "quantile", "sd", "var")
to your NAMESPACE file.
Rd file 'ci.plot.Rd':
  \usage lines wider than 90 characters:
     ci.plot(x, y, se, level = 0.95, ylim = NULL, newplot = TRUE, fun = gaussian()$linkinv, dfun = gaussian()$mu.eta, ...)

These lines will be truncated in the PDF manual.
File ‘tpr/libs/tpr.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’
File ‘tpr/libs/tpr.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 use Fortran I/O
nor system RNGs.
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:
  ...
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: ggplot2

Attaching package: 'trackeR'

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

    append

Warning in download.file(url, destfile = tmp, quiet = !messaging, mode = "wb") :
  cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=57.157231,-2.104296&zoom=13&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false': HTTP status was '403 Forbidden'
Quitting from lines 90-91 (TourDetrackeR.Rmd) 
Error: processing vignette ‘TourDetrackeR.Rmd’ failed with diagnostics:
cannot open URL ‘http://maps.googleapis.com/maps/api/staticmap?center=57.157231,-2.104296&zoom=13&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false’
Execution halted
Running ‘ggplot_extraction.R’ [7s/9s]
  Running ‘trackr-tests.R’ [6s/9s]
Running the tests in ‘tests/trackr-tests.R’ failed.
Complete output:
  > library(trackr)
  Loading required package: histry
  > library(knitr)
  > be = JSONBackend(tempfile())
  > tdb = TrackrDB(backend=be, img_dir = tempdir())
  > defaultTDB(tdb)
  An object of class "TrackrDB"
  Slot "opts":
  An object of class "TrackrOptions"
  Slot "insert_delay":
  [1] 0
  
  Slot "img_dir":
  [1] "/home/hornik/tmp/scratch/RtmpzCY8nP"
  
  Slot "img_ext":
  [1] "png"
  
  Slot "backend_opts":
  list()
  
  
  Slot "backend":
  Reference class object of class "JSONBackend"
  Field "docs":
  DocList (0x0)
  Field ".file":
  [1] "/home/hornik/tmp/scratch/RtmpzCY8nP/filecf73b659502"
  Field "file":
  [1] "/home/hornik/tmp/scratch/RtmpzCY8nP/filecf73b659502"
  
  > 
  > rmdfil = system.file("test_docs/knitr_test.Rmd", package = "trackr")
  > knit_and_record(rmdfil, verbose = TRUE)
  
  
  processing file: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/trackr/test_docs/knitr_test.Rmd
  
  
  processing file: knitr_test.Rmd
    ordinary text without R code
  
  label: plot
  Error in file(file, ifelse(append, "a", "w")) : 
    cannot open the connection
  Calls: knit_and_record ... <Anonymous> -> .handleSimpleError -> h -> cat -> file
  In addition: Warning messages:
  1: In dir.create(dirname(name), recursive = TRUE) :
    cannot create dir 'knitr_test_files/figure-html', reason 'No such file or directory'
  2: In file(file, ifelse(append, "a", "w")) :
    cannot open file 'knitr_test.knit.md': Read-only file system
  Execution halted
Found the following significant warnings:
  libqhull/rboxlib.c:351:5: warning: ‘strncat’ output may be truncated copying between 0 and 199 bytes from a string of length 199 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TukeyRegion.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(udapi)
  > 
  > test_check("udapi")
  ── 1. Failure: specific content can be retrieved (@test_udapi.R#5)  ────────────
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 11 - 10 == 1
  
