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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols 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 use registered native symbols 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.
Packages suggested but not available for checking: ‘gurobi’ ‘rgurobi’
File ‘raptr/libs/raptr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 use registered native symbols 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 use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
datgen: no visible global function definition for ‘rnorm’
optimization.IC: no visible global function definition for ‘optim’
outlier.replace: no visible global function definition for ‘qnorm’
pargen: no visible global function definition for ‘runif’
rav: no visible global function definition for ‘optim’
rav2file: no visible global function definition for ‘write.table’
standardized: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  optim qnorm rnorm runif sd write.table
Consider adding
  importFrom("stats", "optim", "qnorm", "rnorm", "runif", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
File ‘rAverage/libs/rAverage.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Files in the 'vignettes' directory newer than all files in 'inst/doc':
  ‘rbamtools.Rnw’
Running ‘test-all.R’ [2s/2s]
  Running ‘test_bam_align.r’ [0s/0s]
Running the tests in ‘tests/test_bam_align.r’ failed.
Complete output:
  > 
  > 
  > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
  > # test_bam_align: General
  > # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #
  > align <- getNextAlign(reader)
  Error in getNextAlign(reader) : could not find function "getNextAlign"
  Execution halted
Non-portable flags in variable 'PKG_CPPFLAGS':
  -g
File ‘RBerkeley/libs/RBerkeley.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rBeta2009/libs/rBeta2009.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.parse.rhea: no visible global function definition for ‘tail’
get.chebi.all: no visible global function definition for
  ‘download.file’
get.chebi.all: no visible global function definition for ‘read.delim’
get.rhea.all: no visible global function definition for ‘download.file’
get.unipathway.all: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file read.delim tail
Consider adding
  importFrom("utils", "download.file", "read.delim", "tail")
to your NAMESPACE file.
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.
File ‘Rblpapi/libs/Rblpapi.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
ceimOpt: no visible global function definition for ‘dev.new’
ceimOpt: no visible global function definition for ‘runif’
ceimOpt: no visible global function definition for ‘sd’
ceimOpt: no visible global function definition for ‘rnorm’
ceimOpt: no visible global function definition for ‘plot’
ceimOpt: no visible global function definition for ‘grid’
ceimOpt: no visible global function definition for ‘rgb’
ceimOpt: no visible global function definition for ‘lines’
overPlotErrorPolygon: no visible global function definition for
  ‘polygon’
plotEliteDistrib: no visible global function definition for ‘dev.new’
plotEliteDistrib: no visible global function definition for
  ‘split.screen’
plotEliteDistrib: no visible global function definition for ‘screen’
plotEliteDistrib: no visible global function definition for ‘plot’
plotEliteDistrib: no visible global function definition for ‘density’
plotEliteDistrib: no visible global function definition for ‘abline’
plotEliteDistrib: no visible global function definition for ‘text’
plotEliteDistrib: no visible global function definition for
  ‘close.screen’
Undefined global functions or variables:
  abline close.screen density dev.new grid lines plot polygon rgb rnorm
  runif screen sd split.screen text
Consider adding
  importFrom("grDevices", "dev.new", "rgb")
  importFrom("graphics", "abline", "close.screen", "grid", "lines",
             "plot", "polygon", "screen", "split.screen", "text")
  importFrom("stats", "density", "rnorm", "runif", "sd")
to your NAMESPACE file.
.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.
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.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘RcppEigen’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Calls with DUP:
   .Call("hclust_from_distance", data = as.double(x), size = as.integer(attributes(x)$Size), 
       link = as.integer(method), DUP = FALSE, NAOK = FALSE, PACKAGE = "Rclusterpp")
   .Call("hclust_from_data", data = x, link = as.integer(method), 
       dist = as.integer(distance), p = as.numeric(p), DUP = FALSE, 
       NAOK = FALSE, PACKAGE = "Rclusterpp")
DUP is no longer supported and will be ignored.
Rclusterpp.package.skeleton: no visible global function definition for
  ‘packageDescription’
Undefined global functions or variables:
  packageDescription
Consider adding
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
File ‘Rclusterpp/libs/Rclusterpp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
.onAttach: no visible global function definition for ‘palette’
.onAttach: no visible global function definition for ‘dev.off’
helpAboutBCA: no visible global function definition for ‘help’
Undefined global functions or variables:
  dev.off help palette
Consider adding
  importFrom("grDevices", "dev.off", "palette")
  importFrom("utils", "help")
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
Packages in Depends field not imported from:
  ‘orloca’ ‘orloca.es’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rcmdr.new.loca.p: no visible binding for global variable ‘top’
Rcmdr.new.loca.p: no visible binding for global variable ‘buttonsFrame’
Rcmdr.orloca.norm: no visible binding for global variable ‘top’
Rcmdr.orloca.norm : onOK: no visible binding for global variable
  ‘normaVariable’
Rcmdr.orloca.norm: no visible binding for global variable ‘normaFrame’
Rcmdr.orloca.norm: no visible binding for global variable
  ‘buttonsFrame’
Rcmdr.rloca.p: no visible binding for global variable ‘top’
Rcmdr.rloca.p: no visible binding for global variable ‘buttonsFrame’
Rcmdr.zsum: no visible binding for global variable ‘top’
Rcmdr.zsum: no visible binding for global variable ‘buttonsFrame’
Rcmdr.zsummin: no visible binding for global variable ‘top’
Rcmdr.zsummin : onOK: no visible binding for global variable
  ‘algorithmVariable’
Rcmdr.zsummin : onOK: no visible binding for global variable ‘.sol’
Rcmdr.zsummin: no visible binding for global variable ‘algorithmFrame’
Rcmdr.zsummin: no visible binding for global variable ‘buttonsFrame’
Undefined global functions or variables:
  .sol algorithmFrame algorithmVariable buttonsFrame normaFrame
  normaVariable top
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.
Packages in Depends field not imported from:
  ‘Rcmdr’ ‘seeg’ ‘sgeostat’ ‘spatstat’
  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 ‘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.
File ‘Rcoclust/libs/Rcoclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘RcppClassic’
  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.RcppExample
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘RcppClassicExamples/libs/RcppClassicExamples.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols 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 use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘RcppOctave/libs/RcppOctave.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Object: ‘rcpp_octave.o’
File ‘RcppOctave/libs/RcppOctave.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Files in the 'vignettes' directory newer than all files in 'inst/doc':
  ‘RcppShark.Rmd’
blockpfGaussianOpt: no visible global function definition for ‘polygon’
blockpfGaussianOpt: no visible global function definition for ‘lines’
blockpfGaussianOpt: no visible global function definition for ‘points’
getPfLineartBSData: no visible global function definition for
  ‘read.table’
pfLineartBS: no visible global function definition for ‘dev.new’
pfLineartBS: no visible global function definition for ‘par’
pfLineartBSOnlinePlot: no visible global function definition for ‘plot’
simGaussian: no visible global function definition for ‘rnorm’
simLineart: no visible global function definition for ‘rnorm’
simLineart: no visible global function definition for ‘rt’
simNonlin: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  dev.new lines par plot points polygon read.table rnorm rt
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "lines", "par", "plot", "points", "polygon")
  importFrom("stats", "rnorm", "rt")
  importFrom("utils", "read.table")
to your NAMESPACE file.
File ‘RcppSMC/libs/RcppSMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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').
Found the following apparent S3 methods exported but not registered:
  plot.rdacv predict.rda
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Drda1: no visible global function definition for ‘model.matrix’
permute.rows: no visible global function definition for ‘runif’
plot.rdacv: no visible global function definition for ‘par’
rda.plotmat: no visible global function definition for ‘par’
rda.plotmat: no visible global function definition for ‘plot’
rda.plotmat: no visible global function definition for ‘layout’
rda.plotmat: no visible global function definition for ‘image’
rda.plotmat: no visible global function definition for ‘terrain.colors’
rda.plotmat: no visible global function definition for ‘axis’
rda.plotmat: no visible global function definition for ‘points’
rda.plotmat: no visible global function definition for ‘legend’
rda1: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  axis image layout legend model.matrix par plot points runif
  terrain.colors
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "axis", "image", "layout", "legend", "par",
             "plot", "points")
  importFrom("stats", "model.matrix", "runif")
to your NAMESPACE file.
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 use registered native symbols 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 apparent S3 methods exported but not registered:
  dieharder.default plot.dieharder print.dieharder summary.dieharder
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.dieharder: no visible global function definition for ‘par’
plot.dieharder: no visible global function definition for ‘hist’
plot.dieharder: no visible global function definition for ‘lines’
plot.dieharder: no visible global function definition for ‘density’
plot.dieharder: no visible global function definition for ‘plot’
plot.dieharder: no visible global function definition for ‘ecdf’
plot.dieharder: no visible global function definition for ‘segments’
plot.dieharder: no visible global function definition for ‘mtext’
plot.dieharder: no visible global function definition for ‘ks.test’
plot.dieharder: no visible global function definition for ‘wilcox.test’
summary.dieharder: no visible global function definition for ‘stem’
summary.dieharder: no visible global function definition for ‘ks.test’
summary.dieharder: no visible global function definition for
  ‘wilcox.test’
Undefined global functions or variables:
  density ecdf hist ks.test lines mtext par plot segments stem
  wilcox.test
Consider adding
  importFrom("graphics", "hist", "lines", "mtext", "par", "plot",
             "segments", "stem")
  importFrom("stats", "density", "ecdf", "ks.test", "wilcox.test")
to your NAMESPACE file.
File ‘RDieHarder/libs/RDieHarder.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
File ‘RDS/libs/RDS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable 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 use registered native symbols 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:
  .DollarNames.rDVR
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
checkForVServer: 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.
contour.prop.2D: no visible global function definition for ‘contour’
contour.prop.2D: no visible global function definition for
  ‘filled.contour’
plot.grid.1D: no visible global function definition for ‘par’
plot.grid.1D: no visible global function definition for ‘plot’
plot.grid.1D: no visible global function definition for ‘points’
plot.grid.1D: no visible global function definition for ‘legend’
plot.prop.1D: no visible binding for global variable ‘plot’
polar2cart: no visible global function definition for ‘approxfun’
setup.grid.1D: no visible global function definition for ‘uniroot’
setup.grid.1D: no visible global function definition for ‘diffinv’
setup.prop.1D: no visible global function definition for ‘approx’
setup.prop.1D: no visible global function definition for ‘splinefun’
Undefined global functions or variables:
  approx approxfun contour diffinv filled.contour legend par plot
  points splinefun uniroot
Consider adding
  importFrom("graphics", "contour", "filled.contour", "legend", "par",
             "plot", "points")
  importFrom("stats", "approx", "approxfun", "diffinv", "splinefun",
             "uniroot")
to your NAMESPACE file.
File ‘ReacTran/libs/ReacTran.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘readstata13/libs/readstata13.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
allocationTable_offline: no visible global function definition for
  ‘read.csv’
exportArms.redcapApiConnection: no visible global function definition
  for ‘read.csv’
exportEvents.redcapApiConnection: no visible global function definition
  for ‘read.csv’
exportInstruments.redcapApiConnection: no visible global function
  definition for ‘read.csv’
exportMappings.redcapApiConnection: no visible global function
  definition for ‘read.csv’
exportMetaData.redcapApiConnection: no visible global function
  definition for ‘read.csv’
exportRecords.redcapApiConnection: no visible global function
  definition for ‘read.csv’
exportRecords.redcapApiConnection : <anonymous>: no visible global
  function definition for ‘read.csv’
exportRecords_offline: no visible global function definition for
  ‘read.csv’
exportReports.redcapApiConnection: no visible global function
  definition for ‘read.csv’
exportUsers.redcapApiConnection: no visible global function definition
  for ‘read.csv’
importRecords.redcapApiConnection : <anonymous>: no visible global
  function definition for ‘capture.output’
importRecords.redcapApiConnection : <anonymous>: no visible global
  function definition for ‘write.table’
importRecords.redcapApiConnection: no visible global function
  definition for ‘capture.output’
importRecords.redcapApiConnection: no visible global function
  definition for ‘write.table’
validateImport : printLog: no visible global function definition for
  ‘write.table’
validateImport: no visible binding for global variable ‘tail’
validateImport: no visible binding for global variable ‘head’
Undefined global functions or variables:
  capture.output head read.csv tail write.table
Consider adding
  importFrom("utils", "capture.output", "head", "read.csv", "tail",
             "write.table")
to your NAMESPACE file.
File ‘redist/libs/redist.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
mergeNamespace_roclet: no visible global function definition for
  ‘new_roclet’
Undefined global functions or variables:
  new_roclet
File ‘redland/libs/redland.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
File ‘refGenome/libs/refGenome.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Files in the 'vignettes' directory newer than all files in 'inst/doc':
  ‘refGenome.Rnw’
Running ‘test-all.R’ [2s/2s]
  Running ‘test_overlap_juncs.r’ [0s/0s]
Running the tests in ‘tests/test_overlap_juncs.r’ failed.
Last 13 lines of output:
  > 
  > 
  > ##                      1       2       3       4       5       6       7 ##
  > qry<-data.frame(id = 1:7, seqid = "1",
  +             lstart = c(10100L, 11800L, 12220L, 12220L, 12220L, 32000L, 40000L),
  +             lend =   c(10100L, 12000L, 12225L, 12227L, 12227L, 32100L, 40100L),
  +             rstart = c(10200L, 12200L, 12057L, 12613L, 12650L, 32200L, 40200L),
  +             rend =   c(10300L, 12250L, 12179L, 12620L, 12700L, 32300L, 40300L))
  > ##                      1       2       3       4       5       6       7 ##
  > 
  > 
  > # C) 
  > res<-overlapJuncs(qry,junc)
  Error in overlapJuncs(qry, junc) : could not find function "overlapJuncs"
  Execution halted
Foreign function call to a different package:
  .External("do_read_bib", ..., PACKAGE = "bibtex")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  dim.refdata dimnames.refdata names.refdata plot.HanoiTower
  print.HanoiTower print.ref print.refdata row.names.refdata
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
HanoiTower: no visible global function definition for ‘object.size’
plot.HanoiTower: no visible global function definition for ‘plot’
plot.HanoiTower: no visible global function definition for ‘polygon’
plot.HanoiTower: no visible global function definition for ‘text’
Undefined global functions or variables:
  object.size plot polygon text
Consider adding
  importFrom("graphics", "plot", "polygon", "text")
  importFrom("utils", "object.size")
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.
beta.dRUM: no visible global function definition for ‘dlogis’
beta.dRUM: no visible global function definition for ‘runif’
draw.nu: no visible global function definition for ‘rgamma’
predict.reglogit: no visible global function definition for ‘plogis’
reglogit: no visible global function definition for ‘rnorm’
regmlogit: no visible global function definition for ‘rnorm’
rmultnorm: no visible global function definition for ‘rnorm’
z.dRUM: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dlogis plogis rgamma rnorm runif
Consider adding
  importFrom("stats", "dlogis", "plogis", "rgamma", "rnorm", "runif")
to your NAMESPACE file.
File ‘reglogit/libs/reglogit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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.regress summary.regress
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
regress: no visible global function definition for ‘model.frame’
regress: no visible binding for global variable ‘na.pass’
regress: no visible global function definition for ‘model.response’
regress: no visible global function definition for ‘model.matrix’
regress: no visible global function definition for ‘as.formula’
regress: no visible global function definition for ‘var’
regress: no visible binding for global variable ‘nobs’
remlOptimize: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  as.formula model.frame model.matrix model.response na.pass nobs
  optimize var
Consider adding
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response", "na.pass", "nobs", "optimize", "var")
to your NAMESPACE file.
Running ‘BLUP.tests.R’ [1s/1s]
  Running ‘OLS.r’ [0s/0s]
Running the tests in ‘tests/OLS.r’ failed.
Complete output:
  > ## Example of ordinary least squares
  > 
  > x <- rep(1,15)
  > y <- x + rnorm(15)
  > 
  > mod1 <- lm(y~1)
  > mod2 <- regress(y~1)
  Error in regress(y ~ 1) : could not find function "regress"
  Execution halted
File ‘regsem/libs/regsem.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
'library' or 'require' call to ‘tkrplot’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
blockSim: no visible global function definition for ‘txtProgressBar’
blockSim: no visible global function definition for ‘setTxtProgressBar’
breedFst: no visible global function definition for ‘txtProgressBar’
breedFst: no visible global function definition for ‘setTxtProgressBar’
estimateQuantile: no visible global function definition for ‘quantile’
estimateQuantile: no visible global function definition for
  ‘txtProgressBar’
estimateQuantile: no visible global function definition for
  ‘setTxtProgressBar’
maximizeLRPC: no visible global function definition for
  ‘txtProgressBar’
maximizeLRPC: no visible global function definition for ‘runif’
maximizeLRPC: no visible global function definition for
  ‘setTxtProgressBar’
randomChild: no visible global function definition for ‘runif’
randomSample: no visible global function definition for ‘runif’
sim: no visible global function definition for ‘txtProgressBar’
sim: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  quantile runif setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "quantile", "runif")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
File ‘relSim/libs/relSim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
Packages in Depends field not imported from:
  ‘plyr’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘Hmisc:::label.default’
  See the note in ?`:::` about the use of this operator.
Found the following apparent S3 methods exported but not registered:
  as.data.frame.correlation as.data.frame.freq as.data.frame.summarize
  as.data.frame.summarize.by as.data.frame.survival
  as.data.frame.tabular
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'as.data.frame.correlation':
  ‘as.data.frame.correlation’

S3 methods shown with full name in documentation object 'as.data.frame.freq':
  ‘as.data.frame.freq’

S3 methods shown with full name in documentation object 'as.data.frame.summarize':
  ‘as.data.frame.summarize’

S3 methods shown with full name in documentation object 'as.data.frame.summarize.by':
  ‘as.data.frame.summarize.by’

S3 methods shown with full name in documentation object 'as.data.frame.survival':
  ‘as.data.frame.survival’

S3 methods shown with full name in documentation object 'as.data.frame.tabular':
  ‘as.data.frame.tabular’

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

It is good practice to use registered native symbols 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 use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
MakeHierarchyTree: no visible global function definition for
  ‘as.formula’
Undefined global functions or variables:
  as.formula
Consider adding
  importFrom("stats", "as.formula")
to your NAMESPACE file.
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 use registered native symbols 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.
File ‘repeated/libs/repeated.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
manhattan: no visible global function definition for ‘na.omit’
manhattan: no visible global function definition for ‘tail’
manhattan: no visible global function definition for ‘axis’
manhattan: no visible global function definition for ‘abline’
ztobins: no visible global function definition for ‘hist’
ztobins: no visible global function definition for ‘glm’
ztobins: no visible binding for global variable ‘poisson’
ztobins: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline axis glm hist na.omit poisson quantile tail
Consider adding
  importFrom("graphics", "abline", "axis", "hist")
  importFrom("stats", "glm", "na.omit", "poisson", "quantile")
  importFrom("utils", "tail")
to your NAMESPACE file.
File ‘repfdr/libs/repfdr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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 use registered native symbols 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.
File ‘reReg/libs/reReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘reshape2/libs/reshape2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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.
Package suggested but not available for checking: ‘rsolr’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/restfulr.Rcheck/00install.out’ for details.
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘Guide_restorepoint.Rmd’, ‘Guide_restorepoint.html’,
    ‘Guide_restorepoint.md’
Package has no Sweave vignette sources and no VignetteBuilder field.
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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
Found the following significant warnings:
  Warning: GNU Extension: Non-default type object or sequence zz in EQUIVALENCE statement at (1) with objects of different type
  Warning: GNU Extension: Nonstandard type declaration REAL*4 at (1)
  Warning: GNU Extension: Symbol ‘n’ is used before it is typed at (1)
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rexpokit.Rcheck/00install.out’ for details.
'library' or 'require' call to ‘SparseM’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘SparseM’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fermat.test: no visible global function definition for ‘runif’
mat2coo: no visible global function definition for ‘as.matrix.coo’
Undefined global functions or variables:
  as.matrix.coo runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
File ‘rexpokit/libs/rexpokit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.forensicbatwing print.batwing
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.forensicbatwing: no visible global function definition for ‘plot’
print.batwing: no visible global function definition for ‘tail’
Undefined global functions or variables:
  plot tail
Consider adding
  importFrom("graphics", "plot")
  importFrom("utils", "tail")
to your NAMESPACE file.
File ‘rforensicbatwing/libs/rforensicbatwing.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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 use registered native symbols 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.
Found the following apparent S3 methods exported but not registered:
  predict.rgam
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘rgam/libs/rgam.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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
File ‘rgenoud/libs/rgenoud.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘magick’
File ‘rgl/libs/rgl.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.onAttach: no visible global function definition for ‘sessionInfo’
rescaleIndividual: no visible global function definition for ‘cov’
rescaleIndividual: no visible global function definition for ‘var’
server: no visible global function definition for ‘read.csv’
server: no visible global function definition for ‘tail’
server: no visible global function definition for ‘as.formula’
server: no visible global function definition for ‘terms’
server: no visible global function definition for ‘plot’
server: no visible global function definition for ‘legend’
server: no visible global function definition for ‘lines’
server: no visible global function definition for ‘par’
server: no visible global function definition for ‘layout’
server: no visible global function definition for ‘points’
server: no visible global function definition for ‘barplot’
workerProcessRun: no visible global function definition for
  ‘as.formula’
workerProcessRun : <anonymous>: no visible global function definition
  for ‘runif’
workerProcessRun : progressMonitor: no visible global function
  definition for ‘alarm’
workerProcessRun : progressMonitor: no visible global function
  definition for ‘runif’
Undefined global functions or variables:
  alarm as.formula barplot cov layout legend lines par plot points
  read.csv runif sessionInfo tail terms var
Consider adding
  importFrom("graphics", "barplot", "layout", "legend", "lines", "par",
             "plot", "points")
  importFrom("stats", "as.formula", "cov", "runif", "terms", "var")
  importFrom("utils", "alarm", "read.csv", "sessionInfo", "tail")
to your NAMESPACE file.
'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 use registered native symbols 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:
  !.flag &.flag names.GtkObject print.GType |.flag
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
.install_system_dependencies : <anonymous>: no visible global function
  definition for ‘unzip’
.install_system_dependencies : install_system_dep: no visible global
  function definition for ‘menu’
.install_system_dependencies : install_system_dep: no visible global
  function definition for ‘download.file’
as.GParamSpec: no visible global function definition for ‘new’
Undefined global functions or variables:
  download.file menu new unzip
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "download.file", "menu", "unzip")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘RGtk2/libs/RGtk2.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
dbConnect,H2Driver: no visible global function definition for ‘.jgetEx’
dbSendQuery,H2Connection-character: no visible global function
  definition for ‘.jfield’
Undefined global functions or variables:
  .jfield .jgetEx
.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
File ‘RhpcBLASctl/libs/RhpcBLASctl.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols 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.
get_inat_obs: no visible global function definition for ‘read.csv’
get_inat_obs_project: no visible global function definition for
  ‘read.csv’
get_inat_obs_user: no visible global function definition for ‘read.csv’
inat_handle: no visible binding for global variable ‘data’
Undefined global functions or variables:
  data read.csv
Consider adding
  importFrom("utils", "data", "read.csv")
to your NAMESPACE file.
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘margins.sty’, ‘rinatVignette.Rmd’, ‘rinatVignette.html’,
    ‘rinatVignette.md’, ‘rinatVignette.pdf’
Package has no Sweave vignette sources and no VignetteBuilder field.
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 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 use registered native symbols 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_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 the system RNG.
Compiled code should not call non-API entry points in R.
It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Eindex: no visible global function definition for ‘txtProgressBar’
Eindex: no visible global function definition for ‘setTxtProgressBar’
Emc: no visible global function definition for ‘txtProgressBar’
Emc: no visible global function definition for ‘setTxtProgressBar’
Emc: no visible global function definition for ‘ecdf’
Hier2L: no visible global function definition for ‘var’
Null.Hp.RInSp: no visible global function definition for
  ‘txtProgressBar’
Null.Hp.RInSp: no visible global function definition for ‘rmultinom’
Null.Hp.RInSp: no visible global function definition for
  ‘setTxtProgressBar’
PSicalc: no visible global function definition for ‘txtProgressBar’
PSicalc: no visible global function definition for ‘setTxtProgressBar’
PSicalc: no visible global function definition for ‘ecdf’
WTcMC: no visible global function definition for ‘ecdf’
WTdMC: no visible global function definition for ‘ecdf’
import.RInSp: no visible global function definition for ‘read.table’
like.Wi: no visible global function definition for ‘pchisq’
like.Wi: no visible global function definition for ‘qchisq’
sumMC.RInSp: no visible global function definition for ‘hist’
sumMC.RInSp: no visible global function definition for ‘nclass.Sturges’
sumMC.RInSp: no visible global function definition for ‘legend’
sumMC.RInSp: no visible global function definition for ‘segments’
sumMC.RInSp: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  ecdf hist legend nclass.Sturges pchisq qchisq quantile read.table
  rmultinom segments setTxtProgressBar txtProgressBar var
Consider adding
  importFrom("grDevices", "nclass.Sturges")
  importFrom("graphics", "hist", "legend", "segments")
  importFrom("stats", "ecdf", "pchisq", "qchisq", "quantile",
             "rmultinom", "var")
  importFrom("utils", "read.table", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
File ‘RInSp/libs/RInSp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols 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 use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
rite : loadHistory: no visible global function definition for
  ‘savehistory’
rite : saveGist: no visible global function definition for ‘browseURL’
rite : uploadToRPubs : processEntry: no visible global function
  definition for ‘browseURL’
rite : runCode: no visible global function definition for ‘savehistory’
rite : runCode: no visible global function definition for ‘loadhistory’
rite : knittxt: no visible global function definition for ‘Sweave’
rite : knittxt: no visible global function definition for ‘browseURL’
rite : addHighlighting : addHighlight: no visible global function
  definition for ‘packageDescription’
rite : addHighlighting : addHighlight: no visible global function
  definition for ‘na.omit’
rite : about : <anonymous>: no visible global function definition for
  ‘browseURL’
rite : <anonymous>: no visible global function definition for
  ‘capture.output’
rite : <anonymous>: no visible global function definition for
  ‘update.packages’
rite : <anonymous>: no visible global function definition for ‘help’
rite : f1: no visible global function definition for ‘help’
rite : f1: no visible global function definition for ‘help.search’
rite : commandCompletion: no visible global function definition for
  ‘apropos’
rite : findreplace : <anonymous>: no visible global function definition
  for ‘browseURL’
Undefined global functions or variables:
  Sweave apropos browseURL capture.output help help.search loadhistory
  na.omit packageDescription savehistory update.packages
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "Sweave", "apropos", "browseURL", "capture.output",
             "help", "help.search", "loadhistory", "packageDescription",
             "savehistory", "update.packages")
to your NAMESPACE file.
plot.rivernet: no visible global function definition for ‘plot’
plot.rivernet: no visible global function definition for ‘text’
plot.rivernet: no visible global function definition for ‘lines’
plot.rivernet: no visible global function definition for ‘points’
rivernet.read: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  lines plot points read.table text
Consider adding
  importFrom("graphics", "lines", "plot", "points", "text")
  importFrom("utils", "read.table")
to your NAMESPACE file.
colorRampAlpha: no visible global function definition for ‘col2rgb’
colorRampPaletteAlpha : <anonymous>: no visible global function
  definition for ‘rgb’
curveseg: no visible global function definition for ‘polygon’
curveseg: no visible global function definition for ‘lines’
draw.nodes: no visible global function definition for ‘points’
draw.nodes: no visible global function definition for ‘rect’
draw.nodes: no visible global function definition for ‘text’
riverplot: no visible global function definition for ‘plot.new’
riverplot: no visible global function definition for ‘par’
riverplot: no visible global function definition for ‘dev.hold’
riverplot: no visible global function definition for ‘dev.flush’
riverplot: no visible global function definition for ‘strwidth’
Undefined global functions or variables:
  col2rgb dev.flush dev.hold lines par plot.new points polygon rect rgb
  strwidth text
Consider adding
  importFrom("grDevices", "col2rgb", "dev.flush", "dev.hold", "rgb")
  importFrom("graphics", "lines", "par", "plot.new", "points", "polygon",
             "rect", "strwidth", "text")
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.
Tbsb : ksiint: no visible global function definition for ‘pgamma’
Tbsb: no visible global function definition for ‘pchisq’
Tbsc: no visible global function definition for ‘qchisq’
riv_classical: no visible global function definition for ‘cov’
riv_classical: no visible global function definition for ‘pt’
riv_sest: no visible global function definition for ‘pt’
riv_sest: no visible global function definition for ‘mad’
riv_sest: no visible global function definition for ‘mahalanobis’
riv_withDummies: no visible global function definition for ‘coef’
riv_withDummies : <anonymous>: no visible global function definition
  for ‘coef’
Undefined global functions or variables:
  coef cov mad mahalanobis pchisq pgamma pt qchisq
Consider adding
  importFrom("stats", "coef", "cov", "mad", "mahalanobis", "pchisq",
             "pgamma", "pt", "qchisq")
to your NAMESPACE file.
File ‘rivr/libs/rivr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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 use registered native symbols 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 use registered native symbols 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)
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 ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API call to R: ‘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 the system RNG.
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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard file/directory found at top level:
  ‘java-src’
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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
read.pedfile: no visible global function definition for ‘download.file’
read.pedfile.info: no visible global function definition for
  ‘read.table’
read.pedfile.map: no visible global function definition for
  ‘read.table’
write.pedfile: no visible global function definition for ‘is’
Undefined global functions or variables:
  download.file is read.table
Consider adding
  importFrom("methods", "is")
  importFrom("utils", "download.file", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘rJPSGCS/libs/rJPSGCS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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/JSONGlobals.h:43:50: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
  libjson/Source/JSONGlobals.h:44:49: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
  JSONValidator.cpp:394:105: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
  JSONValidator.cpp:397:104: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
rkt: no visible global function definition for ‘median’
rkt: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  median pnorm
Consider adding
  importFrom("stats", "median", "pnorm")
to your NAMESPACE file.
File ‘rkvo/libs/rkvo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rlas.Rcheck/00install.out’ for details.
File ‘rlecuyer/libs/rlecuyer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols 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 use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
File ‘Rmalschains/libs/Rmalschains.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [26s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(rmapshaper)
  > 
  > test_check("rmapshaper")
  1. Failure: ms_simplify works with lines (@test-simplify.R#442) ----------------
  ms_simplify(line_list) not equal to geojson_list(expected_json).
  Component "features": Component 1: Component 2: Component 2: Component 2: Component 2: Mean relative difference: 1.985531e-08
  
  
  testthat results ================================================================
  OK: 252 SKIPPED: 0 FAILED: 1
  1. Failure: ms_simplify works with lines (@test-simplify.R#442) 
  
  Error: testthat unit tests failed
  Execution halted
read.mat: no visible global function definition for ‘download.file’
write.mat,list: no visible global function definition for
  ‘packageVersion’
Undefined global functions or variables:
  download.file packageVersion
Consider adding
  importFrom("utils", "download.file", "packageVersion")
to your NAMESPACE file.
File ‘rmatio/libs/rmatio.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.onLoad: warning in dir(dll.path, pattern = this.ext, full = FALSE):
  partial argument match of ‘full’ to ‘full.names’
diagnos.envel: warning in apply(jumpDistRes, MARG = 2, FUN = quantile,
  probs = perc[1], na.rm = TRUE): partial argument match of ‘MARG’ to
  ‘MARGIN’
diagnos.envel: warning in apply(jumpDistRes, MARG = 2, FUN = quantile,
  probs = perc[2], na.rm = TRUE): partial argument match of ‘MARG’ to
  ‘MARGIN’
diagnos.envel: no visible global function definition for ‘quantile’
diagnos.envel: no visible global function definition for ‘qnorm’
diagnos.envel: no visible binding for global variable ‘quantile’
hrplot: no visible global function definition for ‘plot’
hrplot: no visible global function definition for ‘lines’
hrplot: no visible global function definition for ‘abline’
hrplot: no visible global function definition for ‘text’
sim.chain: no visible global function definition for ‘rnorm’
simRandWalk: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline lines plot qnorm quantile rnorm text
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "text")
  importFrom("stats", "qnorm", "quantile", "rnorm")
to your NAMESPACE file.
File ‘RMC/libs/RMC.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
    Objects: ‘RMC.o’, ‘predict.o’
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘ap.o’
File ‘RMC/libs/RMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘grid’ which was already attached by Depends.
  Please remove these calls from your code.
Found the following apparent S3 methods exported but not registered:
  funnelplot.default funnelplot.meta.DSL funnelplot.meta.MH
  funnelplot.meta.summaries plot.meta.DSL plot.meta.MH plot.meta.cum
  plot.meta.summaries print.meta.DSL print.meta.MH print.meta.cum
  print.meta.summaries print.summary.meta.DSL print.summary.meta.MH
  print.summary.meta.cum print.summary.meta.summaries summary.meta.DSL
  summary.meta.MH summary.meta.cum summary.meta.summaries
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
prepare_Rd: meta.MH.Rd:55: Dropping empty section \references
Rd file 'forestplot.Rd':
  \examples lines wider than 100 characters:
                      c("","OR",format(exp(steroid$logOR),digits=2),NA,format(exp(steroid$logMH),digits=2))

Rd file 'meta.cum.Rd':
  \usage lines wider than 90 characters:
     NULL,  subset = NULL, na.action = na.fail, method = c("meta.MH", "meta.DSL"), statistic = "OR")
     cummeta.summaries(effects,stderrs, conf.level = 0.95, names = NULL,weights=NULL, data= NULL, subset = NULL, na.action = get(getOption(" ... [TRUNCATED]
         summary.line = TRUE, summary.conf = FALSE, main="Cumulative meta-analysis", lwd=1, ...)
  \examples lines wider than 100 characters:
     steroid<-cummeta(n.trt,n.ctrl,ev.trt,ev.ctrl,names=name,data=cochrane,statistic="RR",method="meta.MH")

These lines will be truncated in the PDF manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rmetasim.Rcheck/00install.out’ for details.
File ‘rmgarch/libs/rmgarch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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').
File ‘Rmixmod/libs/Rmixmod.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.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 use registered native symbols 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:
  as.list.stack blandAltman.default blandAltman.formula length.stack
  pairwise.chisq.test.default pairwise.chisq.test.table
  pairwise.fisher.test.default pairwise.fisher.test.table plot.rDist
  plotICC.data.frame plotICC.default plotICC.matrix print.stack
  vswitch.character vswitch.default vswitch.factor
See section ‘Registering S3 methods’ 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.
dbGetDistinct,RMongo-character-character-character: no visible global
  function definition for ‘read.table’
dbGetQueryForKeys,RMongo-character-character-character-numeric-numeric:
  no visible global function definition for ‘read.csv’
Undefined global functions or variables:
  read.csv read.table
Consider adding
  importFrom("utils", "read.csv", "read.table")
to your NAMESPACE file.
Non-standard files/directories found at top level:
  ‘COPYING.LGPL’ ‘configure_script.R’
File ‘Rmpi/libs/Rmpi.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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.
.isPath: no visible global function definition for ‘tail’
.isPath: no visible global function definition for ‘head’
navGraph : <anonymous>: no visible global function definition for
  ‘tail’
navGraph : <anonymous>: no visible global function definition for ‘sd’
navGraph: no visible global function definition for ‘colors’
ng_image_array_gray : <anonymous>: no visible global function
  definition for ‘grey’
scagGraph: no visible global function definition for ‘quantile’
closeViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.off’
initializeViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.new’
initializeViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.cur’
plot,NG_graph-ANY: no visible global function definition for ‘box’
plot,NG_graph-ANY: no visible global function definition for ‘axis’
plot,NG_graph-ANY: no visible global function definition for ‘points’
plot,NG_graph-ANY: no visible global function definition for ‘text’
plot,NG_graph-ANY: no visible global function definition for ‘segments’
updateViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.set’
Undefined global functions or variables:
  axis box colors dev.cur dev.new dev.off dev.set grey head points
  quantile sd segments tail text
Consider adding
  importFrom("grDevices", "colors", "dev.cur", "dev.new", "dev.off",
             "dev.set", "grey")
  importFrom("graphics", "axis", "box", "points", "segments", "text")
  importFrom("stats", "quantile", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
File ‘RnavGraph/libs/DisplaystuffTea.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
File ‘RnavGraph/libs/ImgscaleTea.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
File ‘RnavGraph/libs/RnavGraph.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/progress/include/RProgress.h:172:13: warning: variable length arrays are a C99 feature [-Wvla-extension]
  /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/progress/include/RProgress.h:220:16: warning: variable length arrays are a C99 feature [-Wvla-extension]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rncl.Rcheck/00install.out’ for details.
File ‘rncl/libs/rncl.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.collapse: no visible global function definition for ‘head’
RNGinfo: no visible global function definition for ‘setNames’
RNGlibs: no visible global function definition for ‘tail’
RNGseq : <anonymous>: no visible global function definition for
  ‘nextRNGStream’
RNGseq: no visible global function definition for ‘nextRNGStream’
RNGseq_seed: no visible global function definition for ‘runif’
RNGseq_seed: no visible global function definition for ‘nextRNGStream’
checkRNG: no visible global function definition for ‘checkTrue’
nextRNG: no visible global function definition for ‘runif’
.setRNG,numeric: no visible global function definition for ‘runif’
Undefined global functions or variables:
  checkTrue head nextRNGStream runif setNames tail
Consider adding
  importFrom("stats", "runif", "setNames")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
File ‘robCompositions/libs/robCompositions.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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.
QD2coef.f: no visible global function definition for ‘ppoints’
QD2coef.f: no visible global function definition for ‘lsfit’
QD2funC.f: no visible global function definition for ‘ppoints’
QD2funC.f: no visible global function definition for ‘lsfit’
gminit: no visible global function definition for ‘var’
lywalg: no visible global function definition for ‘median’
qloggamma: no visible global function definition for ‘qgamma’
qloggamma: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  lsfit median ppoints qgamma qnorm var
Consider adding
  importFrom("stats", "lsfit", "median", "ppoints", "qgamma", "qnorm",
             "var")
to your NAMESPACE file.
File ‘robeth/libs/robeth.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package in Depends field not imported from: ‘ROptRegTS’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
RobRSVD: no visible global function definition for ‘median’
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
File ‘RobustAFT/libs/RobustAFT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/RobustEM.Rcheck/00install.out’ for details.
cluster_em_outlier: no visible global function definition for ‘qchisq’
jth_dsty: no visible global function definition for ‘mahalanobis’
k_means: no visible global function definition for ‘kmeans’
mix_rcm: no visible global function definition for ‘median’
Undefined global functions or variables:
  kmeans mahalanobis median qchisq
Consider adding
  importFrom("stats", "kmeans", "mahalanobis", "median", "qchisq")
to your NAMESPACE file.
File ‘RobustEM/libs/RobustEM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols 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 ‘robustrank/libs/robustrank.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: control reaches end of non-void function [-Wreturn-type]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/robust.Rcheck/00install.out’ for details.
Found the following apparent S3 methods exported but not registered:
  anova.glmRoblist anova.lmRoblist plot.covClassic plot.covRob
  plot.glmRob
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘robust/libs/robust.so’:
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘rb.o’
File ‘robust/libs/robust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
File ‘rococo/libs/rococo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
predict.rotationForest: no visible global function definition for
  ‘predict’
rotationForest: no visible global function definition for ‘princomp’
Undefined global functions or variables:
  predict princomp
Consider adding
  importFrom("stats", "predict", "princomp")
to your NAMESPACE file.
File ‘rotations/libs/rotations.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘roxygen2/libs/roxygen2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ 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.
'library' or 'require' calls in package code:
  ‘MASS’ ‘RandomFields’ ‘akima’ ‘denstrip’ ‘geoR’ ‘lattice’ ‘maps’
  ‘mgcv’ ‘rgl’ ‘sm’ ‘tkrplot’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard file/directory found at top level:
  ‘Changelog.TMT’
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.
Found the following apparent S3 methods exported but not registered:
  Mab.coords Mab.pdb Mbc.coords Mbc.pdb Mca.coords Mca.pdb Mxy.coords
  Mxy.pdb Myz.coords Myz.pdb Mzx.coords Mzx.pdb R.coords R.pdb
  Rx.coords Rx.pdb Ry.coords Ry.pdb Rz.coords Rz.pdb Ta.coords Ta.pdb
  Tabc.coords Tabc.pdb Tb.coords Tb.pdb Tc.coords Tc.pdb Tx.coords
  Tx.pdb Txyz.coords Txyz.pdb Ty.coords Ty.pdb Tz.coords Tz.pdb
  abc2xyz.atoms abc2xyz.coords abc2xyz.distances abc2xyz.pdb
  addEleLab.atoms addEleLab.pdb addResLab.atoms addResLab.pdb
  angle.coords angle.pdb atoms.default basis.default basis.pdb
  basis<-.default basis<-.pdb bond.coords bond.pdb cell.coords.cryst1
  cell.coords.default cell.coords.pdb cell.density.default
  cell.density.pdb cell.volume.cryst1 cell.volume.pdb centres.atoms
  centres.coords centres.pdb conect.coords conect.default conect.pdb
  coords.atoms coords.data.frame coords.default coords.matrix
  coords.pdb coords<-.atoms coords<-.pdb cryst1.default dihedral.coords
  dihedral.pdb distances.atoms distances.coords distances.default
  distances.pdb inertia.atoms inertia.coords inertia.pdb info3d.atoms
  info3d.pdb masses.default masses.pdb measure.coords measure.default
  measure.pdb mirror.coords mirror.pdb natom.atoms natom.coords
  natom.pdb norm.distances pdb.default reindex.atoms reindex.pdb
  replicate.atoms replicate.coords replicate.pdb toSymbols.character
  toSymbols.integer toSymbols.numeric unsplit.default visualize.atoms
  visualize.character visualize.coords visualize.data.frame
  visualize.matrix visualize.pdb wrap.atoms wrap.coords wrap.pdb
  xyz2abc.atoms xyz2abc.coords xyz2abc.distances xyz2abc.pdb
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
cell.density.default: no visible binding for global variable
  ‘universalConstants’
conect.pdb: no visible binding for global variable ‘elements’
masses.default: no visible binding for global variable ‘elements’
toSymbols.character: no visible binding for global variable ‘elements’
toSymbols.integer: no visible binding for global variable ‘elements’
visualize.coords: no visible binding for global variable ‘elements’
visualize.coords: no visible binding for global variable ‘rgb’
Undefined global functions or variables:
  elements rgb universalConstants
Consider adding
  importFrom("grDevices", "rgb")
to your NAMESPACE file.
File ‘rpf/libs/rpf.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EAPscores
> ### Title: Compute EAP scores
> ### Aliases: EAPscores
> 
> ### ** Examples
> 
> spec <- list()
> spec[1:3] <- rpf.grm(outcomes=3)
Warning in `[<-`(`*tmp*`, 1:3, value = <S4 object of class "rpf.mdim.grm">) :
  implicit list embedding of S4 objects is deprecated
> param <- sapply(spec, rpf.rparam)
> data <- rpf.sample(5, spec, param)
> colnames(param) <- colnames(data)
> grp <- list(spec=spec, param=param, data=data, minItemsPerScore=1L)
> EAPscores(grp)
*** invalid %N$ use detected ***
Aborted
Running ‘testthat.R’ [8s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rpf)
  Loading required package: parallel
  > 
  > test_check("rpf")
  Loading required package: stats4
  Loading required package: lattice
  *** invalid %N$ use detected ***
  Aborted
File ‘rpg/libs/rpg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Files in the 'vignettes' directory newer than all files in 'inst/doc':
  ‘NEWS.html’
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘TNRSVignette.pdf’, ‘rPlantVignette.pdf’
Package has no Sweave vignette sources and no VignetteBuilder field.
File ‘rplexos/libs/rplexos.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: process_folder
> ### Title: Convert PLEXOS files to SQLite databases
> ### Aliases: process_folder process_input process_solution
> 
> ### ** Examples
> 
> # Process the folder with the solution file provided by rplexos
> location_solution <- location_solution_rplexos()
> process_folder(location_solution)
Error: 'folders' must be a vector of existing folders or the wildcard "*"
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rplexos)
  > 
  > test_check("rplexos")
  Error: 'folders' must be a vector of existing folders or the wildcard "*"
  testthat results ================================================================
  OK: 0 SKIPPED: 6 FAILED: 0
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 44-45 (rplexos.Rmd) 
Error: processing vignette ‘rplexos.Rmd’ failed with diagnostics:
'folders' must be a vector of existing folders or the wildcard "*"
Execution halted
Found the following apparent S3 methods exported but not registered:
  plot.blcTree plot.glcTree predict.blcTree predict.glcTree
  print.blcTree print.glcTree
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘rpms/libs/rpms.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard files/directories found at top level:
  ‘config.guess’ ‘config.sub’ ‘install-sh’
postgresqlImportFile: no visible global function definition for
  ‘count.fields’
postgresqlImportFile: 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.
Rd file 'postgresqlBuildTableDefinition.Rd':
  \usage lines wider than 90 characters:
     postgresqlBuildTableDefinition(dbObj, name, obj, field.types = NULL, row.names = TRUE, ...)

Rd file 'postgresqlSupport.Rd':
  \usage lines wider than 90 characters:
        postgresqlNewConnection(drv, user, password, host, dbname, port, tty, options, forceISOdate = TRUE)

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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’
File ‘rqPen/libs/rqPen.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
plot.rmas: no visible global function definition for ‘rainbow’
plot.tmatrix: no visible global function definition for ‘rainbow’
plot.tmatrix: no visible global function definition for ‘dev.new’
Undefined global functions or variables:
  dev.new rainbow
Consider adding
  importFrom("grDevices", "dev.new", "rainbow")
to your NAMESPACE file.
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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols 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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘RSAgeo/libs/RSAgeo.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Objects: ‘RSAc.o’, ‘lib.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘RSAc.o’
File ‘RSAgeo/libs/RSAgeo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
checkArgs: no visible global function definition for ‘count.fields’
checkArgs: no visible global function definition for ‘read.table’
estimateHap: no visible global function definition for ‘read.table’
estimateHap: no visible global function definition for ‘write.table’
plot.treeoutput: no visible global function definition for ‘par’
plot.treeoutput: no visible global function definition for ‘layout’
plot.treeoutput: no visible global function definition for ‘barplot’
plot.treeoutput: no visible global function definition for ‘plot’
plot.treeoutput: no visible global function definition for ‘lines’
plot.treeoutput: no visible global function definition for ‘lowess’
readArgs: no visible global function definition for ‘read.table’
readOutput: no visible global function definition for ‘read.table’
readTrees: no visible global function definition for ‘count.fields’
restartRun: no visible global function definition for ‘count.fields’
setWeights: no visible global function definition for ‘write.table’
writeTreeoutput: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  barplot count.fields layout lines lowess par plot read.table
  write.table
Consider adding
  importFrom("graphics", "barplot", "layout", "lines", "par", "plot")
  importFrom("stats", "lowess")
  importFrom("utils", "count.fields", "read.table", "write.table")
to your NAMESPACE file.
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.
stripslash: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
f_cal_chk_f: no visible global function definition for ‘qf’
f_main: no visible binding for global variable ‘median’
f_main: no visible binding for global variable ‘sd’
f_main: no visible global function definition for ‘write.table’
f_main_p: no visible global function definition for ‘write.table’
f_main_p: no visible global function definition for ‘runif’
get_random_filename: no visible global function definition for ‘runif’
rSCA.correlation: no visible global function definition for
  ‘read.table’
rSCA.correlation: no visible global function definition for ‘read.csv’
rSCA.correlation: no visible global function definition for ‘cor’
rSCA.inference: no visible global function definition for ‘read.table’
rSCA.inference: no visible global function definition for ‘read.csv’
rSCA.inference: no visible global function definition for ‘na.omit’
rSCA.missing: no visible global function definition for ‘read.table’
rSCA.missing: no visible global function definition for ‘read.csv’
rSCA.modeling: no visible global function definition for ‘read.table’
rSCA.modeling: no visible global function definition for ‘read.csv’
rSCA.modeling: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  cor median na.omit qf read.csv read.table runif sd write.table
Consider adding
  importFrom("stats", "cor", "median", "na.omit", "qf", "runif", "sd")
  importFrom("utils", "read.csv", "read.table", "write.table")
to your NAMESPACE file.
File ‘rscimark/libs/rscimark.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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 use registered native symbols 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:
  as.data.frame.rcomdata as.matrix.rcomdata
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘rscproxy/libs/rscproxy.so’:
  Found non-API calls to R: ‘R_DefParams’, ‘R_ReplDLLinit’,
    ‘R_SetParams’, ‘R_set_command_line_arguments’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’, ‘ptr_R_Busy’, ‘ptr_R_ReadConsole’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’
File ‘rscproxy/libs/rscproxy.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 use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 the system RNG.
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 use registered native symbols 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 the system RNG.
It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls in package code:
  ‘MASS’ ‘codetools’ ‘lattice’ ‘network’ ‘parallel’ ‘tcltk’ ‘xtable’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: ‘utils:::edit.data.frame’
  See the note in ?`:::` about the use of this operator.
Found the following apparent S3 methods exported but not registered:
  print.xtable.sienaFit
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘RSiena/libs/RSiena.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
filterSD: no visible binding for global variable ‘sd’
filterSD: no visible global function definition for ‘quantile’
fit_lasso: no visible global function definition for ‘coef’
fit_prlasso: no visible global function definition for ‘coef’
rsig: no visible binding for global variable ‘mclapply’
rsig.all: no visible binding for global variable ‘mclapply’
rsig.all : <anonymous>: no visible global function definition for
  ‘flush.console’
rsig.all : <anonymous>: no visible global function definition for
  ‘predict’
Undefined global functions or variables:
  coef flush.console mclapply predict quantile sd
Consider adding
  importFrom("stats", "coef", "predict", "quantile", "sd")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
composeMosaicFromImageRandom: no visible global function definition for
  ‘runif’
composeMosaicFromImageRegular: no visible global function definition
  for ‘runif’
computeStatisticalQuantitiesTile: no visible global function definition
  for ‘median’
createLibraryIndexDataFrame: no visible global function definition for
  ‘write.table’
getCloseMatch: no visible global function definition for ‘runif’
Undefined global functions or variables:
  median runif write.table
Consider adding
  importFrom("stats", "median", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
File ‘RSKC/libs/RSKC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Quitting from lines 282-283 (RSNPset.Rnw) 
Error: processing vignette ‘RSNPset.Rnw’ failed with diagnostics:
ERROR: The estimated pi0 <= 0. Check that you have valid p-values or use a different range of lambda.
Execution halted
File ‘Rsomoclu/libs/Rsomoclu.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
exoplantname: no visible global function definition for ‘URLencode’
localgroupname: no visible global function definition for ‘URLencode’
starname: no visible global function definition for ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
rbing.O2: no visible global function definition for ‘runif’
rbing.O2: no visible global function definition for ‘rbeta’
rbing.O2: no visible global function definition for ‘rbinom’
rbing.Op: no visible global function definition for ‘rnorm’
rbing.Op: no visible global function definition for ‘rbinom’
rbing.Op: no visible global function definition for ‘runif’
rbmf.O2: no visible global function definition for ‘runif’
rmf.matrix: no visible global function definition for ‘runif’
rmf.vector: no visible global function definition for ‘rnorm’
rmf.vector: no visible global function definition for ‘rbinom’
rustiefel: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rbeta rbinom rnorm runif
Consider adding
  importFrom("stats", "rbeta", "rbinom", "rnorm", "runif")
to your NAMESPACE file.
File ‘rstiefel/libs/rstiefel.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 ‘rstpm2/libs/rstpm2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard files/directories found at top level:
  ‘docs’ ‘usrfcns’
Rd file 'cvodes.Rd':
  \usage lines wider than 90 characters:
             cvodes(y, times, package, rhs, fndata = NULL, jacfunc = NULL, rootfunc = NULL, numroots = 0, rtol = 1e-6, atol = 1e-6, maxnumst ... [TRUNCATED]

Rd file 'ida.Rd':
  \usage lines wider than 90 characters:
             ida(y, yp, times, package, resfunc, jacfunc = NULL, rootfunc = NULL, fndata = NULL,
                     numroots = 0, rtol = 1e-6, atol = 1e-6, maxnumsteps = 500, maxstep = 0, verbose = FALSE, 

These lines will be truncated in the PDF manual.
Non-portable flags in variable 'PKG_CFLAGS':
  -w
File ‘Rsundials/libs/Rsundials.so’:
  Found ‘printf’, possibly from ‘printf’ (C)
    Objects: ‘nvector_serial.o’, ‘sundials_band.o’,
      ‘sundials_smalldense.o’
  Found ‘putchar’, possibly from ‘putchar’ (C)
    Objects: ‘nvector_serial.o’, ‘sundials_band.o’,
      ‘sundials_smalldense.o’
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Objects: ‘cvodes.o’, ‘sundials_cvodes.o’, ‘sundials_ida.o’
File ‘Rsundials/libs/Rsundials.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 ‘rtdists/libs/rtdists.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 ‘rtfbs/libs/rtfbs.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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:
  addHeader.RTF addNewLine.RTF addPageBreak.RTF addParagraph.RTF
  addPlot.RTF addPng.RTF addSessionInfo.RTF addTOC.RTF addTable.RTF
  addText.RTF addTrellisObject.RTF decreaseIndent.RTF done.RTF
  endParagraph.RTF increaseIndent.RTF setFontSize.RTF
  startParagraph.RTF view.RTF
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
.forest.plot: no visible global function definition for ‘par’
.forest.plot: no visible global function definition for ‘plot’
.forest.plot: no visible global function definition for ‘abline’
.forest.plot: no visible global function definition for ‘arrows’
.forest.plot: no visible global function definition for ‘points’
.forest.plot.scale: no visible global function definition for ‘par’
.forest.plot.scale: no visible global function definition for ‘plot’
.forest.plot.scale: no visible global function definition for ‘axTicks’
.forest.plot.scale : <anonymous>: no visible global function definition
  for ‘lines’
.forest.plot.scale: no visible global function definition for ‘lines’
.forest.plot.scale: no visible global function definition for ‘text’
.rtf.plot: no visible global function definition for ‘png’
.rtf.plot: no visible global function definition for ‘dev.off’
.rtf.trellis.object: no visible global function definition for ‘png’
.rtf.trellis.object: no visible global function definition for
  ‘dev.off’
addSessionInfo.RTF: no visible global function definition for
  ‘sessionInfo’
Undefined global functions or variables:
  abline arrows axTicks dev.off lines par plot png points sessionInfo
  text
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "abline", "arrows", "axTicks", "lines", "par",
             "plot", "points", "text")
  importFrom("utils", "sessionInfo")
to your NAMESPACE file.
File ‘rtiff/libs/rtiff.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘Runuran’ ‘cairoDevice’ ‘gWidgets’ ‘gWidgetsRGtk2’ ‘rvgtest’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘utils:::.getHelpFile’
  See the note in ?`:::` about the use of this operator.
File ‘Runuran/libs/Runuran.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols 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.
File ‘RVowpalWabbit/libs/RVowpalWabbit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package in Depends field not imported from: ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  ‘base:::ifelse’ ‘base:::mapply’ ‘graphics:::abline’ ‘stats:::cor’
  ‘stats:::cov’ ‘stats:::rbeta’ ‘stats:::rbinom’ ‘stats:::rcauchy’
  ‘stats:::rchisq’ ‘stats:::rexp’ ‘stats:::rgamma’ ‘stats:::rhyper’
  ‘stats:::rmultinom’ ‘stats:::rpois’ ‘stats:::rt’ ‘stats:::runif’
  See the note in ?`:::` about the use of this operator.
Found the following apparent S3 methods exported but not registered:
  !.rv Math.rv Ops.rv Summary.rv as.matrix.rv is.matrix.rv
  is.numeric.rvfactor mlplot.default print.rv print.rvfactor
  quantile.rv rep.rv unlist.rv
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: GNU Extension: Different type kinds at (1)
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/rvsel.Rcheck/00install.out’ for details.
File ‘rvsel/libs/rvsel.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: set_location
> ### Title: Specifies location of request
> ### Aliases: set_location
> 
> ### ** Examples
> 
> set_location(zip_code = "90210")
[1] "90210"
> set_location(territory = "Hawaii", city = "Honolulu")
Error in `[.data.frame`(countrycode::countrycode_data, , c("country.name",  : 
  undefined columns selected
Calls: set_location ... is_valid_territory -> list_countries -> [ -> [.data.frame
Execution halted
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 use registered native symbols 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.
File ‘Ryacas/libs/Ryacas.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘vcd’ 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’ ‘ggplot2’ ‘grid’ ‘psych’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘foreign:::adQuote’
  See the note in ?`:::` about the use of this operator.
Found the following apparent S3 methods exported but not registered:
  summary.CrossTable
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
calc.hist.breaks: no visible global function definition for
  ‘nclass.Sturges’
calc.hist.breaks: no visible global function definition for ‘nclass.FD’
calc.hist.breaks: no visible global function definition for
  ‘nclass.scott’
check.class: no visible global function definition for ‘as.formula’
gtkColorSelectionForPlotGetColor: no visible global function definition
  for ‘rgb’
gtkColorSelectionWidgetNew: no visible global function definition for
  ‘colors’
gtkFileChooserDialogFilteredActivate: no visible binding for global
  variable ‘theme_grey’
localize: no visible global function definition for ‘localeToCharset’
summary.CrossTable : twoDimTable: no visible global function definition
  for ‘addmargins’
summary.CrossTable: no visible global function definition for
  ‘assocstats’
write.spss: no visible global function definition for ‘write.table’
write.stata: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  addmargins as.formula assocstats colors localeToCharset nclass.FD
  nclass.Sturges nclass.scott rgb theme_grey write.table
Consider adding
  importFrom("grDevices", "colors", "nclass.FD", "nclass.Sturges",
             "nclass.scott", "rgb")
  importFrom("stats", "addmargins", "as.formula")
  importFrom("utils", "localeToCharset", "write.table")
to your NAMESPACE file.
File ‘s2/libs/s2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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
File ‘sads/libs/sads.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
Found the following apparent S3 methods exported but not registered:
  plot.safidesign plot.safimodel
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.safidesign: no visible global function definition for ‘par’
plot.safidesign: no visible global function definition for ‘matplot’
plot.safidesign: no visible global function definition for ‘axis’
plot.safimodel : plot.coef: no visible global function definition for
  ‘colorRampPalette’
plot.safimodel : plot.coef: no visible global function definition for
  ‘barplot’
plot.safimodel : plot.coef: no visible global function definition for
  ‘axis’
plot.safimodel : plot.coef: no visible global function definition for
  ‘abline’
plot.safimodel : plot.coef: no visible global function definition for
  ‘box’
plot.safimodel: no visible global function definition for ‘par’
safiModel: no visible global function definition for ‘lm’
Undefined global functions or variables:
  abline axis barplot box colorRampPalette lm matplot par
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "abline", "axis", "barplot", "box", "matplot",
             "par")
  importFrom("stats", "lm")
to your NAMESPACE file.
File ‘SALES/libs/SALES.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols 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:
  ‘impute’ ‘matrixStats’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘impute’ ‘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:
  plot.SAMoutput print.SAMoutput
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'samr-internal':
  ‘plot.SAMoutput’ ‘print.SAMoutput’