  ── 2. Failure: random content can be retrieved (@test_udapi.R#10)  ─────────────
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 11 - 10 == 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 9 SKIPPED: 0 FAILED: 2
  1. Failure: specific content can be retrieved (@test_udapi.R#5) 
  2. Failure: random content can be retrieved (@test_udapi.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  include/rapidjson/document.h:1952:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<> >::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::MemoryPoolAllocator<> >’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<> >’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  include/rapidjson/document.h:1952:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::CrtAllocator>’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/validatejsonr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  tabix/razf.c:188:2: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/WhopGenome.Rcheck/00install.out’ for details.
Found the following significant warnings:
  libxlsxwriter/xmlwriter.c:156:17: warning: ‘strncat’ specified bound 5 equals source length [-Wstringop-overflow=]
  libxlsxwriter/xmlwriter.c:160:17: warning: ‘strncat’ specified bound 4 equals source length [-Wstringop-overflow=]
  libxlsxwriter/xmlwriter.c:164:17: warning: ‘strncat’ specified bound 4 equals source length [-Wstringop-overflow=]
  libxlsxwriter/xmlwriter.c:168:17: warning: ‘strncat’ specified bound 6 equals source length [-Wstringop-overflow=]
  libxlsxwriter/xmlwriter.c:198:17: warning: ‘strncat’ specified bound 5 equals source length [-Wstringop-overflow=]
  libxlsxwriter/xmlwriter.c:202:17: warning: ‘strncat’ specified bound 4 equals source length [-Wstringop-overflow=]
  libxlsxwriter/xmlwriter.c:206:17: warning: ‘strncat’ specified bound 4 equals source length [-Wstringop-overflow=]
  tmpfileplus/tmpfileplus.c:172:3: warning: ‘strncpy’ specified bound 4097 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/writexl.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘httr’ ‘progress’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    bootstrapping_example   1.2Mb
    libs                    5.7Mb
Namespaces in Imports field not imported from:
  ‘rARPACK’ ‘sparseLDA’
  All declared Imports should be used.
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but not in PKG_CFLAGS
  src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but not in PKG_CFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    R  13.7Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinydashboard’
  All declared Imports should be used.
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)
Namespace in Imports field not imported from: ‘Benchmarking’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.8Mb
    pictures   2.1Mb
Namespace in Imports field not imported from: ‘filehash’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Namespaces in Imports field not imported from:
  ‘fields’ ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘assertthat’ ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘htmlwidgets’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rjson’ ‘xml2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘base’ ‘methods’ ‘nlme’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(alphavantager)
  > 
  > test_check("alphavantager")
  ── 1. Error: call Technical Indicators (@test_av_get.R#69)  ────────────────────
  Thank you for using Alpha Vantage! Please visit https://www.alphavantage.co/premium/ if you would like to have a higher API call volume.. API parameters used: symbol=MSFT, function=RSI, interval=monthly, time_period=60, series_type=close, apikey=HIDDEN_FOR_YOUR_SAFETY
  1: av_get(symbol, av_fun, interval = interval, time_period = time_period, series_type = series_type) at testthat/test_av_get.R:69
  2: stop(content, call. = F)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 12 SKIPPED: 0 FAILED: 1
  1. Error: call Technical Indicators (@test_av_get.R#69) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data  15.6Mb
Namespace in Imports field not imported from: ‘unmarked’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘gridExtra’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘magrittr’
  All declared Imports should be used.
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    libs  25.1Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rgdal’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    help   4.7Mb
Namespace in Imports field not imported from: ‘caret’
  All declared Imports should be used.
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘httr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pls’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
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.
Found the following significant warnings:
  am.c:275:9: warning: comparison of array 'readByte' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/aqr.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘archivist.github’
Package unavailable to check Rd xrefs: ‘archivist.github’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R             2.3Mb
    help          1.1Mb
    testScripts   1.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.2Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   9.6Mb
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
File ‘audio/libs/audio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘jsonlite’
  All declared Imports should be used.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.6Mb
installed size is 67.2Mb
  sub-directories of 1Mb or more:
    java  67.2Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   8.9Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
    libs   2.9Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘zoo’
  All declared Imports should be used.
installed size is 103.4Mb
  sub-directories of 1Mb or more:
    libs  102.6Mb
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ranger’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.7Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MatrixModels’
  All declared Imports should be used.
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs  16.2Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    1.0Mb
    libs   3.7Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is 58.5Mb
  sub-directories of 1Mb or more:
    libs  57.7Mb
Namespace in Imports field not imported from: ‘inline’
  All declared Imports should be used.
installed size is 29.4Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  24.6Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   4.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    ex-data   4.7Mb
installed size is 89.5Mb
  sub-directories of 1Mb or more:
    libs  89.4Mb
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘matrixStats’ ‘reshape2’ ‘scales’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.2Mb
Namespace in Imports field not imported from: ‘readxl’
  All declared Imports should be used.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 99.5Mb
  sub-directories of 1Mb or more:
    libs  98.1Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘chron’ ‘colorspace’ ‘gtable’ ‘htmltools’ ‘htmlwidgets’
  ‘httpuv’ ‘magrittr’ ‘munsell’ ‘plyr’ ‘scales’ ‘stringi’ ‘xtable’
  ‘yaml’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘crochet’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: replacing previous import ‘ggplot2::sym’ by ‘relations::sym’ when loading ‘benchmark’
See ‘/data/gannet/ripley/R/packages/tests-clang/benchmark.Rcheck/00install.out’ for details.
installed size is 28.8Mb
  sub-directories of 1Mb or more:
    libs  27.7Mb
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
Running ‘testthat.R’ [9s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BGData)
  Loading required package: BEDMatrix
  Loading required package: LinkedMatrix
  Loading required package: symDMatrix
  > 
  > test_check("BGData")
  ── 1. Error: getG_symDMatrix on 1 cores (@test-utils.R#98)  ────────────────────
  blocks need to be of type ColumnLinkedMatrix
  1: getG_symDMatrix(X = W, blockSize = ceiling(nrow(W)/3), folder = paste0(testPath, 
         "test-", randomString()), nTasks = nTasks, nCores = nCores) at testthat/test-utils.R:98
  2: symDMatrix::symDMatrix(blocks, center, scale)
  3: new(structure("symDMatrix", package = "symDMatrix"), ...)
  4: initialize(value, ...)
  5: initialize(value, ...)
  6: stop("blocks need to be of type ColumnLinkedMatrix")
  