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

It is good practice to use registered native symbols 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.
.run_chunk: no visible global function definition for ‘capture.output’
install_sand_packages: no visible global function definition for
  ‘packageDescription’
set_chapter: no visible global function definition for ‘sessionInfo’
Undefined global functions or variables:
  capture.output packageDescription sessionInfo
Consider adding
  importFrom("utils", "capture.output", "packageDescription",
             "sessionInfo")
to your NAMESPACE file.
File ‘sanitizers/libs/sanitizers.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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 use registered native symbols 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 use registered native symbols 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 ‘satellite/libs/satellite.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols 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 use registered native symbols 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.
Found the following apparent S3 methods exported but not registered:
  plot.psgc print.sum.psgc summary.psgc
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.psgc: no visible global function definition for ‘par’
plot.psgc: no visible global function definition for ‘barplot’
plot.psgc: no visible global function definition for ‘hist’
plotci.sA: no visible global function definition for ‘par’
plotci.sA: no visible global function definition for ‘plot’
plotci.sA: no visible global function definition for ‘points’
plotci.sA: no visible global function definition for ‘segments’
plotci.sA: no visible global function definition for ‘abline’
plotci.sA: no visible global function definition for ‘axis’
qM.sM: no visible binding for global variable ‘quantile’
rwish: no visible global function definition for ‘rnorm’
sbgcop.mcmc: no visible global function definition for ‘qnorm’
sbgcop.mcmc: no visible global function definition for ‘rnorm’
sbgcop.mcmc: no visible global function definition for ‘cov’
sbgcop.mcmc: no visible global function definition for ‘runif’
sbgcop.mcmc: no visible global function definition for ‘pnorm’
sbgcop.mcmc: no visible global function definition for ‘quantile’
summary.psgc: no visible global function definition for ‘acf’
Undefined global functions or variables:
  abline acf axis barplot cov hist par plot pnorm points qnorm quantile
  rnorm runif segments
Consider adding
  importFrom("graphics", "abline", "axis", "barplot", "hist", "par",
             "plot", "points", "segments")
  importFrom("stats", "acf", "cov", "pnorm", "qnorm", "quantile",
             "rnorm", "runif")
to your NAMESPACE file.
File ‘sBIC/libs/sBIC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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 use registered native symbols 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 use registered native symbols 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 use registered native symbols 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 use registered native symbols 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’
Found the following apparent S3 methods exported but not registered:
  scagnostics.data.frame scagnostics.default scagnostics.list
  scagnostics.matrix
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
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.
File ‘scales/libs/scales.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
importCol: no visible global function definition for ‘packageVersion’
importMCMC : getL: no visible global function definition for
  ‘read.table’
importMCMC : getP: no visible global function definition for
  ‘read.table’
importMCMC : getB: no visible global function definition for
  ‘read.table’
importMCMC : getR: no visible global function definition for
  ‘read.table’
importProj : getPolicies: no visible global function definition for
  ‘read.table’
importProj : getYears: no visible global function definition for
  ‘read.table’
importProj : getB: no visible global function definition for
  ‘read.table’
importProj : getY: no visible global function definition for
  ‘read.table’
iterate : summaryN: no visible binding for global variable ‘median’
iterate : summarySigmaI: no visible binding for global variable
  ‘median’
plotLA: no visible global function definition for ‘aggregate’
plotN: no visible global function definition for ‘aggregate’
Undefined global functions or variables:
  aggregate median packageVersion read.table
Consider adding
  importFrom("stats", "aggregate", "median")
  importFrom("utils", "packageVersion", "read.table")
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 use registered native symbols 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 use registered native symbols 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 use registered native symbols 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’.
futuresplot: no visible global function definition for ‘rainbow’
plot.schwartz2f.fit: no visible global function definition for
  ‘colorRampPalette’
plot.schwartz2f.fit: no visible global function definition for
  ‘rainbow’
plot,schwartz2f.fit-missing: no visible global function definition for
  ‘colorRampPalette’
plot,schwartz2f.fit-missing: no visible global function definition for
  ‘rainbow’
Undefined global functions or variables:
  colorRampPalette rainbow
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
to your NAMESPACE file.
c,scidbdf: warning in build_dim_schema(x, newname = j): partial
  argument match of ‘newname’ to ‘newnames’
.format: no visible global function definition for ‘capture.output’
.scidbstr: no visible global function definition for ‘capture.output’
glm.fit_scidb: no visible global function definition for ‘gaussian’
glm.fit_scidb: no visible global function definition for ‘pnorm’
glm_scidb: no visible global function definition for ‘gaussian’
glm_scidb: no visible global function definition for ‘as.formula’
iqiter : nextEl: no visible global function definition for ‘read.table’
iquery: no visible global function definition for ‘read.table’
model_scidb: no visible global function definition for ‘as.formula’
model_scidb: no visible global function definition for ‘terms’
model_scidb: no visible global function definition for ‘drop.terms’
predict.glm_scidb: no visible global function definition for ‘coef’
print.glm_scidb: no visible global function definition for ‘coef’
summary.glm_scidb: no visible global function definition for ‘coef’
glm.fit,scidb-ANY-MNSN: no visible global function definition for
  ‘gaussian’
glm.fit,scidb-ANY-MNSN: no visible global function definition for
  ‘pnorm’
glm,ANY-ANY-scidbdf: no visible global function definition for
  ‘gaussian’
glm,ANY-ANY-scidbdf: no visible global function definition for
  ‘as.formula’
image,scidb: no visible global function definition for ‘axis’
Undefined global functions or variables:
  as.formula axis capture.output coef drop.terms gaussian pnorm
  read.table terms
Consider adding
  importFrom("graphics", "axis")
  importFrom("stats", "as.formula", "coef", "drop.terms", "gaussian",
             "pnorm", "terms")
  importFrom("utils", "capture.output", "read.table")
to your NAMESPACE file.
File ‘scidb/libs/scidb.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
bargraph.CI: no visible global function definition for ‘barplot’
bargraph.CI: no visible global function definition for ‘arrows’
bargraph.CI: no visible global function definition for ‘gray.colors’
lineplot.CI : int.plot: no visible global function definition for ‘par’
lineplot.CI : int.plot: no visible global function definition for
  ‘matplot’
lineplot.CI : int.plot : axisInt: no visible global function definition
  for ‘axis’
lineplot.CI : int.plot: no visible global function definition for
  ‘text’
lineplot.CI: no visible global function definition for ‘plot’
lineplot.CI: no visible global function definition for ‘axis’
lineplot.CI: no visible global function definition for ‘arrows’
lineplot.CI: no visible global function definition for ‘points’
Undefined global functions or variables:
  arrows axis barplot gray.colors matplot par plot points text
Consider adding
  importFrom("grDevices", "gray.colors")
  importFrom("graphics", "arrows", "axis", "barplot", "matplot", "par",
             "plot", "points", "text")
to your NAMESPACE file.
ES: no visible global function definition for ‘read.table’
ES: no visible global function definition for ‘sd’
ES: no visible global function definition for ‘var’
ES: no visible global function definition for ‘median’
combine: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  median read.table sd var
Consider adding
  importFrom("stats", "median", "sd", "var")
  importFrom("utils", "read.table")
to your NAMESPACE file.
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 use registered native symbols 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:
  calcscore.default calcscore.formula
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
bdecomp : <anonymous>: no visible global function definition for ‘var’
betafam: no visible global function definition for ‘integrate’
calcscore.formula: no visible global function definition for
  ‘model.response’
plotscore: no visible binding for global variable ‘plot’
plotscore: no visible global function definition for ‘lines’
Undefined global functions or variables:
  integrate lines model.response plot var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "integrate", "model.response", "var")
to your NAMESPACE file.
File ‘scoringRules/libs/scoringRules.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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:
  SK.aov SK.aovlist SK.default SK.nest SK.nest.aov SK.nest.aov
  SK.nest.aovlist SK.nest.aovlist SK.nest.default SK.nest.default
  plot.SK summary.SK summary.SK.nest
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.SK: no visible global function definition for ‘plot’
plot.SK: no visible global function definition for ‘segments’
plot.SK: no visible global function definition for ‘axis’
plot.SK: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  axis mtext plot segments
Consider adding
  importFrom("graphics", "axis", "mtext", "plot", "segments")
to your NAMESPACE file.
File ‘scout/libs/scout.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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:
  WW.default print.WW
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Newsboy: no visible global function definition for ‘qnorm’
Newsboy: no visible global function definition for ‘dnorm’
Newsboy: no visible global function definition for ‘pnorm’
SCperf: no visible global function definition for ‘ARMAtoMA’
SCperf: no visible global function definition for ‘qnorm’
SSL: no visible global function definition for ‘qnorm’
SSL: no visible global function definition for ‘ARMAtoMA’
Undefined global functions or variables:
  ARMAtoMA dnorm pnorm qnorm
Consider adding
  importFrom("stats", "ARMAtoMA", "dnorm", "pnorm", "qnorm")
to your NAMESPACE file.
Rd file 'WW.Rd':
  \examples lines wider than 100 characters:
     #  couple of months, when the winter season will be under way. However, this would necessitate holding

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
File ‘sdat/libs/sdat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 use registered native symbols 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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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 use registered native symbols 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 use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 use registered native symbols 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.
Found the following apparent S3 methods exported but not registered:
  image.seas.sum plot.interarrival plot.seas.norm plot.seas.sum
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘seas/libs/seas.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘car’ ‘sgeostat’ ‘spatstat’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'krige.functions.Rd':
  \usage lines wider than 90 characters:
     plotkriged(dataset, kriged, outpdf="dataset-kriged.pdf", border.sw=FALSE, border.poly="none")

Rd file 'rain.Rd':
  \examples lines wider than 100 characters:
     P <- matrix(c(0.5,0.4,0.0,0.0, 0.0,0.0,0.9,0.5, 0.5,0.6,0.0,0.0, 0.0,0.0,0.1,0.5), ncol=4, byrow=TRUE)
     Ha <- matrix(c(0.025,0.0154,0.0,0.0, 0.0,0.0,0.04,0.02, 0.025,0.0154,0.0,0.0, 0.0,0.0,0.04,0.02), ncol=4, byrow=TRUE)

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Warning: Integer division truncated to constant ‘67108861’ at (1) [-Winteger-division]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/seem.Rcheck/00install.out’ for details.
Rd file 'sim.out.Rd':
  \examples lines wider than 100 characters:
     ## Not run:  The end user would not typically have to call the function. Thus, no examples are provided.

Rd file 'weather.Rd':
  \examples lines wider than 100 characters:
     mtext(side=3,line=-1,paste("Rainy after rainy Pr=0.80","Prop rainy=",round(rainy1$wet.days/ndays,2)),cex=0.8)

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Segmentor3IsBack/libs/Segmentor3IsBack.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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 use registered native symbols 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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘INSTRUCTION.Rmd’
Package has no Sweave vignette sources and no VignetteBuilder field.
File ‘selectiveInference/libs/selectiveInference.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: S3 methods ‘[.xml_missing’, ‘[.xml_nodeset’, ‘[[.xml_missing’, ‘xml_attr<-.xml_missing’, ‘xml_attr<-.xml_node’, ‘xml_attr<-.xml_nodeset’, ‘xml_attrs<-.xml_missing’, ‘xml_attrs<-.xml_node’, ‘xml_attrs<-.xml_nodeset’, ‘xml_name<-.xml_missing’, ‘xml_name<-.xml_node’, ‘xml_name<-.xml_nodeset’, ‘xml_text<-.xml_missing’, ‘xml_text<-.xml_node’, ‘xml_text<-.xml_nodeset’, ‘as.character.xml_document’, ‘as.character.xml_missing’, ‘as.character.xml_node’, ‘as.character.xml_nodeset’, ‘as_list.xml_missing’, ‘as_list.xml_node’, ‘as_list.xml_nodeset’, ‘as_xml_document.character’, ‘as_xml_document.connection’, ‘as_xml_document.list’, ‘as_xml_document.raw’, ‘as_xml_document.response’, ‘as_xml_document.xml_document’, ‘as_xml_document.xml_node’, ‘as_xml_document.xml_nodeset’, ‘format.xml_node’, ‘is.na.xml_missing’, ‘is.na.xml_node’, ‘is.na.xml_nodeset’, ‘nodeset_apply.x [... truncated]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/selectr.Rcheck/00install.out’ for details.
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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
File ‘SemiCompRisks/libs/SemiCompRisks.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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:
  fitted.spm lines.spm plot.spm predict.spm print.spm residuals.spm
  summary.spm
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Packages in Depends field not imported from:
  ‘datautils’ ‘irlba’
  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:
  add.linkinfo check.linkinfo del.linkinfo length.linkinfo
  transform.linkinfo
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
computeKernel: no visible binding for global variable ‘sd’
computeKernel: no visible global function definition for ‘dist’
computeKernel: no visible global function definition for ‘quantile’
computeProjectionFromKernel : <anonymous>: no visible global function
  definition for ‘irlba’
distortions: no visible binding for global variable ‘sd’
distortions: no visible global function definition for ‘dist’
Undefined global functions or variables:
  dist irlba quantile sd
Consider adding
  importFrom("stats", "dist", "quantile", "sd")
to your NAMESPACE file.
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' call to ‘MplusAutomation’ 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:
  semPlotModel.S4
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
'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 ‘sem/libs/sem.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
efficiencies.semsfa: no visible global function definition for ‘dnorm’
efficiencies.semsfa: no visible global function definition for ‘pnorm’
fan: no visible global function definition for ‘pnorm’
plot.semsfa: no visible global function definition for ‘hist’
plot.semsfa: no visible global function definition for ‘plot’
plot.semsfa: no visible global function definition for ‘density’
semsfa: no visible global function definition for ‘residuals’
semsfa: no visible global function definition for ‘loess’
semsfa: no visible global function definition for ‘optimize’
semsfa: no visible global function definition for ‘pnorm’
semsfa: no visible binding for global variable ‘sd’
summary.semsfa: no visible global function definition for ‘pt’
summary.semsfa: no visible global function definition for
  ‘printCoefmat’
Undefined global functions or variables:
  density dnorm hist loess optimize plot pnorm printCoefmat pt
  residuals sd
Consider adding
  importFrom("graphics", "hist", "plot")
  importFrom("stats", "density", "dnorm", "loess", "optimize", "pnorm",
             "printCoefmat", "pt", "residuals", "sd")
to your NAMESPACE file.
File ‘semver/libs/semver.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.IdMap plot.WordCountAna plot.fahst plot.fasnt plot.fast
  print.fahst print.fasnt print.fast
See section ‘Registering S3 methods’ 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 use registered native symbols 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.
Unexported objects imported by ':::' calls:
  ‘igraph:::.igraph.shapes’ ‘igraph:::i.get.arrow.mode’
  ‘igraph:::i.parse.plot.params’ ‘igraph:::igraph.Arrows’
  ‘igraph:::igraph.check.shapes’ ‘igraph:::igraph.polygon’
  See the note in ?`:::` about the use of this operator.
File ‘seqHMM/libs/seqHMM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sequoia
> ### Title: Pedigree Reconstruction
> ### Aliases: sequoia
> 
> ### ** Examples
> 
> data(SimGeno_example, LH_HSg5, package="sequoia")
> 
> SeqOUT <- sequoia(GenoM = SimGeno_example,
+                   LifeHistData = LH_HSg5, MaxSibIter = 0)
At line 127 of file Sequoia.f90
Fortran runtime error: Actual string length is shorter than the declared one for dummy argument 'genofilefr' (-886608328/255)
File ‘seriation/libs/seriation.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following calls to attach():
File ‘sfsmisc/R/sourceAttach.R’:
  attach(ENV, pos = pos, name = name, warn.conflicts = warn.conflicts)
See section ‘Good practice’ in ‘?attach’.
File ‘SGCS/libs/SGCS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols 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.
Malformed Description field: should contain one or more complete sentences.
Deprecated license: BSD
Packages in Depends field not imported from:
  ‘Matrix’ ‘fields’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
distLaplacian: no visible global function definition for ‘sparseMatrix’
gmdDeflation: no visible global function definition for ‘rnorm’
laplacian: no visible global function definition for ‘sparseMatrix’
Undefined global functions or variables:
  rnorm sparseMatrix
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
File ‘sGPCA/libs/sGPCA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
footpoint.nodes: no visible global function definition for
  ‘coordinates’
nt.connect: no visible global function definition for ‘bbox’
nt.connect: no visible global function definition for ‘plot.new’
nt.connect: no visible global function definition for ‘plot.window’
nt.connect: no visible global function definition for ‘title’
nt.connect: no visible global function definition for ‘rainbow’
nt.connect: no visible global function definition for ‘slot’
nt.connect: no visible global function definition for
  ‘as.SpatialLines.SLDF’
nt.connect: no visible global function definition for ‘lines’
nt.connect: no visible global function definition for
  ‘SpatialLinesDataFrame’
points2network: no visible global function definition for ‘is’
ptsinnt.view: no visible global function definition for ‘bbox’
ptsinnt.view: no visible global function definition for ‘plot’
ptsinnt.view: no visible global function definition for ‘points’
ptsinnt.view: no visible global function definition for ‘lines’
ptsinnt.view: no visible global function definition for ‘legend’
readshpnw: no visible global function definition for ‘is’
readshpnw: no visible global function definition for ‘coordinates’
Undefined global functions or variables:
  SpatialLinesDataFrame as.SpatialLines.SLDF bbox coordinates is legend
  lines plot plot.new plot.window points rainbow slot title
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend", "lines", "plot", "plot.new",
             "plot.window", "points", "title")
  importFrom("methods", "is", "slot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘shp2graph/libs/shp2graph.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 use registered native symbols 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').
Found the following apparent S3 methods exported but not registered:
  c.std plot.std summary.std
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.std: no visible global function definition for ‘rainbow’
plot.std: no visible global function definition for ‘legend’
read.std: no visible global function definition for ‘read.table’
std: no visible global function definition for ‘na.exclude’
Undefined global functions or variables:
  legend na.exclude rainbow read.table
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend")
  importFrom("stats", "na.exclude")
  importFrom("utils", "read.table")
to your NAMESPACE file.
.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.
Found the following apparent S3 methods exported but not registered:
  as.data.frame.intersect as.data.frame.receiver
  as.data.frame.transmitter plot.intersect plot.receiver
  plot.transmitter print.intersect print.receiver print.transmitter
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.intersect: no visible global function definition for ‘points’
plot.intersect: no visible global function definition for ‘plot’
plot.receiver: no visible global function definition for ‘points’
plot.receiver: no visible global function definition for ‘plot’
plot.receiver: no visible global function definition for ‘segments’
plot.transmitter: no visible global function definition for ‘points’
plot.transmitter: no visible global function definition for ‘plot’
plot.transmitter: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines plot points segments
Consider adding
  importFrom("graphics", "lines", "plot", "points", "segments")
to your NAMESPACE file.
File ‘signalHsmm/libs/signalHsmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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 use registered native symbols 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.
File ‘SigTree/libs/SigTree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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.
SCIrp: no visible binding for global variable ‘median’
WYht: no visible global function definition for ‘lm’
WYht: no visible global function definition for ‘residuals’
WYht: no visible global function definition for ‘coefficients’
WYht: no visible global function definition for ‘quantile’
mcpHill : alignfunc: no visible global function definition for ‘lm’
mcpHill : alignfunc: no visible global function definition for
  ‘predict’
mcpHill : funcA: no visible global function definition for ‘lm’
mcpHill : funcA: no visible global function definition for ‘residuals’
mcpHill : tstatshort: no visible global function definition for ‘lm’
mcpHill : tstatshort: no visible global function definition for
  ‘coefficients’
mcpHill : tstatshort: no visible global function definition for
  ‘residuals’
tsht: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  coefficients lm median predict quantile residuals
Consider adding
  importFrom("stats", "coefficients", "lm", "median", "predict",
             "quantile", "residuals")
to your NAMESPACE file.
mainalg,mmctestres: no visible global function definition for ‘hist’
Undefined global functions or variables:
  hist
Consider adding
  importFrom("graphics", "hist")
to your NAMESPACE file.
File ‘simctest/libs/simctest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following assignments to the global environment:
File ‘simecol/R/sEdit.R’:
  assign(subx, x, envir = .GlobalEnv)
  assign(subx, x, envir = .GlobalEnv)
  assign(subx, x, envir = .GlobalEnv)
File ‘simecol/libs/simecol.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.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.
Non-standard file/directory found at top level:
  ‘simex-Ex.R’
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘construct.s’ ‘extract.covmat’
Rd file 'simex-package.Rd':
  \examples lines wider than 100 characters:
     (mod_simex1 <- simex(mod_naiv1, SIMEXvariable = "x_het1", measurement.error = sd_me_het1, asymptotic = FALSE))

Rd file 'simex.Rd':
  \examples lines wider than 100 characters:
     (mod_simex1 <- simex(mod_naiv1, SIMEXvariable = "x_het1", measurement.error = sd_me_het1, asymptotic = FALSE))

These lines will be truncated in the PDF manual.
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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
File ‘simone/libs/simone.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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.
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘usingSimpleRCache.Rmd’
Package has no Sweave vignette sources and no VignetteBuilder field.
File ‘simplexreg/libs/simplexreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 ‘simputation/libs/simputation.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
File ‘SiMRiv/libs/SiMRiv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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
evalGrids: no visible global function definition for ‘sessionInfo’
meanAndNormCI: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd sessionInfo
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "sessionInfo")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  plot.CorrAn plot.SimAn summary.CorrAn summary.SimAn
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.CorrAn : SAPplot: no visible global function definition for ‘plot’
plot.CorrAn : SAPtitle: no visible global function definition for
  ‘title’
plot.CorrAn : SAPtitle: no visible global function definition for
  ‘mtext’
plot.CorrAn : SAPplotpuntos: no visible global function definition for
  ‘points’
plot.CorrAn : SAPplotpuntos: no visible global function definition for
  ‘text’
plot.CorrAn: no visible global function definition for ‘dev.new’
plot.SimAn : SAPplot: no visible global function definition for ‘plot’
plot.SimAn : SAPtitle: no visible global function definition for
  ‘title’
plot.SimAn : SAPtitle: no visible global function definition for
  ‘mtext’
plot.SimAn : SAPplotpuntos: no visible global function definition for
  ‘points’
plot.SimAn : SAPplotpuntos: no visible global function definition for
  ‘text’
plot.SimAn: no visible global function definition for ‘dev.new’
plot.SimAn: no visible global function definition for ‘points’
plot.SimAn: no visible global function definition for ‘text’
plot.SimAn: no visible global function definition for ‘par’
plot.SimAn: no visible global function definition for ‘plot’
plot.SimAn: no visible global function definition for ‘title’
plot.SimAn: no visible global function definition for ‘axis’
plot.SimAn: no visible global function definition for ‘arrows’
Undefined global functions or variables:
  arrows axis dev.new mtext par plot points text title
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "arrows", "axis", "mtext", "par", "plot",
             "points", "text", "title")
to your NAMESPACE file.
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.
File ‘sirt/libs/sirt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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:
  logLik.PiecewiseLinear logLik.bent_cable
  plot.LocallyWeightedPolynomial plot.PiecewiseLinear plot.SiZer
  predict.PiecewiseLinear predict.bent_cable print.PiecewiseLinear
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘SKAT/libs/SKAT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ 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 use registered native symbols and to disable
symbol search.

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

See section ‘The DESCRIPTION file’ 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.sla print.sla print.summary.sla sla.default summary.sla
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.sla: no visible global function definition for ‘title’
plot.sla: no visible global function definition for ‘abline’
print.sla: no visible global function definition for ‘coef’
sla.default: no visible global function definition for ‘lm’
sla.default: no visible global function definition for ‘anova’
Undefined global functions or variables:
  abline anova coef lm title
Consider adding
  importFrom("graphics", "abline", "title")
  importFrom("stats", "anova", "coef", "lm")
to your NAMESPACE file.
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 use registered native symbols 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 use registered native symbols 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 use registered native symbols 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 use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols 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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [36s/41s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Data are not available for this date. 2015.03.31 does not exist at ftp://n5eil01u.ecs.nsidc.org/SAN/SMAP/SPL3SMP.003/
  1: find_smap(id = "SPL3SMP", dates = "2015-03-31", version = 3) at testthat/test-extract_smap.R:4
  2: lapply(dates, find_for_date, id = id, version = version)
  3: FUN(X[[i]], ...)
  4: validate_ftp_request(id, date, version)
  5: validate_date(id, version, date)
  6: stop(paste(prefix, suffix))
  
  testthat results ================================================================
  OK: 9 SKIPPED: 14 FAILED: 2
  1. Error: invalid output directories cause errors (@test-download_smap.R#4) 
  2. Error: invalid datasets cause errors (@test-extract_smap.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘SmartSVA/libs/SmartSVA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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:
  fitted.sma
See section ‘Registering S3 methods’ 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.
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 use registered native symbols 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 use registered native symbols 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 use registered native symbols 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 use registered native symbols 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:
  ‘lattice’ ‘splines’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘lattice’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  plot.sme sme.data.frame sme.default sme.list
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
getRoughnessMatrix: no visible global function definition for ‘ns’
plotSmeDiagnostic: no visible global function definition for ‘layout’
plotSmeDiagnostic: no visible global function definition for ‘plot’
plotSmeModel: no visible global function definition for ‘plot’
plotSmeModel: no visible global function definition for ‘lines’
plotSmeModel: no visible global function definition for ‘col2rgb’
plotSmeModel: no visible global function definition for ‘polygon’
plotSmeModel: no visible global function definition for ‘rgb’
plotSmeRaw: no visible global function definition for ‘xyplot’
plotSmeRaw : <anonymous>: no visible global function definition for
  ‘panel.xyplot’
plotSmeRaw : <anonymous>: no visible global function definition for
  ‘panel.lines’
sme.default: no visible global function definition for ‘ns’
sme.list: no visible binding for global variable ‘ns’
sme.list : <anonymous>: no visible global function definition for ‘ns’
vcov.sme: no visible global function definition for ‘ns’
Undefined global functions or variables:
  col2rgb layout lines ns panel.lines panel.xyplot plot polygon rgb
  xyplot
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
  importFrom("graphics", "layout", "lines", "plot", "polygon")
to your NAMESPACE file.
File ‘sme/libs/sme.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: GNU Extension: Symbol ‘ntt’ is used before it is typed at (1)
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/smint.Rcheck/00install.out’ for details.
File ‘smint/libs/smint.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls in package code:
  ‘MASS’ ‘survival’
  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:
  disparity.glm disparity.lm summary.treg
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘Smisc/libs/Smisc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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.
File ‘smoof/libs/smoof.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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:
  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.
'library' or 'require' calls in package code:
  ‘akima’ ‘misc3d’ ‘rgl’ ‘rpanel’ ‘tkrplot’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
File ‘sm/libs/sm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
affinityMatrix: no visible global function definition for ‘dnorm’
displayClusters: no visible global function definition for ‘image’
displayClusters: no visible global function definition for ‘grey’
displayClustersWithHeatmap: no visible global function definition for
  ‘median’
displayClustersWithHeatmap: no visible global function definition for
  ‘heatmap’
Undefined global functions or variables:
  dnorm grey heatmap image median
Consider adding
  importFrom("grDevices", "grey")
  importFrom("graphics", "image")
  importFrom("stats", "dnorm", "heatmap", "median")
to your NAMESPACE file.
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 use registered native symbols 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 use registered native symbols 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 use registered native symbols 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.
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.
File ‘snplist/libs/snplist.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘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 use registered native symbols 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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘Biostrings’ ‘GenomicRanges’ ‘IRanges’ ‘Rsamtools’
  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 ‘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 use registered native symbols 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 use registered native symbols 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.
File ‘sodium/libs/sodium.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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.sod_sq3
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
hsvScale: no visible global function definition for ‘hsv’
plotConcentric: no visible global function definition for ‘plot’
plotConcentric: no visible global function definition for ‘points’
plotConcentric: no visible global function definition for ‘legend’
plotPoints: no visible global function definition for ‘plot’
plotStress: no visible global function definition for ‘plot’
plotStress: no visible global function definition for ‘polygon’
plotStress: no visible global function definition for ‘points’
Undefined global functions or variables:
  hsv legend plot points polygon
Consider adding
  importFrom("grDevices", "hsv")
  importFrom("graphics", "legend", "plot", "points", "polygon")
to your NAMESPACE file.
File ‘SOD/libs/SOD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘aqp’ ‘lattice’ ‘methods’ ‘munsell’ ‘splancs’
  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:
  head.profile.data.frame plot.profile.data.frame
  print.profile.data.frame summary.profile.data.frame
  tail.profile.data.frame
See section ‘Registering S3 methods’ 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.
File ‘solidearthtide/libs/solidearthtide.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ 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 use registered native symbols 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 use registered native symbols 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.
Non-standard files/directories found at top level:
  ‘sandbox’ ‘sos4R-Ex.R’
'library' or 'require' call to ‘rgdal’ 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.
Found the following apparent S3 methods exported but not registered:
  as.data.frame.OmMeasurement as.data.frame.OmObservation
  as.list.OmObservationCollection length.OmObservationCollection
  names.OmMeasurement names.OmObservation names.OmObservationCollection
  plot.SOS plot.SensorML plot.SosObservationOffering
  print.summary.GmlTimePeriod print.summary.OmObservation
  print.summary.OmObservationCollection print.summary.OwsRange
  print.summary.SOS print.summary.SosObservationOffering
  summary.GmlTimePeriod summary.OmObservation
  summary.OmObservationCollection summary.OwsRange summary.SOS
  summary.SosObservationOffering
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘SoundexBR/libs/SoundexBR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘glasso’ ‘limSolve’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
glasso.miss: no visible global function definition for ‘cov’
glasso.miss: no visible global function definition for ‘glasso’
glasso.miss: no visible global function definition for ‘Solve’
space.miss: no visible global function definition for ‘Solve’
Undefined global functions or variables:
  Solve cov glasso
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
Rd file 'glasso.miss.Rd':
  \examples lines wider than 100 characters:
     data(finStocksCn)  ##data of finance sector of Chinese Stock Market, from January 4th, 2011 to July 26th, 2011

Rd file 'space.miss.Rd':
  \examples lines wider than 100 characters:
     data(finStocksCn)  ##data of finance sector of Chinese Stock Market, from January 4th, 2011 to July 26th, 2011

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

It is good practice to use registered native symbols 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 use registered native symbols 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 use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
Found the following significant warnings:
  Warning: GNU Extension: Different type kinds at (1)
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/spanr.Rcheck/00install.out’ for details.
span: no visible global function definition for ‘complete.cases’
spanr: no visible global function definition for ‘model.frame’
spanr: no visible global function definition for ‘complete.cases’
spanr.hull: no visible global function definition for ‘par’
spanr.hull: no visible global function definition for ‘plot.new’
spanr.hull: no visible global function definition for ‘plot.window’
spanr.hull: no visible global function definition for ‘axis’
spanr.hull: no visible global function definition for ‘title’
spanr.hull: no visible global function definition for ‘points’
spanr.hull: no visible global function definition for ‘lines’
spanr.hull: no visible global function definition for ‘abline’
spanr.hull: no visible global function definition for ‘text’
spanr.hull: no visible global function definition for ‘segments’
spanr.hull: no visible global function definition for ‘box’
Undefined global functions or variables:
  abline axis box complete.cases lines model.frame par plot.new
  plot.window points segments text title
Consider adding
  importFrom("graphics", "abline", "axis", "box", "lines", "par",
             "plot.new", "plot.window", "points", "segments", "text",
             "title")
  importFrom("stats", "complete.cases", "model.frame")
to your NAMESPACE file.
File ‘spanr/libs/spanr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Found the following apparent S3 methods exported but not registered:
  plot.HierarchicalSparseCluster plot.HierarchicalSparseCluster.permute
  plot.KMeansSparseCluster plot.KMeansSparseCluster.permute
  print.HierarchicalSparseCluster
  print.HierarchicalSparseCluster.permute print.KMeansSparseCluster
  print.KMeansSparseCluster.permute
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'ColorDendrogram.Rd':
  \usage lines wider than 90 characters:
     ColorDendrogram(hc, y, main = "", branchlength = 0.7, labels = NULL, xlab = NULL, sub = NULL, ylab = "", cex.main = NULL)

Rd file 'HierarchicalSparseCluster.Rd':
  \usage lines wider than 90 characters:
     HierarchicalSparseCluster(x=NULL, dists=NULL,method=c("average","complete", "single","centroid"),
     wbound=NULL,niter=15,dissimilarity=c("squared.distance","absolute.value"), uorth=NULL,silent=FALSE,
  \examples lines wider than 100 characters:
       # faster than   sparsehc <- HierarchicalSparseCluster(x=x,wbound=perm.out$bestw, method="complete")
       sparsehc <- HierarchicalSparseCluster(dists=perm.out$dists, wbound=perm.out$bestw, method="complete", dissimilarity="absolute.value")

Rd file 'HierarchicalSparseCluster.permute.Rd':
  \examples lines wider than 100 characters:
       sparsehc <- HierarchicalSparseCluster(dists=perm.out$dists, wbound=perm.out$bestw, method="complete")

Rd file 'HierarchicalSparseCluster.wrapper.Rd':
  \usage lines wider than 90 characters:
     HierarchicalSparseCluster.wrapper(file,  method=c("average", "complete", "single", "centroid"),
     "single","centroid"),output.cluster.files=TRUE,outputfile.prefix=NULL,maxnumgenes=5000,standardize.arrays=TRUE)

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
Running ‘testthat.r’ [0s/0s]
Running the tests in ‘tests/testthat.r’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
File ‘SparseFactorAnalysis/libs/SparseFactorAnalysis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
rmvn.sparse: no visible global function definition for ‘rnorm’
rmvn.sparse: no visible global function definition for ‘as’
Undefined global functions or variables:
  as rnorm
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "rnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following apparent S3 methods exported but not registered:
  coef.cv.sparsenet
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘sparsenet/libs/sparsenet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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 use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Clarketest: no visible global function definition for ‘pbinom’
Clarketest: no visible global function definition for ‘qbinom’
DIC: no visible global function definition for ‘model.matrix’
LogLike: no visible global function definition for ‘model.matrix’
Vuongtest: no visible global function definition for ‘var’
Vuongtest: no visible global function definition for ‘qnorm’
Vuongtest: no visible global function definition for ‘pnorm’
est.sc: no visible global function definition for ‘model.matrix’
gpind: no visible global function definition for ‘rgamma’
nbind: no visible global function definition for ‘rgamma’
poiind: no visible global function definition for ‘rgamma’
zigpind: no visible global function definition for ‘rbinom’
zigpind: no visible global function definition for ‘rgamma’
zipind: no visible global function definition for ‘rbinom’
zipind: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  model.matrix pbinom pnorm qbinom qnorm rbinom rgamma var
Consider adding
  importFrom("stats", "model.matrix", "pbinom", "pnorm", "qbinom",
             "qnorm", "rbinom", "rgamma", "var")
to your NAMESPACE file.
Rd file 'est.sc.Rd':
  \examples lines wider than 100 characters:
     # gamma.true = vector of spatial effects according to the CAR model with mean 0, psi = 3 and sigma = 1
     nb <- est.sc(sim.Yin, ~1+sim.fm.X[,1]+sim.fm.X[,2], sim.region, model="NB", sim.gmat, sim.nmat, totalit=10)
     gp <- est.sc(sim.Yin, ~1+sim.fm.X[,1]+sim.fm.X[,2], sim.region, model="GP", sim.gmat, sim.nmat, totalit=10)
     zip <- est.sc(sim.Yin, ~1+sim.fm.X[,1]+sim.fm.X[,2], sim.region, model="ZIP", sim.gmat, sim.nmat, totalit=10)
     zigp <- est.sc(sim.Yin, ~1+sim.fm.X[,1]+sim.fm.X[,2], sim.region, model="ZIGP", sim.gmat, sim.nmat, totalit=10)
     Vuong.poi.nb <- Vuongtest(ll.poi, ll.nb, alpha = 0.05, p = DIC.poi$p.D, q = DIC.nb$p.D, correction = TRUE)
     Vuong.poi.gp <- Vuongtest(ll.poi, ll.gp, alpha = 0.05, p = DIC.poi$p.D, q = DIC.gp$p.D, correction = TRUE)
     Vuong.poi.zip <- Vuongtest(ll.poi, ll.zip, alpha = 0.05, p = DIC.poi$p.D, q = DIC.zip$p.D, correction = TRUE)
     Vuong.poi.zigp <- Vuongtest(ll.poi, ll.zigp, alpha = 0.05, p = DIC.poi$p.D, q = DIC.zigp$p.D, correction = TRUE)
     Clarke.poi.nb <- Clarketest(ll.poi, ll.nb, alpha = 0.05, p = DIC.poi$p.D, q = DIC.nb$p.D, correction = TRUE)
     Clarke.poi.gp <- Clarketest(ll.poi, ll.gp, alpha = 0.05, p = DIC.poi$p.D, q = DIC.gp$p.D, correction = TRUE)
     Clarke.poi.zip <- Clarketest(ll.poi, ll.zip, alpha = 0.05, p = DIC.poi$p.D, q = DIC.zip$p.D, correction = TRUE)
     Clarke.poi.zigp <- Clarketest(ll.poi, ll.zigp, alpha = 0.05, p = DIC.poi$p.D, q = DIC.zigp$p.D, correction = TRUE)

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

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: trig.trans
> ### Title: Calculates the trigonomic slope and aspect transformation
> ### Aliases: trig.trans
> 
> ### ** Examples
> 
>  trig.trans(slope = 48.146, aspect = 360.000)
[1] -0.2383874
> 
>  library(raster)
Loading required package: sp
>  elev <- getData('alt', country='CHE')
trying URL 'http://biogeo.ucdavis.edu/data/diva/msk_alt/CHE_msk_alt.zip'
Warning in utils::download.file(url = aurl, destfile = fn, method = "auto",  :
  cannot open URL 'http://biogeo.ucdavis.edu/data/diva/msk_alt/CHE_msk_alt.zip': HTTP status was '403 Forbidden'
Error in utils::download.file(url = aurl, destfile = fn, method = "auto",  : 
  cannot open URL 'http://biogeo.ucdavis.edu/data/diva/msk_alt/CHE_msk_alt.zip'
Calls: getData -> .raster -> .download -> <Anonymous>
Execution halted
File ‘SpatialEpi/libs/SpatialEpi.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols 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.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Old-style initialization at (1)
  Warning: GNU Extension: Different type kinds at (1)
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/spatialkernel.Rcheck/00install.out’ for details.
Malformed Description field: should contain one or more complete sentences.
Deprecated license: CC BY-NC-SA 3.0 + file LICENSE
File ‘spatialkernel/libs/spatialkernel.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
codisp: no visible global function definition for ‘complete.cases’
cor.spatial: no visible global function definition for ‘complete.cases’
modified.ttest: no visible global function definition for
  ‘complete.cases’
modified.ttest: no visible global function definition for ‘cor’
plot.codisp: no visible global function definition for ‘plot’
plot.codisp: no visible global function definition for ‘title’
Undefined global functions or variables:
  complete.cases cor plot title
Consider adding
  importFrom("graphics", "plot", "title")
  importFrom("stats", "complete.cases", "cor")
to your NAMESPACE file.
File ‘spatialsegregation/libs/spatialsegregation.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
bbox_to_SpatialPolygons: no visible global function definition for
  ‘CRS’
bbox_to_SpatialPolygons: no visible global function definition for
  ‘Polygon’
bbox_to_SpatialPolygons: no visible global function definition for
  ‘Polygons’
bbox_to_SpatialPolygons: no visible global function definition for
  ‘SpatialPolygons’
list.raster.files: no visible global function definition for ‘CRS’
list.raster.files: no visible global function definition for
  ‘spTransform’
list.raster.files: no visible global function definition for
  ‘SpatialPolygonsDataFrame’
list.raster.files: no visible global function definition for ‘spChFIDs’
predict_rasterEngine : predict.rasterEngine_function: no visible global
  function definition for ‘complete.cases’
projectRaster_rigorous : chunk_function: no visible global function
  definition for ‘spTransform’
projectRaster_rigorous : chunk_function: no visible global function
  definition for ‘CRS’
spatial_sync_raster: no visible global function definition for ‘bbox’
spatial_sync_vector: no visible global function definition for
  ‘spTransform’
spatial_sync_vector: no visible global function definition for ‘CRS’
Undefined global functions or variables:
  CRS Polygon Polygons SpatialPolygons SpatialPolygonsDataFrame bbox
  complete.cases spChFIDs spTransform
Consider adding
  importFrom("stats", "complete.cases")
to your NAMESPACE file.
File ‘SpatialTools/libs/SpatialTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 ‘spc/libs/spc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 use registered native symbols 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 use registered native symbols 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.specificity summary.specificity
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
randomCorrelations: no visible global function definition for ‘cor’
specGlm : <anonymous>: no visible global function definition for ‘coef’
specLm : <anonymous>: no visible global function definition for ‘coef’
Undefined global functions or variables:
  coef cor
Consider adding
  importFrom("stats", "coef", "cor")
to your NAMESPACE file.
Missing or unexported object: ‘ChemoSpec::readJDX’
File ‘SpecsVerification/libs/SpecsVerification.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
Found the following apparent S3 methods exported but not registered:
  plot.spei print.spei summary.spei
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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:
  ‘ROCR’ ‘rpart’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'partition.tiles.Rd':
  \examples lines wider than 100 characters:
     parti3 = partition.tiles(ecuador, dsplit = 2000, offset = "random", rotation = "random", reassign = TRUE, min.n = 100)

Rd file 'represampling.factor.bootstrap.Rd':
  \examples lines wider than 100 characters:
     fac = partition.tiles(ecuador, return.factor=TRUE, repetition=c(1:3), dsplit=500, min.n=200, rotation="random", offset="random")

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SpherWave.Rcheck/00install.out’ for details.
lambda.global: no visible global function definition for ‘mad’
lambda.global: no visible global function definition for ‘quantile’
lambda.global: no visible global function definition for ‘qnorm’
lambda.global: no visible global function definition for ‘pnorm’
ls.comp: no visible global function definition for ‘lsfit’
modterritory: no visible global function definition for ‘median’
newgotterritory: no visible global function definition for ‘median’
newterritory: no visible global function definition for ‘median’
ridge.comp: no visible global function definition for ‘lsfit’
ridge.diacomp: no visible global function definition for ‘ls.diag’
sw.plot: no visible global function definition for ‘par’
sw.plot: no visible global function definition for ‘plot’
sw.plot: no visible global function definition for ‘points’
sw.plot: no visible global function definition for ‘image’
sw.plot: no visible global function definition for ‘axis’
sw.plot: no visible global function definition for ‘legend’
sw.plot: no visible global function definition for ‘box’
sw.plot: no visible global function definition for ‘title’
thresh.level: no visible global function definition for ‘na.omit’
thresh.level: no visible global function definition for ‘mad’
thresh.level: no visible global function definition for ‘qnorm’
thresh.level: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  axis box image legend ls.diag lsfit mad median na.omit par plot pnorm
  points qnorm quantile title
Consider adding
  importFrom("graphics", "axis", "box", "image", "legend", "par", "plot",
             "points", "title")
  importFrom("stats", "ls.diag", "lsfit", "mad", "median", "na.omit",
             "pnorm", "qnorm", "quantile")
to your NAMESPACE file.
File ‘SpherWave/libs/SpherWave.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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.sphet
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Found the following apparent S3 methods exported but not registered:
  plot.ordinDNA
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Running examples in ‘spider-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: seqStat
> ### Title: Sequence statistics
> ### Aliases: seqStat
> ### Keywords: Barcoding Utilities
> 
> ### ** Examples
> 
> data(anoteropsis)
> seqStat(anoteropsis)
Error in checkDNA(x, gapsAsMissing = TRUE) : object 'output' not found
Calls: seqStat -> sapply -> lapply -> FUN -> checkDNA
Execution halted
File ‘spikeSlabGAM/libs/spikeSlabGAM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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 use registered native symbols 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 ‘splancs/libs/splancs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
NoSep: no visible global function definition for ‘setNames’
Reshape: no visible global function definition for ‘setNames’
Reshape: no visible global function definition for ‘reshape’
read.concat: no visible global function definition for ‘count.fields’
read.concat: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  count.fields read.table reshape setNames
Consider adding
  importFrom("stats", "reshape", "setNames")
  importFrom("utils", "count.fields", "read.table")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  coef.sgpls coef.spls coef.splsda plot.spls predict.sgpls predict.spls
  predict.splsda print.sgpls print.spls print.splsda
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘splus2R/libs/splus2R.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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.equal.list all.equal.list
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘spMC/libs/spMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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 use registered native symbols 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.
File ‘spray/libs/spray.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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.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.
'library' or 'require' call to ‘RankProd’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
pRP: no visible global function definition for ‘plotRP’
pRPadvance: no visible global function definition for ‘plotRP’
pboot: no visible global function definition for ‘runif’
prandomForest.formula: no visible binding for global variable ‘na.fail’
prandomForest.formula: no visible global function definition for
  ‘model.response’
prandomForest.formula: no visible global function definition for
  ‘model.frame’
prandomForest.formula: no visible global function definition for
  ‘terms’
prandomForest.formula: no visible global function definition for
  ‘reformulate’
Undefined global functions or variables:
  model.frame model.response na.fail plotRP reformulate runif terms
Consider adding
  importFrom("stats", "model.frame", "model.response", "na.fail",
             "reformulate", "runif", "terms")
to your NAMESPACE file.
Note: information on .o files is not available
File ‘sprint/libs/sprint.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: GNU Extension: Symbol ‘k’ is used before it is typed at (1)
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/spsmooth.Rcheck/00install.out’ for details.
Found the following apparent S3 methods exported but not registered:
  summary.gam
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
.dpssToEigenvalues: no visible global function definition for ‘mvfft’
smooth.construct.sp.smooth.spec: no visible global function definition
  for ‘str’
Undefined global functions or variables:
  mvfft str
Consider adding
  importFrom("stats", "mvfft")
  importFrom("utils", "str")
to your NAMESPACE file.
File ‘spsmooth/libs/spsmooth.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
File ‘spTimer/libs/spTimer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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:
  chaos.default chaos.spt chaos.st plot.spt plot.st print.spt print.st
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
.GameSPT: no visible global function definition for ‘runif’
.GameSPT: no visible global function definition for ‘points’
.GameST: no visible global function definition for ‘runif’
.GameST: no visible global function definition for ‘points’
.arc: no visible global function definition for ‘lines’
.ptpedal: no visible global function definition for ‘polygon’
.sptpedal2: no visible global function definition for ‘segments’
.sptpedal3: no visible global function definition for ‘polygon’
.sptpedal4: no visible global function definition for ‘polygon’
chaos.spt: no visible global function definition for ‘plot’
chaos.spt: no visible global function definition for ‘polygon’
chaos.spt: no visible global function definition for ‘runif’
chaos.spt: no visible global function definition for ‘points’
chaos.st: no visible global function definition for ‘plot’
chaos.st: no visible global function definition for ‘polygon’
chaos.st: no visible global function definition for ‘runif’
chaos.st: no visible global function definition for ‘points’
plot.spt: no visible global function definition for ‘plot’
plot.spt: no visible global function definition for ‘polygon’
plot.st: no visible global function definition for ‘plot’
plot.st: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  lines plot points polygon runif segments
Consider adding
  importFrom("graphics", "lines", "plot", "points", "polygon",
             "segments")
  importFrom("stats", "runif")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  mean.transectHolder mean.trapTransect print.transectHolder
  print.trapTransect simulate.transectHolder
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
CMCSimulation: no visible global function definition for ‘rexp’
CMCSimulation: no visible global function definition for ‘plot’
CMCSimulation: no visible global function definition for ‘axis’
booking_clerkMC: no visible global function definition for ‘runif’
booking_clerkMC: no visible global function definition for ‘rexp’
fixedpoint_show: no visible global function definition for ‘plot’
fixedpoint_show: no visible global function definition for ‘lines’
mean.trapTransect: no visible global function definition for
  ‘weighted.mean’
newtonraphson_show: no visible global function definition for ‘plot’
newtonraphson_show: no visible global function definition for ‘lines’
print.transectHolder: no visible global function definition for ‘str’
print.trapTransect: no visible global function definition for ‘str’
sd.transectHolder: no visible global function definition for ‘sd’
simulate.transectHolder: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  axis lines plot rexp runif sd str weighted.mean
Consider adding
  importFrom("graphics", "axis", "lines", "plot")
  importFrom("stats", "rexp", "runif", "sd", "weighted.mean")
  importFrom("utils", "str")
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' call to ‘tcltk’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
read.csv.sql: no visible global function definition for ‘download.file’
sqldf: no visible global function definition for ‘modifyList’
sqldf: no visible global function definition for ‘head’
Undefined global functions or variables:
  download.file head modifyList
Consider adding
  importFrom("utils", "download.file", "head", "modifyList")
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 significant warnings:
  Warning: CHARACTER expression will be truncated in assignment (8/9) at (1) [-Wcharacter-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/srd.Rcheck/00install.out’ for details.
draw.srd: no visible global function definition for ‘complete.cases’
draw.srd: no visible global function definition for ‘runif’
draw.srd: no visible global function definition for ‘arrows’
draw.srd: no visible global function definition for ‘text’
draw.srd: no visible global function definition for ‘segments’
draw.srd.enc: no visible global function definition for ‘par’
draw.srd.enc: no visible global function definition for ‘plot.new’
draw.srd.enc: no visible global function definition for ‘plot.window’
draw.srd.enc: no visible global function definition for ‘rgb’
draw.srd.enc: no visible global function definition for ‘polygon’
draw.srd.enc: no visible global function definition for ‘pchisq’
draw.srd.enc: no visible global function definition for ‘text’
draw.srd.enc: no visible global function definition for ‘title’
draw.srd.enc: no visible global function definition for ‘arrows’
drawcell: no visible global function definition for ‘polygon’
drawcell: no visible global function definition for ‘segments’
rotate.srd: no visible global function definition for ‘devAskNewPage’
srd: no visible global function definition for ‘devAskNewPage’
Undefined global functions or variables:
  arrows complete.cases devAskNewPage par pchisq plot.new plot.window
  polygon rgb runif segments text title
Consider adding
  importFrom("grDevices", "devAskNewPage", "rgb")
  importFrom("graphics", "arrows", "par", "plot.new", "plot.window",
             "polygon", "segments", "text", "title")
  importFrom("stats", "complete.cases", "pchisq", "runif")
to your NAMESPACE file.
File ‘srd/libs/srd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 use registered native symbols 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 use registered native symbols 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 use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
calcgroup : probtotrating: no visible global function definition for
  ‘convolve’
enterratdata: no visible global function definition for ‘edit’
gplot.SSrat: no visible global function definition for ‘par’
gplot.SSrat: no visible global function definition for ‘plot’
gplot.SSrat: no visible global function definition for ‘legend’
Undefined global functions or variables:
  convolve edit legend par plot
Consider adding
  importFrom("graphics", "legend", "par", "plot")
  importFrom("stats", "convolve")
  importFrom("utils", "edit")
to your NAMESPACE file.
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.
File ‘stable/libs/stable.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.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 use registered native symbols 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 use registered native symbols 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.
Warning: no function found corresponding to methods exports from ‘stashR’ 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.
cacheVersionFile: no visible global function definition for
  ‘download.file’
getdata: no visible global function definition for ‘download.file’
copyDB,localDB: no visible global function definition for ‘new’
initialize,localDB: no visible global function definition for
  ‘callNextMethod’
initialize,remoteDB: no visible global function definition for
  ‘callNextMethod’
Undefined global functions or variables:
  callNextMethod download.file new
Consider adding
  importFrom("methods", "callNextMethod", "new")
  importFrom("utils", "download.file")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running ‘tests.R’ [0s/1s]
Running the tests in ‘tests/tests.R’ failed.
Last 13 lines of output:
  > ##########################################################################
  > ## Test objects of class 'remoteDB'
  > ## These tests will fail (within a 'try()') if Internet connectivity
  > ## is not available
  > 
  > myurl <- "http://www.biostat.jhsph.edu/MCAPS/data_v0.3/"
  > 
  > ## create a 'remoteDB' object ##
  > db <- new("remoteDB", url= myurl, dir = dir, name= "MCAPS")
  Warning in download.file(rpath, versionFile(db, where = "local"), mode = "w",  :
    cannot open URL 'http://www.biostat.jhsph.edu/MCAPS/data_v0.3/version': HTTP status was '404 Not Found'
  Error in download.file(rpath, versionFile(db, where = "local"), mode = "w",  : 
    cannot open URL 'http://www.biostat.jhsph.edu/MCAPS/data_v0.3/version'
  Calls: new ... initialize -> initialize -> cacheVersionFile -> download.file
  Execution halted
File ‘statcomp/libs/statcomp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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.corsign
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘statip/libs/statip.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ 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:
  decTreeImpFuncCpp.cpp:1677:43: warning: unknown escape sequence '\ ' [-Wunknown-escape-sequence]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/StatMethRank.Rcheck/00install.out’ for details.
File ‘StatMethRank/libs/StatMethRank.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 use registered native symbols 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 use registered native symbols 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 use registered native symbols 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 use registered native symbols 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.
Found the following apparent S3 methods exported but not registered:
  anova.stepplr predict.plr predict.stepplr print.plr print.stepplr
  summary.plr summary.stepplr
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
cv.step.plr: no visible global function definition for ‘binomial’
cv.step.plr: no visible global function definition for ‘predict’
cv.step.plr: no visible binding for global variable ‘var’
plr: no visible global function definition for ‘binomial’
predict.stepplr: no visible global function definition for ‘predict’
summary.plr: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  binomial pnorm predict var
Consider adding
  importFrom("stats", "binomial", "pnorm", "predict", "var")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'plr-internal':
  ‘anova.stepplr’ ‘print.plr’ ‘print.stepplr’ ‘summary.plr’
  ‘summary.stepplr’

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

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

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 ‘stepPlr/libs/stepPlr.so’:
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Object: ‘cg_descent.o’
  Found ‘_gfortran_stop_string’, possibly from ‘stop’ (Fortran)
    Object: ‘cg_descent.o’
File ‘stepPlr/libs/stepPlr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
initialize.emul: no visible global function definition for ‘lm’
make.ranges: no visible global function definition for ‘lm’
optimize.emul: no visible global function definition for ‘nlminb’
optimize.emul: no visible global function definition for ‘runif’
rsurface.plot: no visible global function definition for ‘par’
rsurface.plot: no visible global function definition for
  ‘filled.contour’
rsurface.plot: no visible binding for global variable ‘topo.colors’
rsurface.plot: no visible global function definition for ‘title’
test.all: no visible global function definition for ‘par’
test.all: no visible global function definition for ‘plot’
test.all: no visible global function definition for ‘lines’
test.csv: no visible global function definition for ‘plot.default’
test.csv: no visible global function definition for ‘lines’
Undefined global functions or variables:
  filled.contour lines lm nlminb par plot plot.default runif title
  topo.colors
Consider adding
  importFrom("grDevices", "topo.colors")
  importFrom("graphics", "filled.contour", "lines", "par", "plot",
             "plot.default", "title")
  importFrom("stats", "lm", "nlminb", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/stima.Rcheck/00install.out’ for details.
bos.cat2: no visible global function definition for ‘resid’
bos.cat2: no visible global function definition for ‘lm’
plot.rt: no visible global function definition for ‘plot’
plot.rt: no visible global function definition for ‘text’
plot.rt: no visible global function definition for ‘rect’
plot.rt: no visible global function definition for ‘title’
plot.rt: no visible global function definition for ‘par’
stdata: no visible binding for global variable ‘var’
stima: no visible global function definition for ‘fitted’
stima: no visible global function definition for ‘lm’
stima: no visible global function definition for ‘anova’
stima: no visible global function definition for ‘predict’
stima: no visible global function definition for ‘cor’
stima: no visible global function definition for ‘as.formula’
stima: no visible global function definition for ‘step’
Undefined global functions or variables:
  anova as.formula cor fitted lm par plot predict rect resid step text
  title var
Consider adding
  importFrom("graphics", "par", "plot", "rect", "text", "title")
  importFrom("stats", "anova", "as.formula", "cor", "fitted", "lm",
             "predict", "resid", "step", "var")
to your NAMESPACE file.
File ‘stima/libs/stima.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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:
  na.stinterp.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
na.stinterp.default: no visible global function definition for ‘time’
na.stinterp.default: no visible global function definition for
  ‘na.omit’
Undefined global functions or variables:
  na.omit time
Consider adding
  importFrom("stats", "na.omit", "time")
to your NAMESPACE file.
File ‘stlplus/libs/stlplus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
ConstructMPst: no visible global function definition for ‘na.omit’
ConstructMPst: no visible global function definition for
  ‘txtProgressBar’
ConstructMPst: no visible global function definition for
  ‘setTxtProgressBar’
MedianPolishM.default : Res: no visible binding for global variable
  ‘median’
MedianPolishM.default: no visible binding for global variable ‘median’
MedianPolishM.default: no visible global function definition for
  ‘median’
Mpplot: no visible global function definition for ‘layout’
Mpplot: no visible global function definition for ‘plot’
Mpplot: no visible global function definition for ‘text’
Mpplot: no visible global function definition for ‘axis’
Mpplot: no visible global function definition for ‘mtext’
print.plot.MedianPolishM: no visible global function definition for
  ‘layout’
print.plot.MedianPolishM: no visible global function definition for
  ‘stripchart’
print.plot.MedianPolishM: no visible global function definition for
  ‘ts.plot’
print.plot.MedianPolishM: no visible global function definition for
  ‘plot’
print.plot.MedianPolishM: no visible global function definition for
  ‘legend’
removetrendMPst: no visible global function definition for
  ‘txtProgressBar’
removetrendMPst: no visible global function definition for
  ‘setTxtProgressBar’
splineMPST: no visible global function definition for ‘na.omit’
splineMPST: no visible global function definition for ‘txtProgressBar’
splineMPST: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  axis layout legend median mtext na.omit plot setTxtProgressBar
  stripchart text ts.plot txtProgressBar
Consider adding
  importFrom("graphics", "axis", "layout", "legend", "mtext", "plot",
             "stripchart", "text")
  importFrom("stats", "median", "na.omit", "ts.plot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Rd file 'testPort.Rd':
  \examples lines wider than 100 characters:
     legend('topleft', col=1:5, lty=1:5, legend=c('equal all.', 'none', 'SIM', 'CCM', 'MGM'), pch=c(NA, NA, NA, NA, 1))

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

It is good practice to use registered native symbols 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.
Namespace with empty importFrom: ‘tcltk2’
DetailOpLines: no visible global function definition for
  ‘tkProgressBar’
DetailOpLines: no visible global function definition for
  ‘setTkProgressBar’
MultiTrainWithInventory: no visible global function definition for
  ‘tkProgressBar’
MultiTrainWithInventory: no visible global function definition for
  ‘setTkProgressBar’
SimHistory: no visible global function definition for ‘tkProgressBar’
SimHistory: no visible global function definition for
  ‘setTkProgressBar’
Undefined global functions or variables:
  setTkProgressBar tkProgressBar
File ‘stosim/libs/stosim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: ‘pi’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/stpp.Rcheck/00install.out’ for details.
'library' or 'require' calls in package code:
  ‘rgl’ ‘rpanel’
  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.stpp
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘stpp/libs/stpp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘cubature’ ‘deldir’ ‘splancs’
  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.devresid plot.gridresid plot.stpp plot.superthin plot.supresid
  plot.tessdev plot.tessresid plot.thinresid print.devresid
  print.gridresid print.stgrid print.stpp print.stwin print.superthin
  print.supresid print.tessdev print.tessresid print.thinresid
  summary.superthin summary.supresid summary.thinresid
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'gridresid.Rd':
  \usage lines wider than 90 characters:
     gridresid(X, cifunction, theta = NULL, lambda = NULL, grid = c(10, 10), gf = NULL, resid = c("raw", "pearson", "inverse"), algthm = c(" ... [TRUNCATED]

These lines will be truncated in the PDF manual.
.rdirichlet: no visible global function definition for ‘rgamma’
DGobj.simul.mechanistic: no visible global function definition for
  ‘rbinom’
DGobj.simul.mechanistic: no visible global function definition for
  ‘rpois’
DGobj.simul.mechanistic: no visible global function definition for
  ‘par’
DGobj.simul.mechanistic: no visible global function definition for
  ‘plot’
DGobj.simul.mechanistic: no visible global function definition for
  ‘mtext’
DGobj.simul.mechanistic: no visible global function definition for
  ‘box’
DGobj.simul.regression: no visible global function definition for
  ‘rnorm’
DGobj.simul.regression: no visible global function definition for
  ‘rmultinom’
DGobj.simul.regression: no visible global function definition for ‘par’
DGobj.simul.regression: no visible global function definition for
  ‘plot’
ranking.strains: no visible global function definition for ‘lm’
ranking.strains: no visible global function definition for ‘par’
ranking.strains: no visible global function definition for ‘plot’
ranking.strains: no visible global function definition for ‘points’
ranking.strains: no visible global function definition for ‘hist’
ranking.strains: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline box hist lm mtext par plot points rbinom rgamma rmultinom
  rnorm rpois
Consider adding
  importFrom("graphics", "abline", "box", "hist", "mtext", "par", "plot",
             "points")
  importFrom("stats", "lm", "rbinom", "rgamma", "rmultinom", "rnorm",
             "rpois")
to your NAMESPACE file.
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 ‘strataG/libs/strataG.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
add_b1_takenone: no visible global function definition for ‘quantile’
plot.strata: no visible global function definition for ‘layout’
plot.strata: no visible global function definition for ‘par’
plot.strata: no visible global function definition for ‘hist’
plot.strata: no visible global function definition for ‘rgb’
plot.strata: no visible global function definition for ‘abline’
plot.strata: no visible global function definition for ‘text’
plot.strata: no visible global function definition for ‘mtext’
robust_initpbh: no visible global function definition for ‘var’
strata.LH: no visible global function definition for ‘combn’
strata.LH: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline combn hist layout mtext par quantile rgb text var
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "abline", "hist", "layout", "mtext", "par",
             "text")
  importFrom("stats", "quantile", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
File ‘stratification/libs/stratification.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.icweib print.icweib
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
HRatio: no visible global function definition for ‘qnorm’
icweib: no visible global function definition for ‘model.frame’
icweib: no visible binding for global variable ‘na.pass’
icweib: no visible global function definition for ‘complete.cases’
icweib: no visible global function definition for ‘model.matrix’
icweib: no visible global function definition for ‘optim’
icweib: no visible global function definition for ‘pchisq’
icweib: no visible global function definition for ‘pnorm’
plot.icweib : getstat: no visible global function definition for
  ‘qnorm’
plot.icweib: no visible global function definition for ‘plot’
plot.icweib: no visible global function definition for ‘lines’
plot.icweib: no visible global function definition for ‘legend’
print.icweib: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  complete.cases legend lines model.frame model.matrix na.pass optim
  pchisq plot pnorm qnorm
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "complete.cases", "model.frame", "model.matrix",
             "na.pass", "optim", "pchisq", "pnorm", "qnorm")
to your NAMESPACE file.
File ‘stream/libs/stream.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘ROAuth’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
RMSEA : lower.lambda: no visible global function definition for
  ‘pchisq’
RMSEA: no visible global function definition for ‘uniroot’
RMSEA : upper.lambda: no visible global function definition for
  ‘pchisq’
RMSEA: no visible global function definition for ‘pchisq’
boot.lavaan: no visible global function definition for ‘cov’
boot.lavaan: no visible binding for global variable ‘sd’
factanal.prcomp: no visible global function definition for ‘princomp’
fit.nlminb: no visible global function definition for ‘nlminb’
fit.nlminb: no visible global function definition for ‘pchisq’
pval: no visible global function definition for ‘pnorm’
rmnorm : <anonymous>: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  cov nlminb pchisq pnorm princomp rnorm sd uniroot
Consider adding
  importFrom("stats", "cov", "nlminb", "pchisq", "pnorm", "princomp",
             "rnorm", "sd", "uniroot")
to your NAMESPACE file.
Rd file 'pugesek.Rd':
  \examples lines wider than 100 characters:
     pugesek.threefactors.1 <- sem(pugesek.threefactors.model, data = bumpus.log, fixed.x = FALSE, group =
     pugesek.threefactors.2 <- sem(pugesek.threefactors.model, data = bumpus.log, fixed.x = FALSE, group =