  ── 2. Error: getG_symDMatrix on 2 cores (@test-utils.R#98)  ────────────────────
  blocks need to be of type ColumnLinkedMatrix
  1: getG_symDMatrix(X = W, blockSize = ceiling(nrow(W)/3), folder = paste0(testPath, 
         "test-", randomString()), nTasks = nTasks, nCores = nCores) at testthat/test-utils.R:98
  2: symDMatrix::symDMatrix(blocks, center, scale)
  3: new(structure("symDMatrix", package = "symDMatrix"), ...)
  4: initialize(value, ...)
  5: initialize(value, ...)
  6: stop("blocks need to be of type ColumnLinkedMatrix")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 304 SKIPPED: 0 FAILED: 2
  1. Error: getG_symDMatrix on 1 cores (@test-utils.R#98) 
  2. Error: getG_symDMatrix on 2 cores (@test-utils.R#98) 
  
  Error: testthat unit tests failed
  Execution halted
src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_CFLAGS but no OPENMP macro in PKG_LIBS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
Using a SHLIB_OPENMP_ macro for compilation but none in PKG_LIBS is not
portable and may result in installation errors.
installed size is 144.8Mb
  sub-directories of 1Mb or more:
    include  144.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.9Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   6.1Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
installed size is 28.8Mb
  sub-directories of 1Mb or more:
    libs  28.7Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars: it is not portable to include SHLIB_OPENMP_*' macros in PKG_CPPFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
PKG_CPPFLAGS is used for both C and C++ code so it is not portable to
use it for these macros.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘lattice’ ‘zoo’
  All declared Imports should be used.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   8.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   2.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Package suggested but not available for checking: ‘RQuantLib’
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RGtk2’ ‘cairoDevice’ ‘ergm’ ‘foreign’ ‘gWidgets’ ‘gWidgetsRGtk2’
  ‘haven’ ‘plot3D’ ‘plot3Drgl’ ‘rgl’ ‘sna’ ‘statnet.common’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘gtools’ ‘knitr’ ‘nnet’ ‘parallel’ ‘rJava’ ‘reshape’
  ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
Missing or unexported object: ‘xgboost::predict’
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘blkergm’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘blkergm’
See ‘/data/gannet/ripley/R/packages/tests-clang/blkergm.Rcheck/00install.out’ for details.
installed size is 44.1Mb
  sub-directories of 1Mb or more:
    libs  43.0Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘descriptr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘formula.tools’ ‘plm’
  All declared Imports should be used.
installed size is 32.3Mb
  sub-directories of 1Mb or more:
    libs  32.0Mb
installed size is 64.0Mb
  sub-directories of 1Mb or more:
    libs  63.7Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Found the following significant warnings:
  conditional.least.squares.c:232:20: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  conditional.least.squares.c:233:20: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  conditional.least.squares.c:234:20: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/bnlearn.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.7Mb
src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but not in PKG_CFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
Namespaces in Imports field not imported from:
  ‘knitr’ ‘yaml’
  All declared Imports should be used.
installed size is 376.1Mb
  sub-directories of 1Mb or more:
    include    3.2Mb
    lib      372.6Mb
installed size is 84.3Mb
  sub-directories of 1Mb or more:
    libs  83.9Mb
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘tidyr’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespaces in Imports field not imported from:
  ‘CCA’ ‘brainR’ ‘elasticnet’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
installed size is 37.6Mb
  sub-directories of 1Mb or more:
    libs  37.4Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘profileModel’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R     3.5Mb
    doc   2.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    bin    2.3Mb
    doc    1.1Mb
    libs   2.2Mb
Namespaces in Imports field not imported from:
  ‘rworldxtra’ ‘sp’
  All declared Imports should be used.
Found the following significant warnings:
  helpers.c:365:19: warning: absolute value function 'fabsf' given an argument of type 'double' but has parameter of type 'float' which may cause truncation of value [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/BSquare.Rcheck/00install.out’ for details.
installed size is 32.3Mb
  sub-directories of 1Mb or more:
    libs  31.2Mb
installed size is 98.5Mb
  sub-directories of 1Mb or more:
    libs  97.9Mb
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘btergm’
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘btergm’
See ‘/data/gannet/ripley/R/packages/tests-clang/btergm.Rcheck/00install.out’ for details.
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    libs  18.3Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R        1.1Mb
    data     1.5Mb
    models   2.4Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   3.3Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘cowplot’ ‘dplyr’ ‘ranger’ ‘rms’ ‘survival’ ‘tidyverse’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
ConstructModel: warning in AddDynamicRegression(ss, formula, data =
  data, sigma.mean.prior = sigma.mean.prior): partial argument match of
  'sigma.mean.prior' to 'sigma.mean.prior.DEPRECATED'
Namespace in Imports field not imported from: ‘prettydoc’
  All declared Imports should be used.
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.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  17.7Mb
Found the following significant warnings:
  Warning: replacing previous import ‘BMisc::lhs.vars’ by ‘formula.tools::lhs.vars’ when loading ‘ccfa’
  Warning: replacing previous import ‘BMisc::rhs.vars’ by ‘formula.tools::rhs.vars’ when loading ‘ccfa’
  Warning: replacing previous import ‘BMisc::rhs’ by ‘formula.tools::rhs’ when loading ‘ccfa’
See ‘/data/gannet/ripley/R/packages/tests-clang/ccfa.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ./MCMC_prob.h:2091:41: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/CCMnet.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘units’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lazyeval’ ‘purrr’ ‘roxygen2’
  All declared Imports should be used.
Running examples in ‘CDECRetrieve-Ex.R’ failed
The error most likely occurred in:

> ### Name: cdec_rt
> ### Title: Get a rating table
> ### Aliases: cdec_rt
> 
> ### ** Examples
> 
> cdec_rt("abj") # get the stage to rating curve for ABJ
Error in open.connection(x, "rb") : 
  Timeout was reached: Connection timed out after 10000 milliseconds
Calls: cdec_rt ... %in% -> cdec_rt_list -> <Anonymous> -> read_html.default
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 55-69 (CDECRetrieve.Rmd) 
Error: processing vignette 'CDECRetrieve.Rmd' failed with diagnostics:
Timeout was reached: Connection timed out after 10000 milliseconds
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.3Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   9.3Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.8Mb
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but not in PKG_CFLAGS
  src/Makevars: it is not portable to include SHLIB_OPENMP_*' macros in PKG_CPPFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
PKG_CPPFLAGS is used for both C and C++ code so it is not portable to
use it for these macros.
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Found the following significant warnings:
  costfunctions.c:33:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  costfunctions.c:57:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/changepoint.np.Rcheck/00install.out’ for details.
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars: it is not portable to include SHLIB_OPENMP_*' macros in PKG_CPPFLAGS
  src/Makevars.in: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars.in: it is not portable to include SHLIB_OPENMP_*' macros in PKG_CPPFLAGS
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_CFLAGS but not in PKG_LIBS
  src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_LIBS but not in PKG_CXXFLAGS
  src/Makevars.win: it is not portable to include SHLIB_OPENMP_*' macros in PKG_CPPFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
PKG_CPPFLAGS is used for both C and C++ code so it is not portable to
use it for these macros.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘foreach’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gamlss.dist’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tools’
  All declared Imports should be used.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
Running examples in ‘choroplethr-Ex.R’ failed
The error most likely occurred in:

> ### Name: country_choropleth
> ### Title: Create a country-level choropleth
> ### Aliases: country_choropleth
> 
> ### ** Examples
> 
> # demonstrate default options
> data(df_pop_country)
> country_choropleth(df_pop_country, "2012 World Bank Populate Estimates")
Warning in self$bind() :
  The following regions were missing and are being set to NA: namibia, western sahara, taiwan, antarctica, kosovo
Error in UseMethod("round_any") : 
  no applicable method for 'round_any' applied to an object of class "character"
Calls: <Anonymous> ... <Anonymous> -> f -> <Anonymous> -> f -> number -> round_any
Execution halted
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘stringr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘circlize’
  All declared Imports should be used.
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Files which contain pragma(s) suppressing diagnostics:
  ‘src/cld_3/protos/feature_extractor.pb.h’
  ‘src/cld_3/protos/sentence.pb.h’ ‘src/cld_3/protos/task_spec.pb.h’
installed size is 22.0Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
Namespaces in Imports field not imported from:
  ‘scales’ ‘sp’
  All declared Imports should be used.
Found the following significant warnings:
  ./networkCliqueMSR.h:4:9: warning: 'NETWORKClIQUEMSR_H' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
See ‘/data/gannet/ripley/R/packages/tests-clang/cliqueMS.Rcheck/00install.out’ for details.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘infuser’ ‘purrr’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
    pdf   2.2Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data     3.5Mb
    exdata   5.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   4.2Mb
Namespaces in Imports field not imported from:
  ‘graphics’ ‘pander’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘flashClust’ ‘speedglm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘grid’ ‘gridExtra’
  All declared Imports should be used.
Running examples in ‘colorplaner-Ex.R’ failed
The error most likely occurred in:

> ### Name: color_projections
> ### Title: Color Space Projections
> ### Aliases: YUV_projection color_projections interpolate_projection
> ###   red_blue_projection
> 
> ### ** Examples
> 
> library(ggplot2)
> ggplot(mtcars, aes(x = wt, y = mpg, color = disp, colour2 = hp)) +
+   geom_point() +
+   scale_color_colorplane(color_projection = interpolate_projection,
+                          zero_color = "darkorange2",
+                          horizontal_color = "mediumspringgreen",
+                          vertical_color = "magenta")
Error in guide_train.colorplane(guide, scale, output) : 
  unused argument (output)
Calls: <Anonymous> ... ggplot_gtable.ggplot_built -> build_guides -> guides_train -> guide_train
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 35-54 (colorplaner.Rmd) 
Error: processing vignette 'colorplaner.Rmd' failed with diagnostics:
unused argument (output)
Execution halted
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘PearsonDS’ ‘VGAM’ ‘actuar’ ‘fExtremes’ ‘rmutil’
  All declared Imports should be used.
Found the following significant warnings:
  Utility.c:162:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:187:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:211:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:392:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:417:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:442:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/CompRandFld.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data      6.5Mb
    extdata   2.6Mb
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘MASS’ ‘geepack’
  All declared Imports should be used.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   6.5Mb
Namespaces in Imports field not imported from:
  ‘Rtsne’ ‘scatterplot3d’
  All declared Imports should be used.
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_LIBS but not in PKG_CXXFLAGS
  src/Makevars: it is not portable to include SHLIB_OPENMP_*' macros in PKG_CPPFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
PKG_CPPFLAGS is used for both C and C++ code so it is not portable to
use it for these macros.
installed size is 28.8Mb
  sub-directories of 1Mb or more:
    libs  28.4Mb
Namespace in Imports field not imported from: ‘xtable’
  All declared Imports should be used.
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.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
Running examples in ‘CosmoPhotoz-Ex.R’ failed
The error most likely occurred in:

> ### Name: plotDiagPhotoZ
> ### Title: Plot diagnostics for photometric redshift estimations
> ### Aliases: plotDiagPhotoZ
> ### Keywords: hplot
> 
> ### ** Examples
> 
> # First, generate some mock data
> ppo <- runif(1000, min=0.1, max=2)
> ppo_ph <- rnorm(length(ppo), mean=ppo, sd=0.05)
> 
> # Then generate the plots
> plotDiagPhotoZ(ppo_ph, ppo, type="errordist")
Error in loadNamespace(name) : there is no package called ‘dplyr’
Calls: plotDiagPhotoZ ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   5.2Mb
Namespace in Imports field not imported from: ‘maps’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Namespace in Imports field not imported from: ‘gstat’
  All declared Imports should be used.
src/Makevars: it is not portable to include multiple SHLIB_OPENMP_*' macros in PKG_LIBS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘misc3d’
  All declared Imports should be used.
installed size is 38.8Mb
  sub-directories of 1Mb or more:
    libs  38.6Mb
src/Makevars: incorrect macro SHLIB_OPENMP_CFLAGS included in PKG_CXXFLAGS
  src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but not in PKG_CFLAGS
  src/Makevars.win: incorrect macro SHLIB_OPENMP_CFLAGS included in PKG_CXXFLAGS
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but not in PKG_CFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
QR.cd: no visible global function definition for ‘quantile’
QR.lasso.cd: no visible global function definition for ‘quantile’
cqr.cd: no visible global function definition for ‘quantile’
cqr.lasso.cd: no visible global function definition for ‘quantile’
cqr.lasso.mm: no visible global function definition for ‘quantile’
cqr.mm: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
File ‘cqrReg/libs/cqrReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   6.5Mb
Note: found 11 marked Latin-1 strings
  Note: found 57 marked UTF-8 strings
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Namespaces in Imports field not imported from:
  ‘AnnotationDbi’ ‘clusterProfiler’ ‘org.Hs.eg.db’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘glue’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘r6extended’
  All declared Imports should be used.
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    libs  22.2Mb
Namespace in Imports field not imported from: ‘yaml’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘qte’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    shp   7.8Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data  10.9Mb
Note: found 59670 marked Latin-1 strings
  Note: found 16 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tea’
  All declared Imports should be used.
installed size is 74.4Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
    doc    4.1Mb
    libs  64.1Mb
src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but not in PKG_CFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
installed size is 32.0Mb
  sub-directories of 1Mb or more:
    extdata  31.9Mb
Namespace in Imports field not imported from: ‘pspearman’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘stats’ ‘utils’
  All declared Imports should be used.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    libs   5.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs   1.1Mb
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  20.9Mb
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘Demerelate’ ‘misc3d’ ‘plotly’ ‘quadprog’ ‘rgl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    java  15.2Mb
Namespaces in Imports field not imported from:
  ‘DatabaseConnectorJars’ ‘bit’
  All declared Imports should be used.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    4.5Mb
    libs   3.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
.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.
installed size is 61.4Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  59.4Mb
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
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').
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘gridExtra’ ‘latticeExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘CDM’
  All declared Imports should be used.
Running examples in ‘ddeploy-Ex.R’ failed
The error most likely occurred in:

> ### Name: duke_deploy
> ### Title: Deploy model using REST API
> ### Aliases: duke_deploy
> 
> ### ** Examples
> 
> duke_auth <- list(
+ user_name = "try_it",
+ api_key   = "db1542b66f16aba5768d8a19c27dec4facf9168a",
+ endpoint = "/api/v1.0"
+ )
> example_data <- as.data.frame(cbind(gl(3,50),rnorm(150)));names(example_data) <- c("x","y")
> example_fit  <- lm(y~x,data=example_data)
> duke_deploy(auth_details=duke_auth,model_object=example_fit)
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Connection timed out after 10000 milliseconds
Calls: duke_deploy ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    libs  23.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
'library' or 'require' call to ‘UScensus2010’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘UScensus2010’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘JavaGD’ ‘OpenStreetMap’ ‘maptools’ ‘rgdal’ ‘scales’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
src/Makevars: SHLIB_OPENMP_CFLAGS is included in PKG_CFLAGS but not in PKG_LIBS
  src/Makevars: SHLIB_OPENMP_FFLAGS is included in PKG_FFLAGS but not SHLIB_OPENMP_CFLAGS in PKG_LIBS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
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.
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
Found the following significant warnings:
  DEploid/updateHap.cpp:670:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
  DEploid/updateHap.cpp:678:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
  DEploid/updateHap.cpp:681:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
  DEploid/updateHap.cpp:682:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/DEploid.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_LIBS but not in PKG_CXXFLAGS
  src/Makevars: it is not portable to include SHLIB_OPENMP_*' macros in PKG_CPPFLAGS
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but not in PKG_CFLAGS
  src/Makevars.win: it is not portable to include SHLIB_OPENMP_*' macros in PKG_CPPFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
PKG_CPPFLAGS is used for both C and C++ code so it is not portable to
use it for these macros.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.7Mb
    help   1.4Mb
    libs   1.6Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘methods’
  All declared Imports should be used.
Packages which this enhances but not available for checking:
  ‘gurobi’ ‘Rcplex’ ‘Rmosek’
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  18.4Mb
installed size is 46.4Mb
  sub-directories of 1Mb or more:
    libs  45.9Mb
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  17.4Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
Namespace in Imports field not imported from: ‘mgcv’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: replacing previous import ‘BMisc::lhs.vars’ by ‘formula.tools::lhs.vars’ when loading ‘did’
  Warning: replacing previous import ‘BMisc::rhs.vars’ by ‘formula.tools::rhs.vars’ when loading ‘did’
  Warning: replacing previous import ‘BMisc::rhs’ by ‘formula.tools::rhs’ when loading ‘did’
See ‘/data/gannet/ripley/R/packages/tests-clang/did.Rcheck/00install.out’ for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc   9.3Mb
Namespace in Imports field not imported from: ‘gplots’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘proxy’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    include  16.7Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   2.1Mb
    libs   3.7Mb
Namespaces in Imports field not imported from:
  ‘dbplyr’ ‘randomForest’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘GOstats’ ‘caTools’ ‘fdrtool’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   5.8Mb
Error in re-building vignettes:
  ...
Quitting from lines 284-293 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
`data` must be uniquely named but has duplicate elements
Execution halted
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-clang/dpglasso.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    libs  25.2Mb
Namespaces in Imports field not imported from:
  ‘bit64’ ‘rstudioapi’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   3.5Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Found the following significant warnings:
  compnoreggilks.cpp:31:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compnoreggilks.cpp:90:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:32:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:88:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:150:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:207:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:380:8: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/DPWeibull.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    media       2.2Mb
    shinyapps   2.7Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shapefiles’
  All declared Imports should be used.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   5.1Mb
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.2Mb
    libs  21.1Mb
Namespaces in Imports field not imported from:
  ‘maptools’ ‘tools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘processx’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’ ‘scales’ ‘xtable’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘base64enc’ ‘knitr’ ‘markdown’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘ebimetagenomics-Ex.R’ failed
The error most likely occurred in:

> ### Name: analyseOtu
> ### Title: Analysis of OTU count data
> ### Aliases: analyseOtu
> ### Keywords: EMG
> 
> ### ** Examples
> 
> ps=getProjectSummary("SRP047083")
> samp=projectSamples(ps)
> runs=runsBySample(ps,samp[2])
> otu=getRunOtu(ps,runs[1])
Error in `[.data.frame`(runData, "Release.version") : 
  undefined columns selected
Calls: getRunOtu -> otu.url -> [ -> [.data.frame
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    hac    4.0Mb
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tnet’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dae’ ‘dplyr’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
    doc    1.2Mb
installed size is 53.9Mb
  sub-directories of 1Mb or more:
    libs  53.2Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data  11.5Mb
Namespaces in Imports field not imported from:
  ‘graphics’ ‘maptools’ ‘rgeos’
  All declared Imports should be used.
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  16.3Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    xsd   5.4Mb
'library' or 'require' calls to packages already attached by Depends:
  ‘clusterSim’ ‘earth’
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘clusterSim’ ‘earth’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.3Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.5Mb
Note: found 23639 marked Latin-1 strings
Namespaces in Imports field not imported from:
  ‘BiocParallel’ ‘broom’ ‘reshape2’ ‘rmarkdown’
  All declared Imports should be used.
Running ‘testthat.R’ [42s/50s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(envnames)
  > 
  > test_check("envnames")
  
  Environments involved:
  Current environment: <environment: R_GlobalEnv>
  Parent environment of env1: <environment: R_GlobalEnv>
  Parent environment of env2: <environment: R_GlobalEnv>
  Parent environment of env11: <environment: 0x1a49898>
  R_GlobalEnv env_of_envs       envir 
       "env2"      "env2"      "env2" 
  correct memory address: <0x4796708> 
  observed result: FALSE 
  ── 1. Failure: T21) is_memory_address(): a string obtained as the memory address
  `observed` not equal to `expected`.
  1 element mismatch
  