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols 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.
File ‘subplex/libs/subplex.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.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.
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 use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
print.bws.count: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
GG2.boot: no visible global function definition for ‘integrate’
KM2.pert: no visible global function definition for ‘rexp’
pbc.sample: no visible binding for global variable ‘pbc’
plot.surv2sample: no visible global function definition for ‘plot’
q95: no visible global function definition for ‘quantile’
rmstaug: no visible global function definition for ‘lm’
rmstaug: no visible global function definition for ‘glm’
rmstaug: no visible global function definition for ‘pchisq’
rmstreg: no visible global function definition for ‘lm’
rmstreg: no visible global function definition for ‘glm’
rmstreg: no visible global function definition for ‘pchisq’
surv2sample: no visible binding for global variable ‘sd’
surv2sample: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  glm integrate lm pbc pchisq plot pnorm quantile rexp sd
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "glm", "integrate", "lm", "pchisq", "pnorm",
             "quantile", "rexp", "sd")
to your NAMESPACE file.
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 use registered native symbols 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 use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
dropout : <anonymous>: no visible global function definition for
  ‘na.omit’
encToInt: no visible global function definition for ‘localeToCharset’
intToEnc: no visible global function definition for ‘localeToCharset’
Undefined global functions or variables:
  localeToCharset na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "localeToCharset")
to your NAMESPACE file.
'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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols 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 ‘survPresmooth/libs/survPresmooth.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/survrec.Rcheck/00install.out’ for details.
lines.survfitr: no visible global function definition for ‘lines’
plot.survfitr: no visible global function definition for ‘plot’
plot.survfitr: no visible global function definition for ‘lines’
plot.survfitr: no visible global function definition for ‘qnorm’
print.survfitr : pfun: no visible global function definition for
  ‘median’
survdiffr: no visible global function definition for ‘runif’
survdiffr: no visible global function definition for ‘terms’
survdiffr: no visible global function definition for ‘model.extract’
survfitr: no visible global function definition for ‘terms’
survfitr: no visible global function definition for ‘model.extract’
Undefined global functions or variables:
  lines median model.extract plot qnorm runif terms
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "median", "model.extract", "qnorm", "runif",
             "terms")
to your NAMESPACE file.
File ‘survrec/libs/survrec.so’:
  Found ‘_gfortran_rand’, possibly from ‘rand’ (Fortran)
    Object: ‘bootstrap.o’
File ‘survrec/libs/survrec.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
plot.rmst2: no visible global function definition for ‘par’
plot.rmst2: no visible global function definition for ‘plot’
plot.rmst2: no visible global function definition for ‘polygon’
plot.rmst2: no visible global function definition for ‘lines’
rmst1: no visible global function definition for ‘qnorm’
rmst2: no visible global function definition for ‘qnorm’
rmst2: no visible global function definition for ‘pnorm’
rmst2.sample.data: no visible global function definition for ‘data’
rmst2reg: no visible global function definition for ‘lm’
rmst2reg: no visible global function definition for ‘glm’
rmst2reg: no visible global function definition for ‘pchisq’
rmst2reg: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  data glm lines lm par pchisq plot pnorm polygon qnorm
Consider adding
  importFrom("graphics", "lines", "par", "plot", "polygon")
  importFrom("stats", "glm", "lm", "pchisq", "pnorm", "qnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
File ‘survSNP/libs/survSNP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.jgrRun: no visible global function definition for ‘capture.output’
.macDlgList: no visible global function definition for ‘select.list’
.unixDlgForm: no visible global function definition for ‘as’
.unixDlgMessage: no visible global function definition for ‘alarm’
.winDlgList: no visible global function definition for ‘select.list’
dlgForm.textCLI: no visible global function definition for ‘as’
dlgList.textCLI: no visible global function definition for
  ‘select.list’
dlgMessage.textCLI: no visible global function definition for
  ‘select.list’
dlgSave.textCLI: no visible global function definition for
  ‘select.list’
Undefined global functions or variables:
  alarm as capture.output select.list
Consider adding
  importFrom("methods", "as")
  importFrom("utils", "alarm", "capture.output", "select.list")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
dlgMessage.tcltkGUI: no visible global function definition for ‘alarm’
Undefined global functions or variables:
  alarm
Consider adding
  importFrom("utils", "alarm")
to your NAMESPACE file.
File ‘svd/libs/svd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
svd3dplot: no visible global function definition for ‘wireframe’
svd3dplot: no visible global function definition for ‘levelplot’
Undefined global functions or variables:
  levelplot wireframe
File ‘svglite/libs/svglite.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
completion : finalize : <anonymous>: no visible global function
  definition for ‘existsFunction’
listMethods: no visible global function definition for ‘findFunction’
tempvar: no visible global function definition for ‘runif’
Undefined global functions or variables:
  existsFunction findFunction runif
Consider adding
  importFrom("methods", "existsFunction", "findFunction")
  importFrom("stats", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package in Depends field not imported from: ‘kernlab’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'svmmajcrossval.Rd':
  \usage lines wider than 90 characters:
     svmmajcrossval(X,y,search.grid=list(lambda=2^seq(5,-5,length.out=19)),...,convergence=1e-4, 
                       weights.obs=1, check.positive = TRUE, print.progress=FALSE, ngroup = 5, groups = NULL)

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘svmpath/libs/svmpath.so’:
  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 the system RNG.
It is good practice to use registered native symbols 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.
completeCol: no visible global function definition for ‘colors’
completeCol: no visible global function definition for ‘col2rgb’
completeCol: no visible global function definition for ‘palette’
Undefined global functions or variables:
  col2rgb colors palette
Consider adding
  importFrom("grDevices", "col2rgb", "colors", "palette")
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.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘amap’ ‘gplots’ ‘impute’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘MASS’ ‘amap’ ‘gplots’ ‘impute’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'prince.plot.Rd':
  \examples lines wider than 100 characters:
     ## patient annotations as a data.frame, annotations should be numbers and factors but not characters.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
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').
FECorr: no visible global function definition for ‘is’
FECorr: no visible global function definition for ‘write.csv’
FECorr: no visible global function definition for ‘aggregate’
FECorr: no visible global function definition for ‘lm’
FECorr: no visible global function definition for ‘nlm’
eFBA_gene: no visible global function definition for ‘is’
eFBA_gene: no visible global function definition for ‘as’
eFBA_rxn : adjustTol: no visible global function definition for ‘is’
eFBA_rxn: no visible global function definition for ‘is’
eFBA_rxn: no visible global function definition for ‘as’
findFluxGeneExpr: no visible global function definition for ‘as’
findMDCFlux: no visible global function definition for ‘is’
findMDCFlux: no visible global function definition for ‘as’
gene2Rule: no visible global function definition for ‘is’
Undefined global functions or variables:
  aggregate as is lm nlm write.csv
Consider adding
  importFrom("methods", "as", "is")
  importFrom("stats", "aggregate", "lm", "nlm")
  importFrom("utils", "write.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘symbolicDA/libs/symbolicDA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
integrate.polynomial : f: no visible global function definition for
  ‘dmvnorm’
Undefined global functions or variables:
  dmvnorm
File ‘synchronicity/libs/synchronicity.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package in Depends field not imported from: ‘fields’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cwt_fw: no visible global function definition for ‘fft’
cwt_iw: no visible global function definition for ‘fft’
est_riskshrink_thresh: no visible global function definition for
  ‘median’
Undefined global functions or variables:
  fft median
Consider adding
  importFrom("stats", "fft", "median")
to your NAMESPACE file.
File ‘SynchWave/libs/SynchWave.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
ProgressBAR: no visible global function definition for ‘txtProgressBar’
ProgressBAR: no visible global function definition for
  ‘setTxtProgressBar’
cor.matrix: no visible global function definition for ‘cor’
cor.matrix.partial: no visible global function definition for ‘cor’
optimal: no visible global function definition for ‘combn’
optimal: no visible global function definition for ‘cor’
Undefined global functions or variables:
  combn cor setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "cor")
  importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘RCurl’ ‘RJSONIO’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'available_ranges.Rd':
  \usage lines wider than 90 characters:
       available_ranges(authority = "ensembl", species = "Homo sapiens", domain = "hgnc_symbol")

Rd file 'synergizer.Rd':
  \usage lines wider than 90 characters:
       synergizer(authority = "ensembl", species = "Homo sapiens", domain = "hgnc_symbol", range = "entrezgene", ids = NULL, file = NULL)
  \examples lines wider than 100 characters:
     symbols.ids <- synergizer( authority = "ensembl", species = "Homo sapiens", domain="affy_hg_u95av2", range="hgnc_symbol",ids=c("1939_at ... [TRUNCATED]
     entrez.ids <- synergizer( authority = "ensembl", species = "Homo sapiens", domain="hgnc_symbol", range="entrezgene",ids=c("snph", "pja1 ... [TRUNCATED]

These lines will be truncated in the PDF 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.
Namespaces with empty importFrom:
  ‘Rcpp’ ‘methods’
File ‘synlik/libs/synlik.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.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.
Found the following apparent S3 methods exported but not registered:
  plot.tabu summary.tabu
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.tabu: no visible global function definition for ‘image’
plot.tabu: no visible global function definition for ‘gray’
plot.tabu: no visible global function definition for ‘par’
plot.tabu: no visible global function definition for ‘layout’
plot.tabu: no visible global function definition for ‘plot’
Undefined global functions or variables:
  gray image layout par plot
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "image", "layout", "par", "plot")
to your NAMESPACE file.
File ‘tagcloud/libs/tagcloud.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
File ‘TAQMNGR/libs/TAQMNGR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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.
Found the following apparent S3 methods exported but not registered:
  as.matrix.by stack.list
See section ‘Registering S3 methods’ 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 ‘tau/libs/tau.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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:
  end.TawnyPortfolio start.TawnyPortfolio
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
end.TawnyPortfolio: no visible global function definition for ‘end’
start.TawnyPortfolio: no visible global function definition for ‘start’
Undefined global functions or variables:
  end start
Consider adding
  importFrom("stats", "end", "start")
to your NAMESPACE file.
File ‘tbart/libs/tbart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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.
File ‘tclust/libs/tclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
makeCircles: no visible global function definition for ‘quantile’
targetDiagram: no visible global function definition for ‘as.formula’
targetDiagram: no visible global function definition for ‘modifyList’
targetDiagram: no visible global function definition for ‘extendrange’
tdStats : sdo: no visible global function definition for ‘sd’
tdStats : sdm: no visible global function definition for ‘sd’
tdStats : r2: no visible global function definition for ‘cor’
Undefined global functions or variables:
  as.formula cor extendrange modifyList quantile sd
Consider adding
  importFrom("grDevices", "extendrange")
  importFrom("stats", "as.formula", "cor", "quantile", "sd")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
tdt.quad: no visible global function definition for ‘runif’
tdt.rr: no visible global function definition for ‘pf’
tdt.rr: no visible global function definition for ‘qbeta’
Undefined global functions or variables:
  pf qbeta runif
Consider adding
  importFrom("stats", "pf", "qbeta", "runif")
to your NAMESPACE file.
File ‘tdthap/libs/tdthap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
E.2SI: no visible binding for global variable ‘var’
E.2SI: no visible global function definition for ‘var’
E.BE: no visible global function definition for ‘var’
E.Beta: no visible global function definition for ‘var’
E.PO: no visible global function definition for ‘var’
E.PPS: no visible global function definition for ‘var’
E.SI: no visible global function definition for ‘var’
E.STPPS: no visible global function definition for ‘var’
E.STSI: no visible global function definition for ‘var’
E.STpiPS: no visible global function definition for ‘var’
E.SY: no visible global function definition for ‘var’
E.WR: no visible global function definition for ‘var’
E.piPS: no visible global function definition for ‘var’
GREG.SI: no visible global function definition for ‘var’
S.BE: no visible global function definition for ‘runif’
S.PO: no visible global function definition for ‘runif’
S.PPS: no visible global function definition for ‘runif’
S.SI: no visible global function definition for ‘runif’
S.STPPS: no visible global function definition for ‘runif’
S.WR: no visible global function definition for ‘rbinom’
S.piPS: no visible global function definition for ‘runif’
p.WR: no visible global function definition for ‘dmultinom’
Undefined global functions or variables:
  dmultinom rbinom runif var
Consider adding
  importFrom("stats", "dmultinom", "rbinom", "runif", "var")
to your NAMESPACE file.
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.
File ‘teigen/libs/teigen.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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:
  ^.tensor as.contravariate.character as.covariate.character
  as.tensor.default as.tensor.tensor is.contravariate.character
  is.contravariate.numeric is.contravariate.tensor
  is.covariate.character is.covariate.numeric is.covariate.tensor
  mean.tensor |.tensor
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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
File ‘tergm/libs/tergm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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.df_curves plot.dyntermstrc_nss plot.dyntermstrc_param
  plot.dyntermstrc_yields plot.error plot.fwr_curves plot.ir_curve
  plot.s_curves plot.spot_curves plot.spsearch plot.termstrc_cs
  plot.termstrc_nss plot.zeroyields print.couponbonds
  print.dyncouponbonds print.dyntermstrc_nss print.dyntermstrc_yields
  print.summary.dyntermstrc_nss print.summary.dyntermstrc_param
  print.summary.dyntermstrc_yields print.summary.termstrc_cs
  print.summary.termstrc_nss print.termstrc_cs print.termstrc_nss
  print.zeroyields summary.dyntermstrc_nss summary.dyntermstrc_param
  summary.dyntermstrc_yields summary.termstrc_cs summary.termstrc_nss
  summary.zeroyields
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘termstrc/libs/termstrc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Depends: includes the non-default packages:
  ‘grid’ ‘quadprog’ ‘maps’ ‘maptools’ ‘mapdata’ ‘dichromat’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  ‘dichromat’ ‘grid’ ‘mapdata’ ‘maps’ ‘maptools’ ‘quadprog’
  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.tverify tverify.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘tesseract/libs/tesseract.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘boot’ ‘survrec’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘testthat/libs/testthat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.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.
File ‘text2vec/libs/text2vec.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ 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 use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.dea_create_model: no visible global function definition for
  ‘getSrcFilename’
.wMean: no visible global function definition for ‘weighted.mean’
Undefined global functions or variables:
  getSrcFilename weighted.mean
Consider adding
  importFrom("stats", "weighted.mean")
  importFrom("utils", "getSrcFilename")
to your NAMESPACE file.
transfer: no visible global function definition for ‘rgamma’
transfer: no visible global function definition for ‘rnorm’
transfer: no visible global function definition for ‘rnbinom’
transfer: no visible global function definition for ‘rpois’
transfer: no visible global function definition for ‘rbinom’
transfer: no visible global function definition for ‘runif’
plot,transfer: no visible global function definition for ‘barplot’
plot,transfer: no visible global function definition for ‘axis’
plot,transfer: no visible global function definition for ‘par’
plot,transfer: no visible global function definition for ‘hist’
Undefined global functions or variables:
  axis barplot hist par rbinom rgamma rnbinom rnorm rpois runif
Consider adding
  importFrom("graphics", "axis", "barplot", "hist", "par")
  importFrom("stats", "rbinom", "rgamma", "rnbinom", "rnorm", "rpois",
             "runif")
to your NAMESPACE file.
File ‘TFMPvalue/libs/TFMPvalue.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 use registered native symbols 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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘zoo’ which was already attached by Depends.
  Please remove these calls from your code.
Calls with DUP:
   .C("zstat_pathway_perm", as.double(g), as.integer(m), as.integer(length(m)), 
       as.double(aff), as.integer(length(aff)), as.double(thresh), 
       as.integer(gsubsetmatrix), as.integer(nrow(gsubsetmatrix)), 
       as.integer(use_sign), as.integer(use_weight), as.integer(strategy), 
       as.integer(nperm), ret_pvalue, DUP = FALSE)
   .C("zstat_perm", as.double(g), as.integer(m), as.integer(length(m)), 
       as.double(aff), as.integer(length(aff)), as.double(thresh), 
       as.integer(gsubsetmatrix), as.integer(nrow(gsubsetmatrix)), 
       as.integer(use_sign), as.integer(use_weight), as.integer(strategy), 
       as.integer(nperm), ret_pvalue, DUP = FALSE)
DUP is no longer supported and will be ignored.
File ‘thgenetics/libs/thgenetics.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.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').
read_json: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Files in the 'vignettes' directory newer than same file in 'inst/doc':
  ‘introduction-to-tidyjson.Rmd’
Running ‘test-all.r’ [0s/0s]
Running the tests in ‘tests/test-all.r’ failed.
Complete output:
  > library(testthat)
  > test_check("jplyr")
  Loading required package: jplyr
  Error in loadNamespace(name) : there is no package called 'jplyr'
  Calls: test_check ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  In addition: Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'jplyr'
  Execution halted
File ‘tidyr/libs/tidyr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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 use registered native symbols 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.tight.clust
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.tight.clust: no visible global function definition for ‘hclust’
plot.tight.clust: no visible global function definition for ‘dist’
plot.tight.clust: no visible global function definition for ‘image’
plot.tight.clust: no visible global function definition for
  ‘colorRampPalette’
plot.tight.clust: no visible global function definition for ‘axis’
plot.tight.clust: no visible global function definition for ‘lines’
tight.clust : find.candidates : kmeans.classify: no visible global
  function definition for ‘kmeans’
write.tight.clust: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  axis colorRampPalette dist hclust image kmeans lines write.table
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "image", "lines")
  importFrom("stats", "dist", "hclust", "kmeans")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Rd file 'tight.clust.Rd':
  \usage lines wider than 90 characters:
     tight.clust(x, target, k.min, alpha = 0.1, beta = 0.6, top.can = 7, seq.num = 2, resamp.num = 10, samp.p = 0.7, nstart = 1, remain.p =  ... [TRUNCATED]

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.viterbiTrainingEmission,contHMM-list-list: no visible global function
  definition for ‘var’
sampleObs,tDist-numeric: no visible global function definition for ‘rt’
Undefined global functions or variables:
  rt var
Consider adding
  importFrom("stats", "rt", "var")
to your NAMESPACE file.
File ‘tileHMM/libs/tileHMM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘ggplot2’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘microbenchmark’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
determine_replications: no visible global function definition for
  ‘microbenchmark’
do_timeit: no visible global function definition for ‘Rprof’
do_timeit: no visible global function definition for ‘summaryRprof’
mean.timeit: no visible global function definition for ‘aggregate’
plot.timeit: no visible global function definition for ‘ggplot’
plot.timeit: no visible global function definition for ‘aes’
plot.timeit: no visible global function definition for ‘geom_boxplot’
plot.timeit: no visible global function definition for ‘geom_point’
plot.timeit: no visible global function definition for ‘xlab’
plot.timeit: no visible global function definition for ‘ylab’
plot.timeit: no visible global function definition for ‘ggtitle’
plot.timeit: no visible global function definition for ‘coord_flip’
timeit: no visible binding for global variable ‘median’
Undefined global functions or variables:
  Rprof aes aggregate coord_flip geom_boxplot geom_point ggplot ggtitle
  median microbenchmark summaryRprof xlab ylab
Consider adding
  importFrom("stats", "aggregate", "median")
  importFrom("utils", "Rprof", "summaryRprof")
to your NAMESPACE file.
'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 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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
generatelatencies: no visible binding for global variable ‘allNames’
generatetimedeltas: no visible global function definition for ‘head’
generatetimedeltas: no visible global function definition for ‘tail’
generatevertexedgelist : <anonymous>: no visible global function
  definition for ‘head’
generatevertexedgelist : <anonymous>: no visible global function
  definition for ‘tail’
plotnetworkslices: no visible global function definition for ‘par’
plotnetworkslices: no visible global function definition for ‘text’
plottanet: no visible global function definition for ‘plot’
plottonet: no visible global function definition for ‘plot’
shortesttimepath : <anonymous>: no visible global function definition
  for ‘tail’
Undefined global functions or variables:
  allNames head par plot tail text
Consider adding
  importFrom("graphics", "par", "plot", "text")
  importFrom("methods", "allNames")
  importFrom("utils", "head", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'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
File ‘timereg/libs/timereg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
createHstore.ts: no visible global function definition for ‘time’
exploreDb : <anonymous>: no visible global function definition for
  ‘plot’
exportTsList : <anonymous>: no visible global function definition for
  ‘time’
exportTsList: no visible global function definition for ‘write.csv2’
importTsList: no visible global function definition for ‘read.csv2’
importTsList : <anonymous>: no visible global function definition for
  ‘as.ts’
plot.tslist: no visible global function definition for ‘plot’
plot.tslist : <anonymous>: no visible global function definition for
  ‘time’
plot.tslist: no visible global function definition for ‘par’
plot.tslist: no visible global function definition for ‘legend’
readTimeSeries : <anonymous>: no visible global function definition for
  ‘ts’
resolveOverlap: no visible global function definition for ‘is.ts’
resolveOverlap: no visible global function definition for ‘frequency’
resolveOverlap: no visible global function definition for ‘time’
resolveOverlap: no visible global function definition for ‘ts’
storeTimeSeries: no visible binding for global variable ‘frequency’
zooLikeDateConvert: no visible global function definition for ‘time’
zooLikeDateConvert: no visible global function definition for
  ‘frequency’
zooLikeDateConvert: no visible global function definition for ‘cycle’
Undefined global functions or variables:
  as.ts cycle frequency is.ts legend par plot read.csv2 time ts
  write.csv2
Consider adding
  importFrom("graphics", "legend", "par", "plot")
  importFrom("stats", "as.ts", "cycle", "frequency", "is.ts", "time",
             "ts")
  importFrom("utils", "read.csv2", "write.csv2")
to your NAMESPACE file.
File ‘timetools/libs/timetools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
File ‘tis/libs/tis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘rgl’ ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'par3dsave.Rd':
  \usage lines wider than 90 characters:
     par3dsave(params = c("userMatrix", "scale", "zoom", "FOV"), times = FALSE, dev = rgl.cur())

These lines will be truncated in the PDF 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.
.my.tkdev: no visible global function definition for ‘X11’
tkpersp : draw: no visible global function definition for ‘par’
tkpersp : draw: no visible global function definition for ‘persp’
Undefined global functions or variables:
  X11 par persp
Consider adding
  importFrom("grDevices", "X11")
  importFrom("graphics", "par", "persp")
to your NAMESPACE file.
File ‘tkrplot/libs/tkrplot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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.
File ‘TLMoments/libs/TLMoments.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 ‘tm/libs/tm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
'library' or 'require' calls in package code:
  ‘TeachingDemos’ ‘ash’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
File ‘TP.idm/libs/TP.idm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as.data.frame.survTP
> ### Title: as.data.frame method for a survTP object
> ### Aliases: as.data.frame.survTP
> ### Keywords: manip methods survival
> 
> ### ** Examples
> 
> # Example for the "TPmsm" format
> weiTP <- dgpTP(n=100, corr=1, dist="weibull", dist.par=c(2, 7, 2, 7),
+ model.cens="exponential", cens.par = 6, state2.prob=0.6)
*** invalid %N$ use detected ***
Aborted
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.
File ‘TraMineRextras/libs/TraMineRextras.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DrawViterbiTree
> ### Title: Arranges a Viterbi tree
> ### Aliases: DrawViterbiTree
> ### Keywords: misc
> 
> ### ** Examples
> 
> ## Fit a continous treeHFM ## 
> nHStates = 2;
> ########create observation sequences########
> obs1 <- rbind(runif(10,0,1),runif(10,0,1))
> obs2 <- rbind(runif(8,0,1),runif(8,0,1))
> data=list()
> data[[1]]=obs1
> data[[2]]=obs2
> ######### create guesses for gaussian covariance matrix and means #########
> mc2 <- Mclust(t(cbind(obs1,obs2)), G=2)
> muInit=mc2$parameters$mean;
> SigmaInit=mc2$parameters$variance$sigma
> #########create tree topology####################################
> nodeIndices1=cbind(c(0,1,2,3,3,4,5,6,7,8),c(1,2,3,4,5,6,7,8,9,10));
> nodeIndices2=cbind(c(0,1,2,3,4,4,5,6),c(1,2,3,4,5,6,7,8));
> dataNodeIndices=list()
> dataNodeIndices[[1]]=nodeIndices1;
> dataNodeIndices[[2]]=nodeIndices2;
> ######### create guesses for prior and transition matrices#########
> prior1=array(1,nHStates);
> priorInit = array(1,nHStates)/nHStates;
> transmatInit = matrix(1,nHStates,nHStates)*(1/nHStates);
> transInitDiv= matrix(1,nHStates,nHStates*nHStates)*(1/(nHStates*nHStates))
> #
> hfm=HFMfit(data,nHStates,dataNodeIndices,priorInit,transmatInit,transInitDiv,'c',
+ SigmaInit=SigmaInit, muInit=muInit);

 *** caught segfault ***
address 0x8, cause 'memory not mapped'

Traceback:
 1: .Call("RWrapperBM", priorInit, transmatInit, transInitDiv, emissionProb,     data, nodeIndices, parents, summationIndices, indicesXD,     type, stateIndicesSingle, nHStates, nDStates, nObs, dimData,     nEStates, SigmaInit, muInit)
 2: HFMfit(data, nHStates, dataNodeIndices, priorInit, transmatInit,     transInitDiv, "c", SigmaInit = SigmaInit, muInit = muInit)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
mytree.asymmetric.age: no visible global function definition for
  ‘capture.output’
mytree.asymmetric.age: no visible global function definition for
  ‘collapse.singles’
mytree.asymmetric.age: no visible global function definition for
  ‘drop.fossil’
mytree.asymmetric.taxa: no visible global function definition for
  ‘capture.output’
mytree.asymmetric.taxa: no visible global function definition for
  ‘collapse.singles’
mytree.asymmetric.taxa: no visible global function definition for
  ‘drop.fossil’
mytree.symmetric.age: no visible global function definition for
  ‘capture.output’
mytree.symmetric.age: no visible global function definition for
  ‘collapse.singles’
mytree.symmetric.age: no visible global function definition for
  ‘drop.fossil’
mytree.symmetric.taxa: no visible global function definition for
  ‘capture.output’
mytree.symmetric.taxa: no visible global function definition for
  ‘collapse.singles’
mytree.symmetric.taxa: no visible global function definition for
  ‘drop.fossil’
Undefined global functions or variables:
  capture.output collapse.singles drop.fossil
Consider adding
  importFrom("utils", "capture.output")
to your NAMESPACE file.
File ‘treethresh/libs/treethresh.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
'library' or 'require' call to ‘fpc’ 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.tkm print.tkm
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.tkm: no visible global function definition for ‘plotcluster’
plot.tkm: no visible global function definition for ‘plot’
plot.tkm: no visible global function definition for ‘points’
plot.tkm: no visible global function definition for ‘lines’
plot.tkm: no visible global function definition for ‘discrcoord’
Undefined global functions or variables:
  discrcoord lines plot plotcluster points
Consider adding
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
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 use registered native symbols 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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  Ops.VectorAddr print.VectorAddr update.VectorAddr
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘TRSbook/libs/TRSbook.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
binary.hess: no visible global function definition for ‘as’
trust.optim: 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 ‘trustOptim/libs/trustOptim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard file/directory found at top level:
  ‘changes’
'library' or 'require' calls to packages already attached by Depends:
  ‘leaps’ ‘locfit’ ‘mgcv’
  Please remove these calls from your code.
':::' calls which should be '::':
  ‘stats:::ARMAacf’ ‘stats:::acf’ ‘stats:::arima’
  See the note in ?`:::` about the use of this operator.
Found the following apparent S3 methods exported but not registered:
  fitted.Arima plot.Arima plot.armasubsets predict.TAR rstandard.Arima
  summary.armasubsets tsdiag.Arima tsdiag.TAR
See section ‘Registering S3 methods’ 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.
File ‘tsBSS/libs/tsBSS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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.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.
Running ‘test_code.r’ [0s/0s]
Running the tests in ‘tests/test_code.r’ failed.
Last 13 lines of output:
  +     scoring(fit)
  +   }
  +   if(interv){
  +     interv_test(fit, tau=floor(n/2), delta=0.8, external=FALSE, est_interv=TRUE, ...)
  +     interv_detect(fit, taus=floor(0.45*n):ceiling(0.55*n), delta=0.8, B=3, ...)
  +     interv_multiple(fit, taus=floor(0.45*n):ceiling(0.55*n), deltas=c(0,1), B=3, final.control_bootstrap=NULL, ...)
  +   }
  +   return(TRUE)
  + }
  > 
  > checkfit(model=list(past_obs=1, past_mean=1), param=list(intercept=2, past_obs=0.4, past_mean=0.3), startestims=TRUE, extended=TRUE)
  Error in tsglm.sim(n = n, param = param, model = model, xreg = xreg, link = link,  : 
    could not find function "tsglm.sim"
  Calls: checkfit
  Execution halted
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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
File ‘TSHRC/libs/TSHRC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
arimainterp: no visible binding for global variable ‘head’
arimainterp: no visible binding for global variable ‘na.omit’
arimainterp: no visible binding for global variable ‘tail’
arimapar: no visible binding for global variable ‘na.omit’
arimapar: no visible global function definition for ‘tail’
arimapred: no visible binding for global variable ‘na.omit’
arimapred: no visible global function definition for ‘predict’
marimapar: no visible binding for global variable ‘na.omit’
marimapred: no visible binding for global variable ‘na.omit’
plotarimapred: no visible global function definition for ‘plot’
plotarimapred: no visible global function definition for ‘lines’
Undefined global functions or variables:
  head lines na.omit plot predict tail
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "na.omit", "predict")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
TSgetSQL: no visible global function definition for ‘ts’
TSputSQL: no visible global function definition for ‘is.ts’
TSputSQL: no visible global function definition for ‘frequency’
TSputSQL: no visible global function definition for ‘time’
TSquery: no visible global function definition for ‘ts’
Undefined global functions or variables:
  frequency is.ts time ts
Consider adding
  importFrom("stats", "frequency", "is.ts", "time", "ts")
to your NAMESPACE file.
TT.GS : TT.GS.sp: no visible global function definition for ‘qt’
TT.GS : TT.GS.sp: no visible global function definition for ‘runif’
TT.GS : TT.GS.sp: no visible global function definition for ‘pt’
TT.moment: no visible global function definition for ‘dt’
TT.moment: no visible global function definition for ‘pt’
Undefined global functions or variables:
  dt pt qt runif
Consider adding
  importFrom("stats", "dt", "pt", "qt", "runif")
to your NAMESPACE file.
File ‘TTR/libs/TTR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Found the following apparent S3 methods exported but not registered:
  TukeyC.aov TukeyC.aovlist TukeyC.default TukeyC.nest TukeyC.nest.aov
  TukeyC.nest.aov TukeyC.nest.aovlist TukeyC.nest.aovlist
  TukeyC.nest.default TukeyC.nest.default plot.TukeyC summary.TukeyC
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
http.connection: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘gsl’ ‘igraph’ ‘snowfall’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  predict.TuneParetoModel print.TuneParetoClassifier
  print.TuneParetoModel print.TuneParetoResult
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘TunePareto/libs/TunePareto.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
accelerate: no visible global function definition for ‘modifyList’
boxplot.turbosim: no visible global function definition for ‘par’
boxplot.turbosim: no visible global function definition for ‘axis’
boxplot.turbosim: no visible global function definition for ‘mtext’
dataprof.turbosim: no visible global function definition for ‘quantile’
dataprof.turbosim: no visible global function definition for ‘par’
dataprof.turbosim: no visible global function definition for ‘plot’
dataprof.turbosim: no visible global function definition for ‘lines’
dataprof.turbosim: no visible global function definition for ‘segments’
dataprof.turbosim: no visible global function definition for ‘legend’
line.search: no visible global function definition for ‘optimize’
pairs.turbosim: no visible global function definition for ‘par’
pairs.turbosim: no visible global function definition for ‘plot’
pairs.turbosim: no visible global function definition for ‘legend’
pairs.turbosim: no visible global function definition for ‘axis’
pairs.turbosim: no visible global function definition for ‘title’
pairs.turbosim: no visible global function definition for ‘coef’
pairs.turbosim: no visible global function definition for ‘abline’
pairs.turbosim: no visible global function definition for ‘text’
plot.turbo: no visible global function definition for ‘plot’
plot.turbo: no visible global function definition for ‘lines’
plot.turbo: no visible global function definition for ‘legend’
turboSim: no visible binding for global variable ‘par’
turboem: no visible global function definition for ‘modifyList’
Undefined global functions or variables:
  abline axis coef legend lines modifyList mtext optimize par plot
  quantile segments text title
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "mtext",
             "par", "plot", "segments", "text", "title")
  importFrom("stats", "coef", "optimize", "quantile")
  importFrom("utils", "modifyList")
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.
turtle_param: no visible global function definition for ‘col2rgb’
Undefined global functions or variables:
  col2rgb
Consider adding
  importFrom("grDevices", "col2rgb")
to your NAMESPACE file.
File ‘TUWmodel/libs/TUWmodel.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols 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 use registered native symbols 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 use registered native symbols 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.
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(ubeR)
  > 
  > test_check("ubeR")
  1. Failure: raise error on fail to geocode (@test_utils.R#4) -------------------
  geocode("The Old Biscuit Mill") did not throw an error.
  
  
  testthat results ================================================================
  OK: 8 SKIPPED: 0 FAILED: 1
  1. Failure: raise error on fail to geocode (@test_utils.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘UBL/libs/UBL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘udunits2/libs/udunits2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Rd file 'dataItemExplorer.Rd':
  \usage lines wider than 90 characters:
       apiurl = "http://marketinformation.natgrid.co.uk/MIPIws-public/public/publicwebservice.asmx")

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

It is good practice to use registered native symbols 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.
File ‘unfoldr/libs/unfoldr.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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.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 use registered native symbols 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 ‘uniqueAtomMat/libs/uniqueAtomMat.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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:
  +.census +.count plot.census plot.count plot.preston print.preston
  print.summary.count summary.census summary.count
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Found the following apparent S3 methods exported but not registered:
  plot.upclassfit print.upclassfit summary.upclassfit
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.upclassfit: no visible global function definition for ‘frame’
plot.upclassfit: no visible global function definition for ‘par’
plot.upclassfit: no visible global function definition for ‘axis’
plot.upclassfit: no visible global function definition for ‘matplot’
plot.upclassfit: no visible global function definition for ‘legend’
plot.upclassfit: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis frame legend matplot par title
Consider adding
  importFrom("graphics", "axis", "frame", "legend", "matplot", "par",
             "title")
to your NAMESPACE file.
UPMASKfile: no visible global function definition for ‘read.table’
UPMASKfile: no visible global function definition for ‘write.table’
analyse_randomKde2d: no visible global function definition for ‘hist’
analyse_randomKde2d: no visible global function definition for ‘lines’
analyse_randomKde2d_AutoCalibrated: no visible global function
  definition for ‘hist’
analyse_randomKde2d_AutoCalibrated: no visible global function
  definition for ‘lines’
create_randomKde2d: no visible global function definition for ‘image’
create_randomKde2d: no visible global function definition for ‘points’
getStarsAtHighestDensityRegion: no visible global function definition
  for ‘rgb’
getStarsAtHighestDensityRegion: no visible global function definition
  for ‘dev.new’
getStarsAtHighestDensityRegion: no visible global function definition
  for ‘plot’
getStarsAtHighestDensityRegion: no visible global function definition
  for ‘image’
getStarsAtHighestDensityRegion: no visible global function definition
  for ‘contour’
getStarsAtHighestDensityRegion: no visible global function definition
  for ‘points’
innerLoop: no visible global function definition for ‘dev.new’
innerLoop: no visible global function definition for ‘par’
innerLoop: no visible global function definition for ‘pairs’
innerLoop: no visible global function definition for ‘rainbow’
kde2dForSubset: no visible global function definition for ‘image’
kde2dForSubset: no visible global function definition for ‘points’
Undefined global functions or variables:
  contour dev.new hist image lines pairs par plot points rainbow
  read.table rgb write.table
Consider adding
  importFrom("grDevices", "dev.new", "rainbow", "rgb")
  importFrom("graphics", "contour", "hist", "image", "lines", "pairs",
             "par", "plot", "points")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
File ‘urca/libs/urca.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols 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'.
'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 use registered native symbols 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 the system RNG.
It is good practice to use registered native symbols 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.
File ‘V8/libs/V8.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘foreach’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘foreach’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
constant.post.9mo: no visible global function definition for ‘pexp’
ll.coverage.optim.const.post.9m: no visible global function definition
  for ‘dexp’
make.sample.pop: no visible global function definition for ‘runif’
mcmc.converge: no visible global function definition for ‘par’
mcmc.converge: no visible global function definition for ‘plot’
mcmc.converge: no visible global function definition for ‘points’
mcmc.converge: no visible global function definition for ‘density’
mcmc.converge: no visible global function definition for ‘lines’
mcmc.converge : <anonymous>: no visible global function definition for
  ‘sd’
mcmc.estimate : run.chain: no visible global function definition for
  ‘dexp’
mcmc.estimate : run.chain: no visible global function definition for
  ‘rnorm’
mcmc.estimate : run.chain: no visible global function definition for
  ‘runif’
mcmc.estimate : run.chain: no visible global function definition for
  ‘par’
mcmc.estimate : run.chain: no visible global function definition for
  ‘plot’
mcmc.estimate: no visible global function definition for ‘%dopar%’
mcmc.estimate: no visible global function definition for ‘foreach’
sim.n.vacc.sample.pop : <anonymous>: no visible global function
  definition for ‘runif’
vaccinate.sample.pop: no visible global function definition for ‘runif’
Undefined global functions or variables:
  %dopar% density dexp foreach lines par pexp plot points rnorm runif
  sd
Consider adding
  importFrom("graphics", "lines", "par", "plot", "points")
  importFrom("stats", "density", "dexp", "pexp", "rnorm", "runif", "sd")
to your NAMESPACE file.
Running ‘coverageTest.r’ [0s/0s]
Running the tests in ‘tests/coverageTest.r’ failed.
Last 13 lines of output:
  > #*  
  > #*  $Id: coverageTest.r 378 2012-01-27 02:35:09Z ken $
  > #*  ----------------------------------------------------------------------------
  > 
  > 
  > # TBD: Add file header
  > # TBD: Do I need some 'library( pkg )' or 'source( file )' calls here???
  > 
  > 
  > # source( "../tests/testUtils.r" )
  > source( getTestPaths("vacem","tests/testUtils.r") )
  Error in getTestPaths("vacem", "tests/testUtils.r") : 
    could not find function "getTestPaths"
  Calls: source
  Execution halted
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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘demo.cc.R’, ‘demo.cd.R’, ‘demo.cfw.R’, ‘demo.cytokine.R’,
    ‘demo.leukemia.R’, ‘demo.qtl.R’
Package has no Sweave vignette sources and no VignetteBuilder field.
varComp.fit: no visible binding for global variable ‘combn’
varComp.fit: no visible global function definition for ‘plot’
varComp.fit: no visible global function definition for ‘abline’
wchibarsq: no visible global function definition for ‘combn’
Undefined global functions or variables:
  abline combn plot
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("utils", "combn")
to your NAMESPACE file.
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.
File ‘VariABEL/libs/VariABEL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard file/directory found at top level:
  ‘Todo’
withoutmixture,VSLCMresultsContinuous: no visible global function
  definition for ‘sd’
withoutmixture,VSLCMresultsContinuous: no visible global function
  definition for ‘dnorm’
Undefined global functions or variables:
  dnorm sd
Consider adding
  importFrom("stats", "dnorm", "sd")
to your NAMESPACE file.
File ‘VarSelLCM/libs/VarSelLCM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘MASS’ ‘strucchange’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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 use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols 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 use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
vsetdiff : <anonymous>: no visible global function definition for
  ‘head’
Undefined global functions or variables:
  head
Consider adding
  importFrom("utils", "head")
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.
Found the following assignments to the global environment:
File ‘vegan/R/orditkplot.R’:
  assign(dumpName, xy, envir = .GlobalEnv)
  assign(dumpName, xy, envir = .GlobalEnv)
File ‘vegan/libs/vegan.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:

  Warning: 'lmerTest::lsmeans' is deprecated.
  Warning: 'lmerTest::lsmeans' is deprecated.
  Warning: 'lmerTest::lsmeans' is deprecated.
  Warning: 'lmerTest::lsmeans' is deprecated.
  Warning: 'lmerTest::lsmeans' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
File ‘VGAM/libs/VGAM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols 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.
Malformed Title field: should not end in a period.
License components which are templates and need '+ file LICENSE':
  MIT License
visualize.continuous: no visible global function definition for ‘plot’
visualize.continuous: no visible global function definition for
  ‘polygon’
visualize.continuous: no visible global function definition for ‘axis’
visualize.continuous: no visible global function definition for ‘mtext’
visualize.continuous: no visible global function definition for ‘title’
visualize.discrete: no visible global function definition for ‘barplot’
visualize.discrete: no visible global function definition for ‘axis’
visualize.discrete: no visible global function definition for ‘mtext’
visualize.discrete: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis barplot mtext plot polygon title
Consider adding
  importFrom("graphics", "axis", "barplot", "mtext", "plot", "polygon",
             "title")
to your NAMESPACE file.
File ‘vita/libs/vita.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
add.spread.vowelplot: no visible global function definition for
  ‘points’
add.spread.vowelplot: no visible binding for global variable ‘mtext’
add.spread.vowelplot: no visible global function definition for ‘lines’
add.spread.vowelplot: no visible global function definition for
  ‘prcomp’
add.spread.vowelplot: no visible global function definition for
  ‘arrows’
add.spread.vowelplot: no visible global function definition for
  ‘legend’
add.spread.vowelplot: no visible global function definition for ‘text’
add.vowelplot: no visible global function definition for ‘points’
add.vowelplot: no visible binding for global variable ‘mtext’
add.vowelplot: no visible global function definition for ‘arrows’
add.vowelplot: no visible global function definition for ‘text’
compute.medians: no visible global function definition for ‘median’
compute.sds: no visible global function definition for ‘sd’
load.vowels: no visible global function definition for ‘read.table’
norm.lobanov: no visible global function definition for ‘sd’
vowelplot: no visible global function definition for ‘plot’
vowelplot: no visible global function definition for ‘legend’
vowelplot: no visible global function definition for ‘arrows’
vowelplot: no visible global function definition for ‘text’
Undefined global functions or variables:
  arrows legend lines median mtext plot points prcomp read.table sd
  text
Consider adding
  importFrom("graphics", "arrows", "legend", "lines", "mtext", "plot",
             "points", "text")
  importFrom("stats", "median", "prcomp", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'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.
File ‘VPdtw/libs/VPdtw.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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 the system RNG.
It is good practice to use registered native symbols 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 ‘walkr/libs/walkr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Loading required package: ggplot2
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running ‘texi2dvi’ on ‘walkr.tex’ failed.
LaTeX errors:
! Undefined control sequence.
T1+zi4 ->zifour@spc 
                    
l.879 \section{Using \texttt{walkr}}
                                    
! Undefined control sequence.
T1+zi4 ->zifour@spc 
                    
l.910 \hlstd{A} \hlkwb{<-} \hlkwd{matrix}
                                         \hlstd{(}\hlnum{1}\hlstd{,} \hlkwc{...
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘wand/libs/wand.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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.
Found the following apparent S3 methods exported but not registered:
  plot.wb
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.wb: no visible global function definition for ‘plot’
plot.wb: no visible global function definition for ‘lines’
power.sum: no visible global function definition for ‘plot’
power.sum: no visible global function definition for ‘lines’
test.data: no visible global function definition for ‘var’
test.data: no visible global function definition for ‘rnorm’
test.data: no visible global function definition for ‘plot’
test.data: no visible global function definition for ‘lines’
wave.band: no visible binding for global variable ‘var’
wave.band: no visible global function definition for ‘pnorm’
wave.band: no visible global function definition for ‘qnorm’
wave.band: no visible global function definition for ‘plot’
wave.band: no visible global function definition for ‘lines’
wb.johnson.lims: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  lines plot pnorm qnorm rnorm var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "pnorm", "qnorm", "rnorm", "var")
to your NAMESPACE file.
File ‘waveband/libs/waveband.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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.wvd summary.wvd
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'FWaveD.Rd':
  \usage lines wider than 90 characters:
     FWaveD(y, g = 1, L = 3, deg = 3, F = (log2(length(y)) - 1), thr = rep(0, log2(length(y))), SOFT = FALSE)

Rd file 'WaveD.Rd':
  \usage lines wider than 90 characters:
     WaveD(yobs, g = c(1, rep(0, (length(yobs) - 1))), MC = FALSE, SOFT = FALSE, F = find.j1(g, scale(yobs))[2], L = 3, deg = 3, eta = sqrt( ... [TRUNCATED]

Rd file 'multires.Rd':
  \usage lines wider than 90 characters:
     multires(wcUntrimmed, lowest = 3, coarse = 3, highestplot = NULL, descending = FALSE, sc = 1)

These lines will be truncated in the PDF 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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
wave.multiple.correlation: no visible global function definition for
  ‘qnorm’
Undefined global functions or variables:
  qnorm
Consider adding
  importFrom("stats", "qnorm")
to your NAMESPACE file.
Found the following 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 use registered native symbols 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 use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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:
  knots.WCE
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘wCorr/libs/wCorr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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.
Package in Depends field not imported from: ‘RJSONIO’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
WDI: no visible binding for global variable ‘WDI_data’
WDIcache: no visible global function definition for ‘fromJSON’
WDIsearch: no visible binding for global variable ‘WDI_data’
Undefined global functions or variables:
  WDI_data fromJSON
cleanAndSubsetDetailedData: no visible global function definition for
  ‘read.csv’
cleanAndSubsetObtainedData: no visible global function definition for
  ‘read.csv’
getStationCode: no visible binding for global variable
  ‘USAirportWeatherStations’
getStationCode: no visible binding for global variable ‘IntlWxStations’
getWeatherForDate: no visible global function definition for
  ‘write.csv’
Undefined global functions or variables:
  IntlWxStations USAirportWeatherStations read.csv write.csv
Consider adding
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
File ‘webp/libs/webp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Title field: should not end in a period.
Deprecated license: BSD
Non-standard file/directory found at top level:
  ‘webvis_0.0.1.tar.gz’
Found the following apparent S3 methods exported but not registered:
  +.webvis
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘webvis/R/zzz.R’:
  .onLoad calls:
    print("Welcome to the webvis pacakge.")

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

[1] "Welcome to the webvis pacakge."
render.webvis: no visible global function definition for ‘browseURL’
unfold.webvis : <anonymous>: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  browseURL runif
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "browseURL")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'plot.webvis':
  ‘plot.webvis’

S3 methods shown with full name in documentation object '"+.webvis"':
  ‘+.webvis’

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
print.palette: no visible global function definition for ‘par’
print.palette: no visible global function definition for ‘image’
print.palette: no visible global function definition for ‘rect’
print.palette: no visible global function definition for ‘rgb’
print.palette: no visible global function definition for ‘text’
wes_palette: no visible global function definition for
  ‘colorRampPalette’
Undefined global functions or variables:
  colorRampPalette image par rect rgb text
Consider adding
  importFrom("grDevices", "colorRampPalette", "rgb")
  importFrom("graphics", "image", "par", "rect", "text")
to your NAMESPACE file.
File ‘wfe/libs/wfe.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package in Depends field not imported from: ‘snpStats’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Z.value: no visible global function definition for ‘sd’
Z.value: no visible global function definition for ‘pnorm’
pairtest: no visible global function definition for ‘is’
pairtest: no visible global function definition for ‘new’
pairtest: no visible global function definition for ‘rbind2’
pairtest: no visible global function definition for ‘p.value’
pairtest: no visible global function definition for ‘single.snp.tests’
scoretest: no visible global function definition for ‘pchisq’
varplot : <anonymous>: no visible global function definition for ‘var’
varplot: no visible global function definition for ‘plot’
varplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline is new p.value pchisq plot pnorm rbind2 sd single.snp.tests
  var
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("methods", "is", "new", "rbind2")
  importFrom("stats", "pchisq", "pnorm", "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
plot.whatif: no visible global function definition for ‘na.fail’
plot.whatif : do.plot: no visible global function definition for
  ‘lines’
plot.whatif : do.plot: no visible global function definition for
  ‘lowess’
plot.whatif: no visible global function definition for ‘postscript’
plot.whatif: no visible global function definition for ‘plot’
plot.whatif: no visible global function definition for ‘dev.off’
whatif: no visible global function definition for ‘read.table’
whatif: no visible global function definition for ‘complete.cases’
whatif: no visible global function definition for ‘terms’
whatif: no visible global function definition for ‘model.matrix’
whatif: no visible global function definition for ‘model.frame’
whatif: no visible global function definition for ‘update.formula’
whatif: no visible global function definition for ‘na.omit’
whatif: no visible global function definition for ‘na.fail’
Undefined global functions or variables:
  complete.cases dev.off lines lowess model.frame model.matrix na.fail
  na.omit plot postscript read.table terms update.formula
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "complete.cases", "lowess", "model.frame",
             "model.matrix", "na.fail", "na.omit", "terms",
             "update.formula")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Files in the 'vignettes' directory newer than all files in 'inst/doc':
  ‘gk.bib’, ‘gkpubs.bib’, ‘whatif.pdf’, ‘whatif.tex’
Package has no Sweave vignette sources and no VignetteBuilder field.
'library' or 'require' call to ‘markdown’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
download_img_data: no visible global function definition for
  ‘download.file’
smooth_hist: no visible global function definition for ‘quantile’
whitestripe: no visible global function definition for ‘hist’
whitestripe: no visible global function definition for ‘quantile’
whitestripe: no visible global function definition for ‘sd’
whitestripe_norm: no visible global function definition for ‘sd’
Undefined global functions or variables:
  download.file hist quantile sd
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "quantile", "sd")
  importFrom("utils", "download.file")
to your NAMESPACE file.
File ‘WhopGenome/libs/WhopGenome.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fai_close
> ### Title: Closes a file previously opened with fai_open
> ### Aliases: fai_close
> 
> ### ** Examples
> 
> 
> ##
> ##	Example :
> ##
> faifile  <- system.file("extdata", "ex.fasta", package = "WhopGenome")
> faifh <- fai_open( faifile )
> stopifnot( faifh != NULL )
Error in faifh != NULL : 
  comparison (2) is possible only for atomic and list types
Calls: stopifnot
Execution halted
File ‘wicket/libs/wicket.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 use registered native symbols 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 use registered native symbols 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’.
Packages suggested but not available for checking:
  ‘AnomalyDetection’ ‘BreakoutDetection’
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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Unexported objects imported by ':::' calls:
  ‘circular:::DensityCircularRad’ ‘circular:::DvonmisesRad’
  ‘circular:::DwrappednormalRad’ ‘circular:::MlevonmisesRad’
  ‘circular:::MlewrappednormalRad’
  See the note in ?`:::` about the use of this operator.
File ‘wle/libs/wle.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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 use registered native symbols 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.
File ‘Wmisc/libs/Wmisc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'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 use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
  Cardinality of sample space is less than 20 for one more groups. Type I error might not be controlled!
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running ‘texi2dvi’ on ‘WRS2.tex’ failed.
LaTeX errors:
! Dimension too large.
\fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa 
                                                  \fb@putboxa #1\fb@afterfra...
l.2320 ...() or as.vector() instead.}}\end{kframe}
                                                  
! Dimension too large.
\fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa 
                                                  \fb@putboxa #1\fb@afterfra...
l.2320 ...() or as.vector() instead.}}\end{kframe}
                                                  
! Dimension too large.
\fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa 
                                                  \fb@putboxa #1\fb@afterfra...
l.2320 ...() or as.vector() instead.}}\end{kframe}
                                                  
! Dimension too large.
\fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa 
                                                  \fb@putboxa #1\fb@afterfra...
l.232
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘wrswoR/libs/wrswoR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ 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.
Found the following apparent S3 methods exported but not registered:
  +.CellStyle CellBlock.default CellStyle.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
.xssfcolor: no visible global function definition for ‘col2rgb’
Undefined global functions or variables:
  col2rgb
Consider adding
  importFrom("grDevices", "col2rgb")
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 no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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’
[[,XMLCodeFile: possible error in updateIds(doc, save = x): unused
  argument (save = x)
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 the system RNG.

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 use registered native symbols 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 use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.xpose.multiple.plot
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘xseq/libs/xseq.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls in package code:
  ‘chron’ ‘fts’ ‘its’ ‘timeDate’ ‘timeSeries’ ‘tseries’
  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:
  as.environment.xts dimnames.xts dimnames<-.xts
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘xyz/libs/xyz.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols 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 ‘yaImpute/libs/yaImpute.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols 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.
File ‘yaml/libs/yaml.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘deSolve’ ‘triangle’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘zic/libs/zic.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Deprecated license: CC BY-SA 2.0 + file LICENSE
Rd file 'lnre_bootstrap.Rd':
  \usage lines wider than 90 characters:
       lnre.bootstrap(model, N, ESTIMATOR, STATISTIC, replicates=100, simplify=FALSE, verbose=TRUE, ...)

Rd file 'plot_spc.Rd':
  \examples lines wider than 100 characters:
     plot(zm.spc,log="x",main="Expected Spectrum with Confidence Interval",xlab="spectrum elements",ylab="expected type counts")

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
piczoeppritz: no visible global function definition for ‘locator’
piczoeppritz: no visible global function definition for ‘rect’
piczoeppritz: no visible global function definition for ‘grey’
piczoeppritz: no visible global function definition for ‘segments’
piczoeppritz: no visible global function definition for ‘arrows’
piczoeppritz: no visible global function definition for ‘text’
plotzoeppritz: no visible global function definition for ‘plot’
plotzoeppritz: no visible global function definition for ‘par’
plotzoeppritz: no visible global function definition for ‘lines’
plotzoeppritz: no visible global function definition for ‘abline’
plotzoeppritz: no visible global function definition for ‘grey’
plotzoeppritz: no visible global function definition for ‘strheight’
plotzoeppritz: no visible global function definition for ‘text’
plotzoeppritz: no visible global function definition for ‘legend’
pzoeppritz: no visible global function definition for ‘par’
pzoeppritz: no visible global function definition for ‘plot’
pzoeppritz: no visible global function definition for ‘title’
pzoeppritz: no visible global function definition for ‘text’
Undefined global functions or variables:
  abline arrows grey legend lines locator par plot rect segments
  strheight text title
Consider adding
  importFrom("grDevices", "grey")
  importFrom("graphics", "abline", "arrows", "legend", "lines",
             "locator", "par", "plot", "rect", "segments", "strheight",
             "text", "title")
to your NAMESPACE file.
.getPath: no visible global function definition for ‘predict’
ZIClass: no visible binding for global variable ‘na.omit’
ZIClass: no visible global function definition for ‘predict’
analyzeClass: no visible global function definition for ‘plot’
calibrate : findmax: no visible global function definition for ‘lowess’
calibrate: no visible global function definition for ‘lm’
calibrate: no visible global function definition for ‘anova’
calibrate: no visible global function definition for ‘coef’
focusGraph: no visible global function definition for ‘dev.list’
getTrain: no visible global function definition for ‘na.omit’
makeClass : selectVars: no visible global function definition for
  ‘as.formula’
predict.ZIClass: no visible global function definition for ‘predict’
processSampleAll: no visible global function definition for ‘predict’
viewResults: no visible global function definition for ‘par’
viewResults: no visible global function definition for ‘plot’
viewResults: no visible global function definition for ‘points’
viewResults: no visible global function definition for ‘text’
zidbDrawVignette: no visible global function definition for ‘dev.size’
zidbDrawVignette: no visible global function definition for ‘par’
zidbDrawVignette: no visible global function definition for ‘dev.cur’
zidbDrawVignette: no visible global function definition for
  ‘rasterImage’
zidbPlotNew: no visible global function definition for ‘par’
zidbPlotNew: no visible global function definition for ‘plot’
Undefined global functions or variables:
  anova as.formula coef dev.cur dev.list dev.size lm lowess na.omit par
  plot points predict rasterImage text
Consider adding
  importFrom("grDevices", "dev.cur", "dev.list", "dev.size")
  importFrom("graphics", "par", "plot", "points", "rasterImage", "text")
  importFrom("stats", "anova", "as.formula", "coef", "lm", "lowess",
             "na.omit", "predict")
to your NAMESPACE file.
ztable.glm: no visible global function definition for ‘confint’
ztable.glm: no visible global function definition for ‘coef’
ztable.nls: no visible global function definition for ‘formula’
Undefined global functions or variables:
  coef confint formula
Consider adding
  importFrom("stats", "coef", "confint", "formula")
to your NAMESPACE file.
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/221s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1: expect_null(check_assertions(temp)) at testthat/test-assertions.R:18
  2: expect(is.null(object), sprintf("%s is not null.", lab), info = info)
  3: as.expectation(exp, ..., srcref = srcref)
  4: check_assertions(temp)
  5: ala_fields("assertions", as_is = TRUE)
  6: cached_get(this_url, type = "json")
  7: download_to_file(url, binary_file = identical(type, "binary_filename"), verbose = verbose, 
         on_redirect = on_redirect, on_client_error = on_client_error, on_server_error = on_server_error)
  8: check_status_code(h$value()[["status"]], on_redirect = on_redirect, on_client_error = on_client_error, 
         on_server_error = on_server_error, extra_info = diag_message)
  9: stop("HTTP status code ", xstatus, " received.\n", diag_msg)
  
  DONE ===========================================================================
  Error: Test failures
  Execution halted
Running ‘units.R’ [8s/8s]
Running the tests in ‘tests/units.R’ failed.
Last 13 lines of output:
  2: condition(object)
  3: expect_equal(x, expected, ..., expected.label = label)
  4: compare(object, expected, ...)
  5: protein_inference.ProteinInference(peptide_data, peptide_method = "all", peptide_summary = "median", 
         fasta = NA, apex_model = NA, combine_precursors = FALSE, consensus_peptides = FALSE)
  6: data.dt[, list(response = median(peptide_intensity)), by = key(data.dt)]
  7: `[.data.table`(data.dt, , list(response = median(peptide_intensity)), by = key(data.dt))
  8: gforce(thisEnv, jsub, o__, f__, len__, irows)
  9: gmedian(peptide_intensity)
  
  DONE ===========================================================================
  Error: Test failures
  In addition: Warning message:
  Placing tests in `inst/tests/` is deprecated. Please use `tests/testthat/` instead 
  Execution halted
File ‘allelic/libs/allelic.so’:
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Object: ‘newallelic.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: namespace ‘unmarked’ is not available and has been replaced
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/AMModels.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]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/audio.Rcheck/00install.out’ for details.
File ‘audio/libs/audio.so’:
  Found non-API call to R: ‘R_checkActivity’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: GNU Extension: Different type kinds at (1)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/basicspace.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BayesFM.Rcheck/00install.out’ for details.
File ‘BayesSAE/libs/BayesSAE.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘HBsae.o’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Nonstandard type declaration INTEGER*4 at (1)
  Warning: Integer division truncated to constant ‘67108863’ at (1) [-Winteger-division]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/BEANSP.Rcheck/00install.out’ for details.
File ‘bifactorial/libs/bifactorial.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘misc.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Objects: ‘krit.o’, ‘pv.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: GNU Extension: Different type kinds at (1)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/blockmodeling.Rcheck/00install.out’ for details.
File ‘BMN/libs/BMN.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
    Objects: ‘JunctionTree.o’, ‘pseudoLikelihood.o’

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: control reaches end of non-void function [-Wreturn-type]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cold.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [10s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  8: essgraph$repr()
  9: score$create.dag()
  10: tryCatch(new(.pardag.class, nodes = .nodes), error = function(e) stop(paste("Instance of class '", 
         .pardag.class, "' cannot be created.", sep = "")))
  11: tryCatchList(expr, classes, parentenv, handlers)
  12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  13: value[[3L]](cond)
  14: stop(paste("Instance of class '", .pardag.class, "' cannot be created.", sep = ""))
  
  testthat results ================================================================
  OK: 19 SKIPPED: 0 FAILED: 1
  1. Error: Checks output type for ges (@test_getParents_defaults_all_methods.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cslogistic.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [36s/84s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > test_check("dataone")
  Loading required package: dataone
  1. Failure: CNode object index query works with query list param (@test.D1Node.R#37) 
  result[[1]]$abstract does not match "chlorophyll".
  Actual value: "Two YSI water quality sondes and loggers were installed onto a navigation light pole in Kentucky Lake KY, one at a depth of one meter below the lake surface, the other at one meter above the lake bottom in February 2005.  Water Temperature, pH, dissolved oxygen, conductivity, oxidation reduction potential, and turbidity data are collected from each sonde every 15 minutes.  Chlorophyll a data are collected from the one meter depth.  Lake elevations are estimated from depth data collected from the sonde anchored near the lake bottom."
  
  
  testthat results ================================================================
  OK: 197 SKIPPED: 31 FAILED: 1
  1. Failure: CNode object index query works with query list param (@test.D1Node.R#37) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘test-all.r’ [2s/2s]
Running the tests in ‘tests/test-all.r’ failed.
Last 13 lines of output:
  5: stop(gettextf("'%s' is not an exported object from 'namespace:%s'", name, getNamespaceName(ns)), 
         call. = FALSE, domain = NA)
  
  2. Error: NA acts differently for stats vs dendextendRcpp (@test-labels_dendrogram.r#52) 
  dendrogram entries must be 1,2,..,6 (in any order), to be coercible to "hclust"
  1: as.hclust(sub_dend_iris) at /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/dendextendRcpp/tests/test-labels_dendrogram.r:52
  2: as.hclust.dendrogram(sub_dend_iris)
  3: stop(gettextf("dendrogram entries must be 1,2,..,%d (in any order), to be coercible to \"hclust\"", 
         n), domain = NA)
  
  DONE ===========================================================================
  Error: Test failures
  In addition: Warning message:
  Placing tests in `inst/tests/` is deprecated. Please use `tests/testthat/` instead 
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DNAprofiles.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Symbol ‘nsave’ is used before it is typed at (1)
  Warning: GNU Extension: Different type kinds at (1)
  Warning: GNU Extension: Nonstandard type declaration INTEGER*4 at (1)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DPpackage.Rcheck/00install.out’ for details.
File ‘DPpackage/libs/DPpackage.so’:
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDBDPdensity.o’, ‘LDDPdensity.o’,
      ‘LDDPsurvival.o’, ‘LDPDdoublyintsba.o’, ‘LDTFPdensity.o’,
      ‘LDTFPglmmpois.o’, ‘LDTFPsurvival.o’, ‘PSgamgam.o’,
      ‘PSgamgauss.o’, ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: Integer division truncated to constant ‘1’ at (1) [-Winteger-division]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/EMMIXcontrasts.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: Integer division truncated to constant ‘1’ at (1) [-Winteger-division]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/EMMIXskew.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: ‘i’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fAsianOptions.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: GNU Extension: Different type kinds at (1)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fastcox.Rcheck/00install.out’ for details.
File ‘fastmatch/libs/fastmatch.so’:
  Found non-API call to R: ‘match5’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FastRWeb.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fUnitRoots.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: GNU Extension: Different type kinds at (1)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gglasso.Rcheck/00install.out’ for details.
File ‘gnmf/libs/gnmf.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘FactorMatrix.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘FactorMatrix.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘run-tests.R’ [1s/1s]
Running the tests in ‘tests/run-tests.R’ failed.
Last 13 lines of output:
  +   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 ‘testthat.R’ [13s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Loading required package: coda
  Loading required package: MASS
  ##
  ## Markov Chain Monte Carlo Package (MCMCpack)
  ## Copyright (C) 2003-2017 Andrew D. Martin, Kevin M. Quinn, and Jong Hee Park
  ##
  ## Support provided by the U.S. National Science Foundation
  ## (Grants SES-0350646 and SES-0350613)
  ##
  testthat results ================================================================
  OK: 104 SKIPPED: 0 FAILED: 1
  1. Failure: caching in reap with long sample (@test-caching.R#76) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘hSDM/libs/hSDM.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘useful.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Objects: ‘hSDM.Nmixture.o’, ‘hSDM.Nmixture.iCAR.o’, ‘hSDM.ZIB.o’,
      ‘hSDM.ZIB.iCAR.alteration.o’, ‘hSDM.ZIB.iCAR.o’, ‘hSDM.ZIP.o’,
      ‘hSDM.ZIP.iCAR.alteration.o’, ‘hSDM.ZIP.iCAR.o’,
      ‘hSDM.binomial.o’, ‘hSDM.binomial.iCAR.o’, ‘hSDM.poisson.o’,
      ‘hSDM.poisson.iCAR.o’, ‘hSDM.siteocc.o’, ‘hSDM.siteocc.iCAR.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(ids)
  > 
  > test_check("ids")
  1. Failure: functional interface (@test-adjective-animal.R#64) -----------------
  all(grepl(re, x)) isn't true.
  
  
  testthat results ================================================================
  OK: 97 SKIPPED: 0 FAILED: 1
  1. Failure: functional interface (@test-adjective-animal.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
   # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/igraph.Rcheck/00install.out’ for details.
File ‘iotools/libs/iotools.so’:
  Found non-API call to R: ‘getConnection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: Return value of function ‘subsnv’ at (1) not set [-Wreturn-type]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/JohnsonDistribution.Rcheck/00install.out’ for details.
File ‘jointDiag/libs/jointDiag.so’:
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Object: ‘jedi.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/largeVis.Rcheck/00install.out’ for details.
File ‘leaps/libs/leaps.so’:
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Object: ‘leaps.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [1s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  # of Infringing URLs:  19
  # of Copyrighted URLs: 11
  