  Now inside function g 
  Environment name of calling function (using environmentName() function):  ""
  Environment name of calling function as returned by get_fun_calling(): env1$f
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 265 SKIPPED: 14 FAILED: 1
  1. Failure: T21) is_memory_address(): a string obtained as the memory address of an object is identified as a valid memory address (@test-functions.r#109) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    doc    3.3Mb
    help   3.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘ROCR’ ‘c060’ ‘methods’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘colorspace’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘llogistic’ ‘logitnorm’
  All declared Imports should be used.
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Found the following significant warnings:
  utilities.c:175:32: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/Equalden.HD.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘ergm.count’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘ergm.count’
See ‘/data/gannet/ripley/R/packages/tests-clang/ergm.count.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘ergm::colMeans.mcmc.list’ by ‘statnet.common::colMeans.mcmc.list’ when loading ‘ergm.ego’
  Warning: replacing previous import ‘ergm::sweep.mcmc.list’ by ‘statnet.common::sweep.mcmc.list’ when loading ‘ergm.ego’
See ‘/data/gannet/ripley/R/packages/tests-clang/ergm.ego.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘ergm.graphlets’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘ergm.graphlets’
See ‘/data/gannet/ripley/R/packages/tests-clang/ergm.graphlets.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘ergm.rank’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘ergm.rank’
See ‘/data/gannet/ripley/R/packages/tests-clang/ergm.rank.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘ergm.userterms’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘ergm.userterms’
See ‘/data/gannet/ripley/R/packages/tests-clang/ergm.userterms.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘signal’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘searcher’
  All declared Imports should be used.
installed size is 26.6Mb
  sub-directories of 1Mb or more:
    libs  26.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘msm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘EnvStats’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
Namespaces in Imports field not imported from:
  ‘curl’ ‘openxlsx’ ‘stringr’
  All declared Imports should be used.
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
Namespaces in Imports field not imported from:
  ‘CodeDepends’ ‘DT’ ‘PKI’ ‘shinycssloaders’ ‘tictoc’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘polynom’
  All declared Imports should be used.
print.cdf : numform: warning in formatC(x, dig = digits): partial
  argument match of 'dig' to 'digits'
print.cdf: warning in get("x", env = environment(x)): partial argument
  match of 'env' to 'envir'
print.cdf: warning in get("y", env = environment(x)): partial argument
  match of 'env' to 'envir'
print.ogive : numform: warning in formatC(x, dig = digits): partial
  argument match of 'dig' to 'digits'
print.ogive: warning in get("x", env = environment(x)): partial
  argument match of 'env' to 'envir'
print.ogive: warning in get("y", env = environment(x)): partial
  argument match of 'env' to 'envir'
quantile.expert: warning in formatC(paste(100 * probs, "%", sep = ""),
  format = "fg", wid = 1, digits = dig): partial argument match of
  'wid' to 'width'
MS: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
Error in re-building vignettes:
  ...
Warning: Removed 37 rows containing non-finite values (stat_summary).
Warning: Removed 37 rows containing non-finite values (stat_summary).
Warning: Removed 37 rows containing non-finite values (stat_summary).
Warning: Removed 37 rows containing non-finite values (stat_summary).
Warning: Removed 37 rows containing non-finite values (stat_summary).
Warning: Removed 37 rows containing non-finite values (stat_summary).
Warning: Removed 37 rows containing non-finite values (stat_summary).
Warning: Removed 37 rows containing non-finite values (stat_summary).
Warning in make_onset_data(response_window_clean, onset_time = 15500, fixation_window_length = 1,  :
  Very few trials have a legitimate first AOI! Possible incorrect onset time?
Warning in max(SwitchAOI) :
  no non-missing arguments to max; returning -Inf
Warning in min(SwitchAOI) :
  no non-missing arguments to min; returning Inf
Warning in max(df_plot$.Time) :
  no non-missing arguments to max; returning -Inf
Quitting from lines 91-93 (onset_contingent_analysis_vignette.Rmd) 
Error: processing vignette 'onset_contingent_analysis_vignette.Rmd' failed with diagnostics:
replacement has 1 row, data has 0
Execution halted
Namespace in Imports field not imported from: ‘refund’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘forcats’ ‘formula.tools’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.9Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  15.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.1Mb
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
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 ‘/data/gannet/ripley/R/packages/tests-clang/FastRWeb.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘whisker’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.7Mb
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
  Warning: 'cBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is 54.3Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  51.2Mb
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    libs  22.2Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   7.2Mb
Namespaces in Imports field not imported from:
  ‘cellranger’ ‘knitr’
  All declared Imports should be used.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Namespaces in Imports field not imported from:
  ‘RStoolbox’ ‘rgdal’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘desc’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Quitting from lines 83-87 (fiftystater.Rmd) 
Error: processing vignette 'fiftystater.Rmd' failed with diagnostics:
unused argument (output)
Execution halted
Namespace in Imports field not imported from: ‘rappdirs’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘fingertipsR’ ‘mapproj’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘XML’ ‘gglasso’ ‘methods’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
src/Makevars: it is not portable to include multiple SHLIB_OPENMP_*' macros in PKG_LIBS
  src/Makevars.win: SHLIB_OPENMP_FCFLAGS is included in PKG_FCFLAGS but not in PKG_LIBS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R   6.4Mb
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
Namespaces in Imports field not imported from:
  ‘base’ ‘pbapply’ ‘stringr’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    libs  21.2Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
src/Makevars: it is not portable to include SHLIB_OPENMP_*' macros in PKG_CPPFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
PKG_CPPFLAGS is used for both C and C++ code so it is not portable to
use it for these macros.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
Package suggested but not available for checking: ‘dggrids’
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    2.1Mb
Namespaces in Imports field not imported from:
  ‘R.utils’ ‘grDevices’ ‘graphics’ ‘matrixStats’ ‘stats’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    data  16.2Mb
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    libs  18.0Mb
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_LIBS but not in PKG_CXXFLAGS
  src/Makevars: it is not portable to include SHLIB_OPENMP_*' macros in PKG_CPPFLAGS
  src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_LIBS but not in PKG_CXXFLAGS
  src/Makevars.win: it is not portable to include SHLIB_OPENMP_*' macros in PKG_CPPFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for F77: see the manual).
PKG_CPPFLAGS is used for both C and C++ code so it is not portable to
use it for these macros.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
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
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘maptools’ ‘rgeos’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘gamlss’
  All declared Imports should be used.
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').
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   8.6Mb
installed size is 63.5Mb
  sub-directories of 1Mb or more:
    libs  63.0Mb
installed size is 83.4Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     80.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘roxygen2’ ‘testthat’ ‘utils’ ‘withr’
  All declared Imports should be used.
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  16.3Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Found the following significant warnings:
  cGetHCS.c:9:33: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  cIdentical.c:9:34: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/gdmp.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘rootSolve’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘NMF’ ‘RColorBrewer’ ‘VennDiagram’ ‘clValid’ ‘data.table’ ‘grid’
  ‘gtools’ ‘pca3d’ ‘rmarkdown’ ‘scales’ ‘shinydashboard’ ‘shinyjs’
  ‘statmod’ ‘stringr’
  All declared Imports should be used.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    4.7Mb
    libs   1.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    exdata   5.1Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.7Mb
Namespaces in Imports field not imported from:
  ‘maptools’ ‘rgdal’ ‘rgeos’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    help   1.2Mb
    libs   3.7Mb
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    data  26.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R         3.5Mb
    extdata   1.4Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  12.3Mb
Namespace in Imports field not imported from: ‘velociraptr’
  All declared Imports should be used.
Found the following assignments to the global environment:
File ‘geoR/R/auxiliar.R’:
  assign(".objfuncQQ", objfunc, pos = 1)
  assign(".bounds.list", .bounds.list, pos = 1)
  assign("madtonormalQQ", madtonormalQQ, pos = 1)
File ‘geoR/R/likGRF.R’:
  assign(".likGRF.dists.vec", lapply(split(as.data.frame(coords), 
    realisations), vecdist), pos = 1)
  assign(".likGRF.dists.vec", lapply(split(as.data.frame(coords), 
    realisations), vecdist), pos = 1)
  assign(".likGRF.dists.vec", lapply(split(as.data.frame(coords.c), 
    temp.list$realisations), vecdist), pos = 1)
  assign(".temp.lower.lambda", -2, pos = 1)
  assign(".temp.upper.lambda", 2, pos = 1)
File ‘geoR/R/profiles.R’:
  assign(".temp.list", list(n = n, z = data, beta.size = dim(trend)[2], 
    kappa = obj.likfit$kappa, xmat = trend, method.lik = obj.likfit$method.lik, 
    dists.lowertri = dists.vec, cov.model = obj.likfit$cov.model, 
    fix.lambda = obj.likfit$transform.info$fix.lambda, lambda = obj.likfit$lambda, 
    lower.phi = lower.phi, upper.phi = upper.phi, lower.sigmasq = lower.sigmasq, 
    phi.est = phi, tausq.rel.est = tausq.rel, tausq.est = tausq, 
    sigmasq.est = sigmasq), pos = 1)
  assign(".temp.temp.list", get(".temp.list", pos = 1), pos = 1)
  assign(".temp.list", .temp.temp.list, pos = 1)
  assign(".temp.lambda", lambda, pos = 1)
  assign(".temp.lambda", lambda, pos = 1)
File ‘geoR/R/simul.R’:
  assign("setRF", geoR2RF(cov.model = cov.model, cov.pars = cov.pars, 
    nugget = nugget, kappa = kappa, aniso.pars = aniso.pars), 
    pos = 1)
File ‘geoR/R/variofit.R’:
  assign(".temp.theta", NULL, pos = 1)
  assign(".temp.theta", theta, pos = 1)
  assign(".IND.geoR.variog.model.env", TRUE, pos = 1)
File ‘geoR/R/variogram.R’:
  assign(".variog4.nomessage", TRUE, pos = 1)