  1. Failure: Search Works (@tests.R#28) -----------------------------------------
  length(s2) not equal to 2.
  1/1 mismatches
  [1] 1 - 2 == -1
  
  
  testthat results ================================================================
  OK: 4 SKIPPED: 0 FAILED: 1
  1. Failure: Search Works (@tests.R#28) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 264-270 (estimaterates.Rmd) 
Error: processing vignette ‘estimaterates.Rmd’ failed with diagnostics:
cannot open the connection
Execution halted
File ‘maxent/libs/maxent.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘sgd.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘medSTC/libs/medSTC.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Objects: ‘medstc/medstc.o’, ‘medstc/corpus.o’,
      ‘svmlight/svm_common.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘medstc/corpus.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘MigClim/libs/MigClim.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Objects: ‘genclust.o’, ‘migrate.o’, ‘src_cell.o’, ‘validate.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Objects: ‘genclust.o’, ‘migrate.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Loading required package: rtkore
Loading required package: Rcpp

Attaching package: ‘rtkore’

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

    LdFlags


Error: processing vignette ‘Introduction-Mixtures.Rnw’ failed with diagnostics:
 chunk 13 
Error in cov.wt(as.matrix(Y), x@tik[, k], method = "ML") : 
  'x' must contain finite values only
Execution halted
File ‘mph/libs/mph.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘mph.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘mph.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: GNU Extension: Symbol ‘n’ is used before it is typed at (1)
  Warning: Pointer at (1) in pointer assignment might outlive the pointer target [-Wtarget-lifetime]
  Warning: GNU Extension: Different type kinds at (1)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mra.Rcheck/00install.out’ for details.
File ‘MRwarping/libs/MRwarping.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘interfaceRC_warp.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: GNU Extension: Symbol ‘k’ is used before it is typed at (1)
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Different type kinds at (1)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/multitaper.Rcheck/00install.out’ for details.
File ‘NeatMap/libs/NeatMap.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘nMDS_R.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘nMDS_R.o’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Symbol ‘n’ is used before it is typed at (1)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/nmcdr.Rcheck/00install.out’ for details.
File ‘obliclus/libs/obliclus.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘random_cluster_C.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘random_cluster_C.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration INTEGER*4 at (1)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/oblique.tree.Rcheck/00install.out’ for details.
File ‘oblique.tree/libs/oblique.tree.so’:
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/OBsMD.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: GNU Extension: Different type kinds at (1)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/oc.Rcheck/00install.out’ for details.
File ‘parmigene/libs/parmigene.so’:
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.o’

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

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘test-that.r’ [1s/1s]
Running the tests in ‘tests/test-that.r’ failed.
Last 13 lines of output:
  1: expect_that(get_metric(NULL), is_true()) at /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/plspm/tests/test-get-metric.r:4
  2: is_true()
  3: is_TRUE(x)
  
  11. Error: check_manifest_scaling works for right scaling (@test-manifest-scaling.r#10) 
  argument "x" is missing, with no default
  1: expect_that(check_manifest_scaling(MV, good_scaling), is_true()) at /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/plspm/tests/test-manifest-scaling.r:10
  2: is_true()
  3: is_TRUE(x)
  
  DONE ===========================================================================
  Error: Test failures
  In addition: Warning message:
  Placing tests in `inst/tests/` is deprecated. Please use `tests/testthat/` instead 
  Execution halted
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*4 at (1)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/popsom.Rcheck/00install.out’ for details.
File ‘PottsUtils/libs/PottsUtils.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘sw.o’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: GNU Extension: Different type kinds at (1)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PSM.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: GNU Extension: Symbol ‘n’ is used before it is typed at (1)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/pvrank.Rcheck/00install.out’ for details.
File ‘QUIC/libs/QUIC.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘QUIC.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘QUIC.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘loadlibs.r’ [0s/0s]
  Running ‘test.r’ [0s/1s]
Running the tests in ‘tests/test.r’ failed.
Last 13 lines of output:
  
  The following object is masked from 'package:utils':
  
      combn
  
  WARNING: ignoring environment value of R_HOME
  make[1]: Entering directory '/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Quor.Rcheck/tests'
  make[1]: *** No rule to make target '../src/core.o', needed by '../src/Quor.so'.
  make[1]: Target 'all' not remade because of errors.
  make[1]: Leaving directory '/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Quor.Rcheck/tests'
  Error in dyn.load(file.path(package.loc, "src", "Quor.so")) : 
    unable to load shared object '/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Quor.Rcheck/tests/../src/Quor.so':
    /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Quor.Rcheck/tests/../src/Quor.so: cannot open shared object file: No such file or directory
  Calls: loadlibs -> dyn.load
  Execution halted
File ‘qVarSel/libs/qVarSel.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘qVarSelH.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘qVarSelH.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Loading required package: fingerprint
Segmentation fault
File ‘RcppOctave/libs/RcppOctave.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Object: ‘rcpp_octave.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Files in the 'vignettes' directory newer than all files in 'inst/doc':
  ‘rdnb_vignette.html’
Package has no Sweave vignette sources and no VignetteBuilder field.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/restfulr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: GNU Extension: Non-default type object or sequence zz in EQUIVALENCE statement at (1) with objects of different type
  Warning: GNU Extension: Nonstandard type declaration REAL*4 at (1)
  Warning: GNU Extension: Symbol ‘n’ is used before it is typed at (1)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rexpokit.Rcheck/00install.out’ for details.
File ‘RGtk2/libs/RGtk2.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.
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_ReplDLLinit’, ‘R_RunExitFinalizers’,
    ‘R_SetParams’, ‘R_SignalHandlers’, ‘R_TempDir’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API call to R: ‘R_GlobalContext’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  libjson/Source/JSONGlobals.h:43:50: warning: invoking macro json_global_decl argument 3: empty macro arguments are undefined in ISO C++98 [-Wpedantic]
  libjson/Source/JSONGlobals.h:44:49: warning: invoking macro json_global_decl argument 3: empty macro arguments are undefined in ISO C++98 [-Wpedantic]
  JSONValidator.cpp:394:105: warning: invoking macro JSON_ASSERT_SAFE argument 3: empty macro arguments are undefined in ISO C++98 [-Wpedantic]
  JSONValidator.cpp:397:104: warning: invoking macro JSON_ASSERT_SAFE argument 3: empty macro arguments are undefined in ISO C++98 [-Wpedantic]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RJSONIO.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [35s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(rmapshaper)
  > 
  > test_check("rmapshaper")
  1. Failure: ms_simplify works with lines (@test-simplify.R#442) ----------------
  ms_simplify(line_list) not equal to geojson_list(expected_json).
  Component "features": Component 1: Component 2: Component 2: Component 2: Component 2: Mean relative difference: 1.985531e-08
  
  
  testthat results ================================================================
  OK: 252 SKIPPED: 0 FAILED: 1
  1. Failure: ms_simplify works with lines (@test-simplify.R#442) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘RMC/libs/RMC.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
    Objects: ‘RMC.o’, ‘predict.o’
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘ap.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-portable flags in variable 'PKG_CFLAGS':
  -g
Non-portable flags in variable 'PKG_CXXFLAGS':
  -g
Running ‘clustering1test.R’ [1s/1s]
  Running ‘clusteringParametertest.R’ [1s/1s]
  Running ‘clusteringPartitiontest.R’ [1s/1s]
  Running ‘heterogeneousDAtest.R’ [0s/0s]
  Running ‘heterogeneousclusteringtest.R’ [1s/1s]
  Running ‘ssupervised.R’ [1s/1s]
  Running ‘test.R’ [17s/17s]
Running the tests in ‘tests/test.R’ failed.
Last 13 lines of output:
                           Proportion =  0.2398 
                                Means =  2.1284 56.2987 
                            Variances = |        NaN        NaN |
                                        |        NaN        NaN |
  *                  Cluster  6 : 
                           Proportion =  0.1801 
                                Means =  4.4925 86.2012 
                            Variances = |        NaN        NaN |
                                        |        NaN        NaN |
  *          Log-likelihood =  -864.6805 
  **************************************************************
  > plot(xem.geyser)
  Error in eigen(A) : infinite or missing values in 'x'
  Calls: plot -> plot -> .local -> plotCluster -> ellipse -> eigen
  Execution halted
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RobustEM.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: control reaches end of non-void function [-Wreturn-type]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/robust.Rcheck/00install.out’ for details.
File ‘robust/libs/robust.so’:
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘rb.o’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rscproxy/libs/rscproxy.so’:
  Found non-API calls to R: ‘R_DefParams’, ‘R_ReplDLLinit’,
    ‘R_SetParams’, ‘R_set_command_line_arguments’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’, ‘ptr_R_Busy’, ‘ptr_R_ReadConsole’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rsgcc/libs/rsgcc.so’:
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Rsundials/libs/Rsundials.so’:
  Found ‘printf’, possibly from ‘printf’ (C)
    Objects: ‘nvector_serial.o’, ‘sundials_band.o’,
      ‘sundials_smalldense.o’
  Found ‘putchar’, possibly from ‘putchar’ (C)
    Objects: ‘nvector_serial.o’, ‘sundials_band.o’,
      ‘sundials_smalldense.o’
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Objects: ‘cvodes.o’, ‘sundials_cvodes.o’, ‘sundials_ida.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: GNU Extension: Different type kinds at (1)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rvsel.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: Integer division truncated to constant ‘67108861’ at (1) [-Winteger-division]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/seem.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: S3 methods ‘[.xml_missing’, ‘[.xml_nodeset’, ‘[[.xml_missing’, ‘xml_attr<-.xml_missing’, ‘xml_attr<-.xml_node’, ‘xml_attr<-.xml_nodeset’, ‘xml_attrs<-.xml_missing’, ‘xml_attrs<-.xml_node’, ‘xml_attrs<-.xml_nodeset’, ‘xml_name<-.xml_missing’, ‘xml_name<-.xml_node’, ‘xml_name<-.xml_nodeset’, ‘xml_text<-.xml_missing’, ‘xml_text<-.xml_node’, ‘xml_text<-.xml_nodeset’, ‘as.character.xml_document’, ‘as.character.xml_missing’, ‘as.character.xml_node’, ‘as.character.xml_nodeset’, ‘as_list.xml_missing’, ‘as_list.xml_node’, ‘as_list.xml_nodeset’, ‘as_xml_document.character’, ‘as_xml_document.connection’, ‘as_xml_document.list’, ‘as_xml_document.raw’, ‘as_xml_document.response’, ‘as_xml_document.xml_document’, ‘as_xml_document.xml_node’, ‘as_xml_document.xml_nodeset’, ‘format.xml_node’, ‘is.na.xml_missing’, ‘is.na.xml_node’, ‘is.na.xml_nodeset’, ‘nodeset_apply.x [... truncated]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/selectr.Rcheck/00install.out’ for details.
Running examples in ‘sequoia-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sequoia
> ### Title: Pedigree Reconstruction
> ### Aliases: sequoia
> 
> ### ** Examples
> 
> data(SimGeno_example, LH_HSg5, package="sequoia")
> 
> SeqOUT <- sequoia(GenoM = SimGeno_example,
+                   LifeHistData = LH_HSg5, MaxSibIter = 0)
At line 127 of file Sequoia.f90
Fortran runtime error: Actual string length is shorter than the declared one for dummy argument 'genofilefr' (-390258662/255)
Running ‘testthat.R’ [41s/48s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Data are not available for this date. 2015.03.31 does not exist at ftp://n5eil01u.ecs.nsidc.org/SAN/SMAP/SPL3SMP.003/
  1: find_smap(id = "SPL3SMP", dates = "2015-03-31", version = 3) at testthat/test-extract_smap.R:4
  2: lapply(dates, find_for_date, id = id, version = version)
  3: FUN(X[[i]], ...)
  4: validate_ftp_request(id, date, version)
  5: validate_date(id, version, date)
  6: stop(paste(prefix, suffix))
  
  testthat results ================================================================
  OK: 9 SKIPPED: 14 FAILED: 2
  1. Error: invalid output directories cause errors (@test-download_smap.R#4) 
  2. Error: invalid datasets cause errors (@test-extract_smap.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: GNU Extension: Symbol ‘ntt’ is used before it is typed at (1)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/smint.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: GNU Extension: Different type kinds at (1)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/spanr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Old-style initialization at (1)
  Warning: GNU Extension: Different type kinds at (1)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/spatialkernel.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SpherWave.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: GNU Extension: Symbol ‘k’ is used before it is typed at (1)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/spsmooth.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: CHARACTER expression will be truncated in assignment (8/9) at (1) [-Wcharacter-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/srd.Rcheck/00install.out’ for details.
Found the following significant warnings:
  decTreeImpFuncCpp.cpp:1677:42: warning: unknown escape sequence: '\040'
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/StatMethRank.Rcheck/00install.out’ for details.
File ‘stepPlr/libs/stepPlr.so’:
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Object: ‘cg_descent.o’
  Found ‘_gfortran_stop_string’, possibly from ‘stop’ (Fortran)
    Object: ‘cg_descent.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/stima.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: ‘pi’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/stpp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/survrec.Rcheck/00install.out’ for details.
File ‘survrec/libs/survrec.so’:
  Found ‘_gfortran_rand’, possibly from ‘rand’ (Fortran)
    Object: ‘bootstrap.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘svmpath/libs/svmpath.so’:
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’

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

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: umxCP
> ### Title: umxCP: Build and run a Common pathway twin model
> ### Aliases: umxCP
> 
> ### ** Examples
> 
> require(umx)
> data(twinData) 
> zygList = c("MZFF", "MZMM", "DZFF", "DZMM", "DZOS")
> twinData$ZYG = factor(twinData$zyg, levels = 1:5, labels = zygList)
> selDVs = c("ht", "wt")
> mzData <- subset(twinData, ZYG == "MZFF", umx_paste_names(selDVs, "", 1:2))
> dzData <- subset(twinData, ZYG == "DZFF", umx_paste_names(selDVs, "", 1:2))
> m1 = umxCP(selDVs = selDVs, dzData = dzData, mzData = mzData, suffix = "")
Running CP with 13 parameters
Warning: In model 'CP' Optimizer returned a non-zero status code 10. Starting values are not feasible. Consider mxTryHard()
Error: The job for model 'CP' exited abnormally with the error message: fit is not finite (Continuous covariance (loc2) is not positive definite in data 'DZ.data' row 170. Detail:
covariance =  matrix(c(    # 4x4
 3.61319e+42, 7.71285e+41, 1.81688e+42, 3.87837e+41
, 7.71285e+41, 1.64641e+41, 3.87837e+41, 8.27891e+40
, 1.81688e+42, 3.87837e+41, 3.61319e+42, 7.71285e+41
, 3.87837e+41, 8.27891e+40, 7.71285e+41, 1.64641e+41), byrow=TRUE, nrow=4, ncol=4)
)
Execution halted
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’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   5.0Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘httr’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    R  13.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
Running examples in ‘ActuDistns-Ex.R’ failed
The error most likely occurred in:

> ### Name: dgumbeld
> ### Title: Gumbel pdf
> ### Aliases: dgumbeld
> ### Keywords: Gumbel distribution
> 
> ### ** Examples
> x=runif(10,min=0,max=1)
> y=dgumbeld(x)
Error in dgumbel(x, mu = mu, sigma = sigma) : 
  unused arguments (mu = mu, sigma = sigma)
Calls: dgumbeld -> ifelse
Execution halted
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)
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data       2.8Mb
    pictures   2.1Mb
Namespace in Imports field not imported from: ‘filehash’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Namespaces in Imports field not imported from:
  ‘fields’ ‘knitr’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Loading required package: maps

Attaching package: 'maps'

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

    ozone

Quitting from lines 190-195 (ALA4R.Rmd) 
Error: processing vignette 'ALA4R.Rmd' failed with diagnostics:
replacement has 2 rows, data has 0
Execution halted
Namespaces in Imports field not imported from:
  ‘rjson’ ‘xml2’
  All declared Imports should be used.
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    data  15.6Mb
Running examples in ‘anametrix-Ex.R’ failed
The error most likely occurred in:

> ### Name: authenticate
> ### Title: authenticate
> ### Aliases: authenticate
> 
> ### ** Examples
> 
> username <- "demo.user@demoanametrix.com"
> password <- "password"
> auth     <- authenticate("https://demo.anametrix.com/api", username, password)
Failed to authenticate with Anametrix API 
Error: Connection timed out after 100000 milliseconds 
Error in xmlTreeParse(resp) : object 'resp' not found
Calls: authenticate -> xmlTreeParse
Execution halted
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
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.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.0Mb
File ‘audio/libs/audio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘htmlwidgets’
  All declared Imports should be used.
installed size is 64.3Mb
  sub-directories of 1Mb or more:
    java  64.2Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
Package suggested but not available for checking: ‘sybilSBML’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   1.3Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘osd’
  All declared Imports should be used.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/BAMBI.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: GNU Extension: Different type kinds at (1)
See ‘/data/gannet/ripley/R/packages/tests-clang/basicspace.Rcheck/00install.out’ for details.
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  11.2Mb
installed size is 21.9Mb
  sub-directories of 1Mb or more:
    libs  20.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    ex-data   5.4Mb
installed size is 63.4Mb
  sub-directories of 1Mb or more:
    libs  63.3Mb
Namespace in Imports field not imported from: ‘inline’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘readxl’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Nonstandard type declaration INTEGER*4 at (1)
  Warning: Integer division truncated to constant ‘67108863’ at (1) [-Winteger-division]
See ‘/data/gannet/ripley/R/packages/tests-clang/BEANSP.Rcheck/00install.out’ for details.
installed size is 46.1Mb
  sub-directories of 1Mb or more:
    libs  45.1Mb
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.
Namespaces in Imports field not imported from:
  ‘FinTS’ ‘Rcpp’ ‘TSA’ ‘TTR’ ‘colorspace’ ‘fpp’ ‘fracdiff’ ‘gtable’
  ‘htmlwidgets’ ‘lmtest’ ‘normtest’ ‘quadprog’ ‘rugarch’ ‘scales’
  ‘stringi’ ‘testthat’ ‘timeDate’ ‘tseries’ ‘viridis’
  All declared Imports should be used.
installed size is 126.8Mb
  sub-directories of 1Mb or more:
    include  126.8Mb
Error in re-building vignettes:
  ...
Quitting from lines 138-140 (bibliometrix-vignette.Rmd) 
Error: processing vignette 'bibliometrix-vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Namespace in Imports field not imported from: ‘maptools’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   4.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   3.8Mb
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    libs  27.8Mb
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
Running examples in ‘bioimagetools-Ex.R’ failed
The error most likely occurred in:

> ### Name: readBMP
> ### Title: Read bitmap files
> ### Aliases: readBMP
> 
> ### ** Examples
> 
> bi<-readBMP("http://www.statistik.lmu.de/institut/ag/bioimg/bit/ratbert.bmp")
Warning in file(file, "rb") :
  cannot open URL 'http://www.statistik.lmu.de/institut/ag/bioimg/bit/ratbert.bmp': HTTP status was '404 Not Found'
Error in file(file, "rb") : cannot open the connection
Calls: readBMP -> file
Execution halted
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Running examples in ‘BioPET-Ex.R’ failed
The error most likely occurred in:

> ### Name: enrichment_analysis
> ### Title: Prognostic Enrichment with Real Data
> ### Aliases: enrichment_analysis
> 
> ### ** Examples
> 
> data(dcaData)
> 
> ## using a single biomarker in the dataset
> analysis.single.marker <- enrichment_analysis(Cancer ~ Marker1,
+ data=dcaData,
+ reduction.under.treatment=0.3,
+ cost.screening=100,
+ cost.keeping=1000)
Warning in mean.default(response) :
  argument is not numeric or logical: returning NA
Error: Unsupported use of matrix or array for column indexing
Execution halted
Package suggested but not available for checking: ‘RQuantLib’
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
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’
installed size is 35.0Mb
  sub-directories of 1Mb or more:
    libs  33.9Mb
Found the following significant warnings:
  Warning: GNU Extension: Different type kinds at (1)
See ‘/data/gannet/ripley/R/packages/tests-clang/blockmodeling.Rcheck/00install.out’ for details.
'library' or 'require' calls in package code:
  ‘Matrix’ ‘sna’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
installed size is 29.3Mb
  sub-directories of 1Mb or more:
    libs  29.0Mb
File ‘BMN/libs/BMN.so’:
  Found ‘_ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
    Objects: ‘JunctionTree.o’, ‘pseudoLikelihood.o’
File ‘BMN/libs/BMN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘compiler’
  All declared Imports should be used.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.7Mb
installed size is 243.2Mb
  sub-directories of 1Mb or more:
    include    2.7Mb
    lib      240.3Mb
installed size is 40.9Mb
  sub-directories of 1Mb or more:
    libs  40.6Mb
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rworldxtra’ ‘sp’
  All declared Imports should be used.
installed size is 49.0Mb
  sub-directories of 1Mb or more:
    libs  48.6Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data     1.5Mb
    models   2.2Mb
Namespace in Imports field not imported from: ‘Matrix’
  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 15.2Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘rgdal’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   9.3Mb
get.switch.time: warning in uniroot(f = switch.func, int =
  c(last_boundary, boundary), lower = last_boundary, upper = boundary,
  maxiter = 1000, tol = tol, e): partial argument match of 'int' to
  'interval'
plot.cggd: warning in axis(4, at = b[nrow(b), ], label = paste(cnums),
  cex = 0.8, adj = 0): partial argument match of 'label' to 'labels'
plot.cggd: no visible global function definition for ‘gen.beta’
plotCVcggd: no visible binding for global variable ‘cv’
plotCVcggd: no visible binding for global variable ‘cv.error’
predict.cggd: no visible binding for global variable ‘max.tk’
predict.cggd: no visible global function definition for ‘gen.beta’
Undefined global functions or variables:
  cv cv.error gen.beta max.tk
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
installed size is 59.7Mb
  sub-directories of 1Mb or more:
    data  59.6Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘stringr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    extdata  12.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
    pdf   2.2Mb
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data     3.5Mb
    exdata   5.5Mb
Package suggested but not available for checking: ‘CNVtools’
Found the following significant warnings:
  Warning: control reaches end of non-void function [-Wreturn-type]
  Warning: ‘result’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-clang/cold.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [23s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(CompareCausalNetworks)
  > 
  > test_check("CompareCausalNetworks")
  1. Error: Checks output type for ges (@test_getParents_defaults_all_methods.R#19) 
  Instance of class 'GaussParDAG' cannot be created.
  1: expect_is(Ahat <- getParents(X, environment, method = method, alpha = 0.1), "Matrix") at testthat/test_getParents_defaults_all_methods.R:19
  2: klass(object)
  3: paste(class(x), collapse = "/")
  4: getParents(X, environment, method = method, alpha = 0.1)
  5: runGES(X, parentsOf, variableSelMat, setOptions, directed, verbose, result)
  6: pcalg::ges(ncol(X), score, fixedGaps = if (is.null(variableSelMat)) NULL else (!variableSelMat), 
         turning = optionsList$turning, maxDegree = optionsList$maxDegree, verbose = verbose)
  7: caus.inf("GIES", score = score, labels = labels, targets = list(integer(0)), fixedGaps = fixedGaps, 
         adaptive = adaptive, phase = phase, iterate = iterate, maxDegree = maxDegree, 
         verbose = verbose, ...)
  8: essgraph$repr()
  9: score$create.dag()
  10: tryCatch(new(.pardag.class, nodes = .nodes), error = function(e) stop(paste("Instance of class '", 
         .pardag.class, "' cannot be created.", sep = "")))
  11: tryCatchList(expr, classes, parentenv, handlers)
  12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  13: value[[3L]](cond)
  14: stop(paste("Instance of class '", .pardag.class, "' cannot be created.", sep = ""))
  
  testthat results ================================================================
  OK: 19 SKIPPED: 0 FAILED: 1
  1. Error: Checks output type for ges (@test_getParents_defaults_all_methods.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    app   2.6Mb
    doc   2.2Mb
installed size is  9.3Mb
  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.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Quitting from lines 775-800 (CopulaDTA_Vignette.Rmd) 
Error: processing vignette 'CopulaDTA_Vignette.Rmd' failed with diagnostics:
formal argument "axis.title.y" matched by multiple actual arguments
Execution halted
installed size is 10.7Mb
  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.
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    libs  23.8Mb
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  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 31.3Mb
  sub-directories of 1Mb or more:
    libs  31.1Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   4.8Mb
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
Namespace in Imports field not imported from: ‘httpcode’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    shp   7.8Mb
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
See ‘/data/gannet/ripley/R/packages/tests-clang/cslogistic.Rcheck/00install.out’ for details.
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
Found the following significant warnings:
  ./ctl.h:38:23: warning: token pasting of ',' and __VA_ARGS__ is a GNU extension [-Wgnu-zero-variadic-macro-arguments]
  ./ctl.h:36:25: warning: token pasting of ',' and __VA_ARGS__ is a GNU extension [-Wgnu-zero-variadic-macro-arguments]
See ‘/data/gannet/ripley/R/packages/tests-clang/ctl.Rcheck/00install.out’ for details.
installed size is 32.0Mb
  sub-directories of 1Mb or more:
    extdata  31.9Mb
Running examples in ‘curlconverter-Ex.R’ failed
The error most likely occurred in:

> ### Name: make_req
> ### Title: Turn parsed cURL command lines into 'httr' request functions
> ### Aliases: make_req
> 
> ### ** Examples
> 
> library(httr)
> 
> my_ip <- straighten("curl 'https://httpbin.org/ip'") %>% make_req()
curl 'https://httpbin.org/ip'
Error: Clipboard on X11 requires 'xclip' (recommended) or 'xsel'.
Execution halted
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
Package suggested but not available for checking: ‘gputools’
Package unavailable to check Rd xrefs: ‘gputools’
.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.
Running ‘testthat.R’ [68s/212s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("dataone")
  Loading required package: dataone
  1. Failure: CNode object index query works with query list param (@test.D1Node.R#37) 
  result[[1]]$abstract does not match "chlorophyll".
  Actual value: "Two YSI water quality sondes and loggers were installed onto a navigation light pole in Kentucky Lake KY, one at a depth of one meter below the lake surface, the other at one meter above the lake bottom in February 2005.  Water Temperature, pH, dissolved oxygen, conductivity, oxidation reduction potential, and turbidity data are collected from each sonde every 15 minutes.  Chlorophyll a data are collected from the one meter depth.  Lake elevations are estimated from depth data collected from the sonde anchored near the lake bottom."
  
  
  testthat results ================================================================
  OK: 197 SKIPPED: 31 FAILED: 1
  1. Failure: CNode object index query works with query list param (@test.D1Node.R#37) 
  
  Error: testthat unit tests failed
  Execution halted
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  5.1Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
installed size is 21.5Mb
  sub-directories of 1Mb or more:
    libs  21.4Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(debugme)
  
  Attaching package: 'debugme'
  
  The following object is masked from 'package:base':
  
      debug
  
  > 
  > test_check("debugme")
  1. Failure: get a package style (@test-colors.R#32) ----------------------------
  `ret` not equal to quote(debug_data$palette[pkg]).
  Modes of target, current: function, call
  target, current do not match when deparsed
  
  
  2. Failure: debugme (@test-package.R#34) ---------------------------------------
  env$f2() produced no output
  
  
  3. Failure: debugme (@test-package.R#36) ---------------------------------------
  env$.hidden() produced no output
  
  
  testthat results ================================================================
  OK: 34 SKIPPED: 0 FAILED: 3
  1. Failure: get a package style (@test-colors.R#32) 
  2. Failure: debugme (@test-package.R#34) 
  3. Failure: debugme (@test-package.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
'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.
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.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.7Mb
    help   1.3Mb
    libs   1.1Mb
Packages suggested but not available for checking: ‘gurobi’ ‘Rcplex’
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  16.5Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/dfpk.Rcheck/00install.out’ for details.
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    bin  13.3Mb
    doc   1.7Mb
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.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    extdata       2.4Mb
    htmlwidgets   4.7Mb
    img           2.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    2.2Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/DNAprofiles.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Namespaces in Imports field not imported from:
  ‘GOstats’ ‘caTools’ ‘fdrtool’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Symbol ‘nsave’ is used before it is typed at (1)
  Warning: GNU Extension: Different type kinds at (1)
  Warning: GNU Extension: Nonstandard type declaration INTEGER*4 at (1)
See ‘/data/gannet/ripley/R/packages/tests-clang/DPpackage.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘shapefiles’
  All declared Imports should be used.
perturbFBM: warning in circFBM(n, H, plot = FALSE): partial argument
  match of 'plot' to 'plotfBm'
circFBM: no visible global function definition for ‘fft’
circFBM: no visible global function definition for ‘rnorm’
circFBM: no visible global function definition for ‘par’
circFBM: no visible global function definition for ‘plot’
dvFBM: no visible global function definition for ‘filter’
dvFBM: no visible global function definition for ‘quantile’
dvFBM: no visible global function definition for ‘lm’
dvFBM: no visible global function definition for ‘plot’
dvFBM: no visible global function definition for ‘abline’
filt: no visible global function definition for ‘wavDaubechies’
perturbFBM: no visible global function definition for ‘rnorm’
perturbFBM: no visible global function definition for ‘rbinom’
perturbFBM: no visible global function definition for ‘par’
perturbFBM: no visible global function definition for ‘segments’
perturbFBM: no visible global function definition for ‘points’
Undefined global functions or variables:
  abline fft filter lm par plot points quantile rbinom rnorm segments
  wavDaubechies
Consider adding
  importFrom("graphics", "abline", "par", "plot", "points", "segments")
  importFrom("stats", "fft", "filter", "lm", "quantile", "rbinom",
             "rnorm")
to your NAMESPACE file.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    2.9Mb
    libs   6.7Mb
bootstrapCI: no visible global function definition for ‘lpepa’
bootstrapCI: no visible global function definition for ‘var’
bootstrapCI: no visible global function definition for ‘quantile’
dynamicCorrelation: no visible global function definition for ‘lpepa’
dynamicCorrelation: no visible global function definition for ‘var’
Undefined global functions or variables:
  lpepa quantile var
Consider adding
  importFrom("stats", "quantile", "var")
to your NAMESPACE file.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    models   4.3Mb
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.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    hac    4.0Mb
Package suggested but not available for checking: ‘ComplexHeatmap’
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘ComplexHeatmap’
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is 41.2Mb
  sub-directories of 1Mb or more:
    libs  40.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    examples   4.6Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data  11.5Mb
Namespaces in Imports field not imported from:
  ‘prettyunits’ ‘ratelimitr’ ‘rgdal’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘FNN’ ‘ggmap’ ‘simFrame’
  All declared Imports should be used.
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  14.5Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    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.
Found the following significant warnings:
  Warning: Integer division truncated to constant ‘1’ at (1) [-Winteger-division]
See ‘/data/gannet/ripley/R/packages/tests-clang/EMMIXcontrasts.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: Integer division truncated to constant ‘1’ at (1) [-Winteger-division]
See ‘/data/gannet/ripley/R/packages/tests-clang/EMMIXskew.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    Sweave   6.0Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    help   3.3Mb
File ‘ETAS/libs/ETAS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package unavailable to check Rd xrefs: ‘DNAprofiles’
Namespace in Imports field not imported from: ‘EnvStats’
  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.
Found the following significant warnings:
  Warning: iteration 7 invokes undefined behavior [-Waggressive-loop-optimizations]
See ‘/data/gannet/ripley/R/packages/tests-clang/expoRkit.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘affy’
  All declared Imports should be used.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Namespace in Imports field not imported from: ‘FactoMineR’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: ‘i’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-clang/fAsianOptions.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: GNU Extension: Different type kinds at (1)
See ‘/data/gannet/ripley/R/packages/tests-clang/fastcox.Rcheck/00install.out’ for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  12.7Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
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  5.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.4Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is 41.1Mb
  sub-directories of 1Mb or more:
    libs  40.4Mb
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   6.3Mb
Namespaces in Imports field not imported from:
  ‘ncdf4’ ‘rgeos’
  All declared Imports should be used.
Found the following significant warnings:
  ff.cpp:256:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ff.cpp:256:54: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/ff.Rcheck/00install.out’ for details.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Running examples in ‘fheatmap-Ex.R’ failed
The error most likely occurred in:

> ### Name:  Column Annotations 
> ### Title: Annotations of columns in "fheatmap_data"
> ### Aliases: ' annotation_col '
> ### Keywords: annotation_col
> 
> ### ** Examples
> 
> data(annotation_col)
> fheatmap(fheatmap_data,annotation_col=annotation_col)
Error in theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),  : 
  formal argument "plot.margin" matched by multiple actual arguments
Calls: fheatmap -> draw_tree -> theme_blank
Execution halted
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Namespace in Imports field not imported from: ‘rgdal’
  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
Running examples in ‘forega-Ex.R’ failed
The error most likely occurred in:

> ### Name: ForecastArima
> ### Title: Floating-Point Genetic Algorithms with Statistical Forecast
> ###   Based Inheritance Operator
> ### Aliases: ForecastArima
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
> # Required package forega
> require("forega")
> 
> set.seed(12345)
> 
> # This function has the global minimum at x_1 = pi and x_2 = exp(1)
> f <- function (x){
+ 	return( (x[1]-pi)^2 + (x[2]-2.71828)^2 )
+ }
> 
> # Performing a floating-point genetic algorithm search with forecast probability of 0.10
> res <- forecasting_ga(evalFunc=f, chsize=2, minv=rep(-10.0,2),
+                       maxv=rep(10.0,2), crossprob=0.80, mutationprob=0.01, 
+                       popsize=100, maxiter=1000, MinimumForecastLength=20, 
+                       ForecastFunction=ForecastArima, elitism=2, forecastprob=0.01)
Error in forecasting_ga(evalFunc = f, chsize = 2, minv = rep(-10, 2),  : 
  only replacement of elements is allowed
Calls: forecasting_ga -> .Call
Execution halted
Namespaces in Imports field not imported from:
  ‘maptools’ ‘rgdal’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
Namespaces in Imports field not imported from:
  ‘R.utils’ ‘grDevices’ ‘graphics’ ‘matrixStats’ ‘stats’
  All declared Imports should be used.
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
See ‘/data/gannet/ripley/R/packages/tests-clang/fUnitRoots.Rcheck/00install.out’ for details.
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
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 10.4Mb
  sub-directories of 1Mb or more:
    data    3.7Mb
    doc     2.9Mb
    tests   2.8Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    1.0Mb
    libs   7.1Mb
installed size is 50.5Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     47.7Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  14.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    java   5.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   4.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(GeneralTree)
  Loading required package: R6
  > 
  > test_check("GeneralTree")
  1. Error: plotting a tree works (@test_plot.R#64) ------------------------------
  'create_nodes' is not an exported object from 'namespace:DiagrammeR'
  1: expect_identical(plot(tree)$x$diagram, diagram) at testthat/test_plot.R:64
  2: identical(object, expected)
  3: plot(tree)
  4: plot.GeneralTree(tree)
  5: generate_grViz(x, ...)
  6: do.call(DiagrammeR::create_nodes, create_nodes_call)
  7: DiagrammeR::create_nodes
  8: getExportedValue(pkg, name)
  9: stop(gettextf("'%s' is not an exported object from 'namespace:%s'", name, getNamespaceName(ns)), 
         call. = FALSE, domain = NA)
  
  testthat results ================================================================
  OK: 118 SKIPPED: 0 FAILED: 1
  1. Error: plotting a tree works (@test_plot.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 102-103 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
'create_nodes' is not an exported object from 'namespace:DiagrammeR'
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    exdata   5.1Mb
Running ‘test-that.r’
Running the tests in ‘tests/test-that.r’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc        1.4Mb
    examples   1.5Mb
    vign       1.0Mb
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    data  26.0Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Namespace in Imports field not imported from: ‘agricolae’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘plotly’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggmap’ ‘gridExtra’ ‘scales’ ‘tnet’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘lazyeval’ ‘readr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘XML’ ‘mapproj’ ‘moonBook’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: GNU Extension: Different type kinds at (1)
See ‘/data/gannet/ripley/R/packages/tests-clang/gglasso.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘NHANES’ ‘gridExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘randomForest’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Found the following significant warnings:
  dataStructure.cpp:146:13: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  dataStructure.cpp:148:70: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  dataStructure.cpp:149:27: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/glmBfp.Rcheck/00install.out’ for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    libs  37.3Mb
Package suggested but not available for checking: ‘cplexAPI’
Warning in fun(libname, pkgname) :
  JRI.jar seems to be missing from the classpath.The graphical user interface will most likely not be available.Compile R with shared library enabled (--enable-R-shlib option)and reinstall rJava to use JRI functionality.

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

Probably some imports need to be declared in the NAMESPACE file.
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
Namespace in Imports field not imported from: ‘googleCloudStorageR’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘roxygen2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘BiasedUrn’
  All declared Imports should be used.
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
Namespace in Imports field not imported from: ‘rrcov’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rvest’
  All declared Imports should be used.
Running ‘run-tests.R’
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 /data/gannet/ripley/R/test-clang/gWidgets2/tests/button.R
  Loading required package: gWidgets2tcltk
  Loading required package: memoise
  Loading required package: tcltk
  testing /data/gannet/ripley/R/test-clang/gWidgets2/tests/calendar.R
  testing /data/gannet/ripley/R/test-clang/gWidgets2/tests/checkbox.R
  testing /data/gannet/ripley/R/test-clang/gWidgets2/tests/combobox.R
  testing /data/gannet/ripley/R/test-clang/gWidgets2/tests/containers.R
  Error: svalue(cards) not equal to 1.
  Modes: logical, numeric
  target is logical, current is numeric
  Execution halted
installed size is 62.5Mb
  sub-directories of 1Mb or more:
    java  61.2Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
Found the following significant warnings:
  ./City.h:82:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:93:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:94:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:95:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:96:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:87:8: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:89:8: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:267:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:268:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ./Spooky.h:285:36: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/hashFunction.Rcheck/00install.out’ for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Namespace in Imports field not imported from: ‘hms’
  All declared Imports should be used.
installed size is 112.6Mb
  sub-directories of 1Mb or more:
    libs  111.5Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    doc          13.7Mb
    htmlwidgets   1.9Mb
Namespace in Imports field not imported from: ‘quantmod’
  All declared Imports should be used.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    highlight   1.1Mb
    libs        6.2Mb
Namespace in Imports field not imported from: ‘colorspace’
  All declared Imports should be used.
Running examples in ‘horizon-Ex.R’ failed
The error most likely occurred in:

> ### Name: horizonSearch
> ### Title: Horizon elevation angle from DEM RasterLayer
> ### Aliases: horizonSearch
> 
> ### ** Examples
> 
> r <- getData('alt', country='ALB')
trying URL 'http://biogeo.ucdavis.edu/data/diva/msk_alt/ALB_msk_alt.zip'
Warning in utils::download.file(url = aurl, destfile = fn, method = "auto",  :
  cannot open URL 'http://biogeo.ucdavis.edu/data/diva/msk_alt/ALB_msk_alt.zip': HTTP status was '403 Forbidden'
Error in utils::download.file(url = aurl, destfile = fn, method = "auto",  : 
  cannot open URL 'http://biogeo.ucdavis.edu/data/diva/msk_alt/ALB_msk_alt.zip'
Calls: getData -> .raster -> .download -> <Anonymous>
Execution halted
print.summary.hotspots: warning in sort(x$data, dec = TRUE): partial
  argument match of 'dec' to 'decreasing'
print.summary.hotspots: warning in sort(x$disprop$positive, dec =
  TRUE): partial argument match of 'dec' to 'decreasing'
print.summary.hotspots: warning in sort(x$disprop$negative, dec =
  TRUE): partial argument match of 'dec' to 'decreasing'
Lchs: no visible global function definition for ‘plot’
Lchs: no visible global function definition for ‘points’
disprop: no visible global function definition for ‘median’
hotspots: no visible global function definition for ‘median’
hotspots: no visible global function definition for ‘qnorm’
hotspots: no visible global function definition for ‘qt’
plot.hotspots: no visible global function definition for ‘par’
summary.hotspots: no visible global function definition for ‘median’
Undefined global functions or variables:
  median par plot points qnorm qt
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "median", "qnorm", "qt")
to your NAMESPACE file.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Found the following significant warnings:
  language.c:41:5: warning: flexible array initialization is a GNU extension [-Wgnu-flexible-array-initializer]
See ‘/data/gannet/ripley/R/packages/tests-clang/htmltidy.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    dict   1.3Mb
    doc    1.1Mb
    libs   3.8Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘ggplot2’ ‘pander’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   4.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   2.6Mb
Note: found 14 marked Latin-1 strings
  Note: found 39 marked UTF-8 strings
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.2Mb
    libs   7.7Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
Error in re-building vignettes:
  ...
Error in (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  : 
  there is no package called 'states2k'
Quitting from lines 24-109 (US-Engineering-Weather-Map.Rmd) 
Error: processing vignette 'US-Engineering-Weather-Map.Rmd' failed with diagnostics:
object 'states2k_map' not found
Execution halted
Package suggested but not available for checking: ‘RcppOctave’
Found the following significant warnings:
  # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
See ‘/data/gannet/ripley/R/packages/tests-clang/igraph.Rcheck/00install.out’ for details.
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    help   1.2Mb
    libs  14.5Mb
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       3.4Mb
    include   2.6Mb
    libs     15.5Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R  10.8Mb
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘count_compare’
Namespace in Imports field not imported from: ‘prodlim’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘png’
  All declared Imports should be used.
File ‘ipft/libs/ipft.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.5Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   5.3Mb
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘GPArotation’ ‘PMCMR’ ‘afex’ ‘car’ ‘lsmeans’
  ‘lsr’ ‘multcomp’ ‘psych’ ‘vcd’ ‘vcdExtra’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: Return value of function ‘subsnv’ at (1) not set [-Wreturn-type]
See ‘/data/gannet/ripley/R/packages/tests-clang/JohnsonDistribution.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.1Mb
Namespace in Imports field not imported from: ‘lme4’
  All declared Imports should be used.
installed size is 206.0Mb
  sub-directories of 1Mb or more:
    extdata  205.2Mb
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Warning: parse error in file '02_fromLongitudinalData.r':
invalid multibyte character in parser at line 1
'library' or 'require' call not declared from: ‘codetools’
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Package in Depends field not imported from: ‘cluster’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   2.8Mb
Running ‘testthat.R’ [0m/10m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(kokudosuuchi)
  このサービスは、「国土交通省　国土数値情報（カテゴリ名）」をもとに加工者が作成
  以下の国土数値情報ダウンロードサービスの利用約款をご確認の上ご利用ください：
  
  http://nlftp.mlit.go.jp/ksj/other/yakkan.html
  > 
  > test_check("kokudosuuchi")
  trying URL 'http://nlftp.mlit.go.jp/ksj/gml/data/W05/W05-07/W05-07_03_GML.zip'
  Content type 'application/zip' length 10927086 bytes (10.4 MB)
  ==================================================
  downloaded 10.4 MB
  
  OGR data source with driver: ESRI Shapefile 
  Source: "/tmp/Rtmp5Dq6p5/1d9e3cbd8c67c8289c3e955f4a925569", layer: "W05-07_03-g_Stream"
  with 7597 features
  It has 10 fields
  OGR data source with driver: ESRI Shapefile 
  Source: "/tmp/Rtmp5Dq6p5/1d9e3cbd8c67c8289c3e955f4a925569", layer: "W05-07_03-g_RiverNode"
  with 7534 features
  It has 3 fields
  1. Failure: getKSJData works (@test-getData.R#6) -------------------------------
  names(d) not equal to c("W05-07_03-g_RiverNode", "W05-07_03-g_Stream").
  2/2 mismatches
  x[1]: "W05-07_03-g_Stream"
  y[1]: "W05-07_03-g_RiverNode"
  
  x[2]: "W05-07_03-g_RiverNode"
  y[2]: "W05-07_03-g_Stream"
  
  
  testthat results ================================================================
  OK: 3 SKIPPED: 0 FAILED: 1
  1. Failure: getKSJData works (@test-getData.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    java   6.0Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tibble’
  All declared Imports should be used.
kztp: warning in rowMeans(kztp, dim = 2): partial argument match of
  'dim' to 'dims'
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    2.4Mb
    help   1.1Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/largeVis.Rcheck/00install.out’ for details.
Running examples in ‘laser-Ex.R’ failed
The error most likely occurred in:

> ### Name: agamids
> ### Title: Ultrametric Phylogeny of Australian Agamid Lizards
> ### Aliases: agamids
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(agamids)
> agbtimes <- getBtimes(string = agamids)
Error in getBtimes(string = agamids) : Tree is not ultrametric!
Execution halted
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    dataset   1.5Mb
    include  16.0Mb
    libs      5.7Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘rgeos’
  All declared Imports should be used.
File ‘lidR/libs/lidR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    doc        1.8Mb
    libs      18.7Mb
    testdata   1.5Mb
lmec: warning in qr.Q(qrZ, compl = TRUE): partial argument match of
  'compl' to 'complete'
lmec: warning in qr.Q(qra, compl = TRUE): partial argument match of
  'compl' to 'complete'
lmec: no visible global function definition for ‘lm’
lmec: no visible global function definition for ‘pnorm’
lmec: no visible global function definition for ‘dnorm’
lmec : vtrnorm2: no visible global function definition for ‘runif’
lmec : vtrnorm2: no visible global function definition for ‘qnorm’
lmec : vtrnorm2: no visible global function definition for ‘pnorm’
lmec: no visible global function definition for ‘rnorm’
lmec: no visible global function definition for ‘ar’
Undefined global functions or variables:
  ar dnorm lm pnorm qnorm rnorm runif
Consider adding
  importFrom("stats", "ar", "dnorm", "lm", "pnorm", "qnorm", "rnorm",
             "runif")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘boot’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: ‘nsimp’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-clang/localdepth.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘distr’
  All declared Imports should be used.
Package in Depends field not imported from: ‘logcondens’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Note: found 143 marked Latin-1 strings
  Note: found 833 marked UTF-8 strings
Namespace in Imports field not imported from: ‘tcltk2’
  All declared Imports should be used.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    data  16.0Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    TS_files     5.9Mb
    base_files   6.3Mb
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    libs  23.5Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘cmprsk’ ‘colorspace’ ‘etm’ ‘fracdiff’ ‘gtable’ ‘munsell’
  ‘numDeriv’ ‘plyr’ ‘quadprog’ ‘scales’ ‘timeDate’ ‘tseries’ ‘zoo’
  All declared Imports should be used.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
Found the following significant warnings:
  #warning Using clang version 3, assuming nullptr defined
See ‘/data/gannet/ripley/R/packages/tests-clang/ManifoldOptim.Rcheck/00install.out’ for details.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
File ‘ManifoldOptim/libs/ManifoldOptim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 32.7Mb
  sub-directories of 1Mb or more:
    mapdata  32.6Mb
Error in re-building vignettes:
  ...
Quitting from lines 264-270 (estimaterates.Rmd) 
Error: processing vignette 'estimaterates.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.5Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   4.5Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
File ‘maxent/libs/maxent.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   9.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   2.8Mb
installed size is 26.6Mb
  sub-directories of 1Mb or more:
    libs  25.9Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘glmgraph’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   5.0Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.5Mb
Error in re-building vignettes:
  ...
Quitting from lines 101-107 (Getting-started.rnw) 
Error: processing vignette 'Getting-started.rnw' failed with diagnostics:
1: Unknown IO error2: failed to load external entity "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nucleotide&term=cytB%20%5Ball%5D%20OR%20Cytb%20%5Ball%5D%20OR%20CYTB%20%5Ball%5D%20OR%20cytb%20%5Ball%5D%20OR%20CytB%20%5Ball%5D&rettype=gb&retmode=xml"
Execution halted
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘RGtk2’ ‘RNifti’ ‘cairoDevice’ ‘gtools’ ‘jsonlite’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   2.1Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.1Mb
Running ‘test_all.r’
Running the tests in ‘tests/test_all.r’ failed.
Complete output:
  > library('Metrics')
  > library('RUnit')
  Error in library("RUnit") : there is no package called 'RUnit'
  Execution halted
Namespaces in Imports field not imported from:
  ‘ggmap’ ‘plotly’
  All declared Imports should be used.
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
    misc   1.1Mb
File ‘mFilter/R/zzz.R’:
  .onLoad calls:
    writeLines(strwrap(txt, indent = 4, exdent = 4))

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

.onLoad: warning in packageDescription("mFilter", lib = mylib): partial
  argument match of 'lib' to 'lib.loc'
bkfilter: warning in ts(x.cycle, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
bkfilter: warning in ts(x.trend, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
bkfilter: warning in ts(x, star = tsp.x[1], frequency = tsp.x[3]):
  partial argument match of 'star' to 'start'
bwfilter: warning in ts(x.cycle, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
bwfilter: warning in ts(x.trend, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
bwfilter: warning in ts(x, star = tsp.x[1], frequency = tsp.x[3]):
  partial argument match of 'star' to 'start'
cffilter: warning in ts(x.cycle, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
cffilter: warning in ts(x.trend, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
cffilter: warning in ts(x, star = tsp.x[1], frequency = tsp.x[3]):
  partial argument match of 'star' to 'start'
hpfilter: warning in ts(x.cycle, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
hpfilter: warning in ts(x.trend, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
hpfilter: warning in ts(x, star = tsp.x[1], frequency = tsp.x[3]):
  partial argument match of 'star' to 'start'
Package suggested but not available for checking: ‘grasp2db’
Namespaces in Imports field not imported from:
  ‘DiceDesign’ ‘MaxPro’ ‘doSNOW’
  All declared Imports should be used.
cdf.pval: no visible global function definition for ‘median’
cdf.pval: no visible binding for global variable ‘ecdf’
find_hits: no visible global function definition for ‘na.omit’
mad.scores: no visible global function definition for ‘as.formula’
mad.scores: no visible binding for global variable ‘median’
mad.scores: no visible binding for global variable ‘mad’
rm.outliers: no visible global function definition for ‘as.formula’
rm.outliers: no visible binding for global variable ‘median’
rm.outliers: no visible binding for global variable ‘mad’
Undefined global functions or variables:
  as.formula ecdf mad median na.omit
Consider adding
  importFrom("stats", "as.formula", "ecdf", "mad", "median", "na.omit")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cluster’ ‘dendextend’ ‘npmv’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Namespace in Imports field not imported from: ‘rjags’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘broom’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   6.4Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   6.9Mb
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.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Found the following significant warnings:
  Warning: GNU Extension: Symbol ‘n’ is used before it is typed at (1)
  Warning: Pointer at (1) in pointer assignment might outlive the pointer target [-Wtarget-lifetime]
  Warning: GNU Extension: Different type kinds at (1)
See ‘/data/gannet/ripley/R/packages/tests-clang/mra.Rcheck/00install.out’ for details.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
installed size is 29.7Mb
  sub-directories of 1Mb or more:
    libs  29.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    examples   1.8Mb
    libs       3.2Mb
installed size is 26.7Mb
  sub-directories of 1Mb or more:
    libs  26.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Found the following significant warnings:
  Warning: GNU Extension: Symbol ‘k’ is used before it is typed at (1)
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Different type kinds at (1)
See ‘/data/gannet/ripley/R/packages/tests-clang/multitaper.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    java  13.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.4Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
Error in re-building vignettes:
  ...

Attaching package: 'lubridate'

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

    date

Quitting from lines 110-111 (naptime.Rmd) 
Error: processing vignette 'naptime.Rmd' failed with diagnostics:
unhandled input for naptime(): Error: unhandled input for naptime(): Error in validObject(.Object): invalid class "Period" object: periods must have integer values

Execution halted
Running ‘test-all.r’
Running the tests in ‘tests/test-all.r’ failed.
Complete output:
  > library(testthat)
  > library(nat.templatebrains)
  Loading required package: rgl
  Loading required package: nat
  Some nat functions depend on a CMTK installation. See ?cmtk and README.md for details.
  
  Attaching package: 'nat'
  
  The following object is masked from 'package:rgl':
  
      as.mesh3d
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, union
  
  > test_check("nat.templatebrains")
  1. Failure: bridging graph and friends work (@test-transformation.r#82) --------
  `df2` not equal to `df`.
  Attributes: < Component "row.names": Mean relative difference: 0.04081633 >
  
  
  skipping transformation tests since CMTK is not installed
  testthat results ================================================================
  OK: 42 SKIPPED: 1 FAILED: 1
  1. Failure: bridging graph and friends work (@test-transformation.r#82) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.5Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   5.0Mb
File ‘NetRep/libs/NetRep.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
Namespace in Imports field not imported from: ‘htmlTable’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    CppCode        2.6Mb
    R              2.5Mb
    classic-bugs   1.6Mb
    include        3.9Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.3Mb
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Symbol ‘n’ is used before it is typed at (1)
See ‘/data/gannet/ripley/R/packages/tests-clang/nmcdr.Rcheck/00install.out’ for details.
Package unavailable to check Rd xrefs: ‘RcppOctave’
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rms’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘mclust’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
Note: found 13172 marked Latin-1 strings
installed size is 39.0Mb
  sub-directories of 1Mb or more:
    extdata  38.9Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   8.7Mb
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())
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
installed size is 23.5Mb
  sub-directories of 1Mb or more:
    libs  23.4Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration INTEGER*4 at (1)
See ‘/data/gannet/ripley/R/packages/tests-clang/oblique.tree.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
See ‘/data/gannet/ripley/R/packages/tests-clang/OBsMD.Rcheck/00install.out’ for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R            1.4Mb
    test_files   4.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    help   2.1Mb
Found the following significant warnings:
  Warning: GNU Extension: Different type kinds at (1)
See ‘/data/gannet/ripley/R/packages/tests-clang/oc.Rcheck/00install.out’ for details.
installed size is 103.6Mb
  sub-directories of 1Mb or more:
    libs  103.2Mb
Running examples in ‘onlineCPD-Ex.R’ failed
The error most likely occurred in:

> ### Name: findCP
> ### Title: Wisely Pick Changepoints
> ### Aliases: findCP
> 
> ### ** Examples
> 
> ## Two changepoints within \code{buffer} points:
> set.seed(5)
> y <- c(rnorm(15,0.5,0.01),0.505,0.51,0.015,0.52,rnorm(15,0.6,0.05))
> res <- offlineCPD(y)
> plot(res,buffer=10)     ## Will replace the two changepoints
Error: Aesthetics must be either length 1 or the same as the data (1): x, y, xend, yend, alpha
Execution halted
Package suggested but not available for checking: ‘RAppArmor’
installed size is 119.1Mb
  sub-directories of 1Mb or more:
    R         1.1Mb
    libs    110.9Mb
    models    4.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    java     1.2Mb
    models   6.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
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.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    nifti   3.8Mb
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.
Namespace in Imports field not imported from: ‘bitops’
  All declared Imports should be used.
[,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'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data        1.6Mb
    localdata   3.1Mb
Namespace in Imports field not imported from: ‘RSQLite’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
Found the following significant warnings:
  Warning: CHARACTER expression at (1) is being truncated (6/1) [-Wcharacter-truncation]
  Warning: CHARACTER expression will be truncated in assignment (1/9) at (1) [-Wcharacter-truncation]
  Warning: CHARACTER expression will be truncated in assignment (1/19) at (1) [-Wcharacter-truncation]
  Warning: CHARACTER expression will be truncated in assignment (1/16) at (1) [-Wcharacter-truncation]
  Warning: CHARACTER expression will be truncated in assignment (1/12) at (1) [-Wcharacter-truncation]
See ‘/data/gannet/ripley/R/packages/tests-clang/pbdSLAP.Rcheck/00install.out’ for details.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    lib   9.4Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc        1.5Mb
    examples   1.7Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   2.1Mb
    libs   5.8Mb
Running examples in ‘pcalg-Ex.R’ failed
The error most likely occurred in:

> ### Name: GaussL0penIntScore-class
> ### Title: Class '"GaussL0penIntScore"'
> ### Aliases: GaussL0penIntScore-class local.score,GaussL0penIntScore-method
> ###   global.score,GaussL0penIntScore-method
> ###   local.mle,GaussL0penIntScore-method
> ###   global.mle,GaussL0penIntScore-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> ##################################################
> ## Using Gaussian Data
> ##################################################
> ## Load predefined data
> data(gmInt)
> 
> ## Define the score object
> score <- new("GaussL0penIntScore", gmInt$x, gmInt$targets, gmInt$target.index) 
Warning in if (sort(unique(object$pp.dat$target.index)) != 1:length(object$pp.dat$targets)) return("Data from all intervention targets must be available") :
  the condition has length > 1 and only the first element will be used
Warning in if (unique(object$pp.dat$scatter.index) != 1:length(object$pp.dat$scatter)) { :
  the condition has length > 1 and only the first element will be used
Error in validObject(.Object) : 
  invalid class “GaussL0penIntScore” object: The scatter matrices have invalid dimensions.
Calls: new -> initialize -> initialize -> validObject
Execution halted
Error in re-building vignettes:
  ...
Loading required package: Rgraphviz
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect,
    is.unsorted, lapply, lengths, mapply, match, mget, order,
    paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans,
    rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: grid
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf

Error: processing vignette 'pcalgDoc.Rnw' failed with diagnostics:
 chunk 17 (label = pcExpl-plot) 
Error in value[[3L]](cond) : 
  Instance of class 'GaussParDAG' cannot be created.
Execution halted
Namespace in Imports field not imported from: ‘fda’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘car’ ‘sandwich’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
File ‘pgam/R/zzz.r’:
  .onLoad calls:
    require("stats", character.only = TRUE, quietly = TRUE, warn.conflicts = FALSE)
    require("utils", character.only = TRUE, quietly = TRUE, warn.conflicts = FALSE)
    cat("This is pgam library version", ver, "\n", sep = " ")

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

This is pgam library version 0.4.12 
pgam: warning in assign("loglik", NULL, env = pgam.env): partial
  argument match of 'env' to 'envir'
pgam: warning in get("loglik", env = pgam.env): partial argument match
  of 'env' to 'envir'
pgam.likelihood: warning in assign("loglik", loglik, env = env):
  partial argument match of 'env' to 'envir'
envelope.pgam: no visible global function definition for ‘par’
periodogram: no visible global function definition for ‘axis’
periodogram: no visible global function definition for ‘title’
periodogram: no visible global function definition for ‘lines’
plot.pgam: no visible global function definition for ‘plot’
Undefined global functions or variables:
  axis lines par plot title
Consider adding
  importFrom("graphics", "axis", "lines", "par", "plot", "title")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘quanteda’
  All declared Imports should be used.
installed size is 40.1Mb
  sub-directories of 1Mb or more:
    libs  39.4Mb
Namespaces in Imports field not imported from:
  ‘gplots’ ‘phytools’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Namespace in Imports field not imported from: ‘ape’
  All declared Imports should be used.
installed size is 29.2Mb
  sub-directories of 1Mb or more:
    libs  29.1Mb
Namespaces in Imports field not imported from:
  ‘hexbin’ ‘quantreg’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   2.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
Namespaces in Imports field not imported from:
  ‘jsonlite’ ‘readr’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*4 at (1)
See ‘/data/gannet/ripley/R/packages/tests-clang/popsom.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
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 ‘/data/gannet/ripley/R/packages/tests-clang/powell.Rcheck/00install.out’ for details.
Registration problems:
  Evaluating ‘paste("stat", stat.index, sep = "")’ during check gives error
‘object 'stat.index' not found’:
   .C(paste("stat", stat.index, sep = ""), 0, 0L, 0, 0L, name = c("1", 
       rep(" ", 49)), 1L, 0, 0L, 0, 0, 0, 0L, 0L, 0L, 0, 0)
  Evaluating ‘paste("stat", stat.index, sep = "")’ during check gives error
‘object 'stat.index' not found’:
   .C(paste("stat", stat.index, sep = ""), 0, 0L, 0, 0L, name = c("1", 
       rep(" ", 49)), 1L, 0, 0L, 0, 0, 0, 0L, 0L, 0L, 0, 0)
  Evaluating ‘paste("stat", stat.index, sep = "")’ during check gives error
‘object 'stat.index' not found’:
   .C(paste("stat", stat.index, sep = ""), 0, 0L, 0, 0L, name = c("1", 
       rep(" ", 49)), 1L, 0, 0L, 0, 0, 0, 0L, 0L, 0L, 0, 0)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
Missing or unexported object: ‘cowplot::switch_axis_position’
Namespaces in Imports field not imported from:
  ‘graphics’ ‘stats’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.3Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    extdata  10.9Mb
    libs      1.1Mb
Package suggested but not available for checking: ‘qtbase’
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
Namespaces in Imports field not imported from:
  ‘forecast’ ‘knitr’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Found the following significant warnings:
  Warning: GNU Extension: Different type kinds at (1)
See ‘/data/gannet/ripley/R/packages/tests-clang/PSM.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    dict   5.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc        3.5Mb
    examples   2.3Mb
Found the following significant warnings:
  Warning: GNU Extension: Symbol ‘n’ is used before it is typed at (1)
See ‘/data/gannet/ripley/R/packages/tests-clang/pvrank.Rcheck/00install.out’ for details.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
Package suggested but not available for checking: ‘biom’
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  11.8Mb
Namespace in Imports field not imported from: ‘xts’
  All declared Imports should be used.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/qtbase.Rcheck/00install.out’ for details.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    contrib   3.8Mb
    doc       2.9Mb
    libs      1.2Mb
Package required but not available: ‘qtbase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    2.3Mb
    libs   5.6Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   4.1Mb
Note: found 21 marked Latin-1 strings
  Note: found 7 marked UTF-8 strings
Namespaces in Imports field not imported from:
  ‘afex’ ‘data.table’ ‘dplyr’ ‘lmerTest’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    Output   2.2Mb
    bin      2.6Mb
Namespace in Imports field not imported from: ‘car’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘AlgDesign’ ‘psych’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   1.4Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    htmlwidgets   6.4Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   3.6Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.7Mb
    libs  10.3Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    etc    1.9Mb
    po     1.2Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    blp    7.1Mb
    libs   5.0Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    java   7.8Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    cont  25.5Mb
Package suggested but not available for checking: ‘ROpenOffice’
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   4.0Mb
    po    2.2Mb
Namespace in Imports field not imported from: ‘FSA’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    include   4.7Mb
    libs      1.1Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    lib    4.9Mb
    libs   1.5Mb
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    include   4.6Mb
    libs     21.9Mb
Error in re-building vignettes:
  ...
Loading required package: inline
installed size is 50.1Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib      37.3Mb
    libs     10.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    include   6.3Mb
    libs      3.1Mb
Registration problem:
  symbol ‘symbol’ in the local frame:
   .Call(symbol)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
installed size is 147.4Mb
  sub-directories of 1Mb or more:
    include    4.4Mb
    lib      108.0Mb
    libs      34.9Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘smcure’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rcompression’
dieharder.default: no visible binding for global variable
  ‘.dieharder.generators’
dieharder.default: no visible binding for global variable
  ‘.dieharder.tests’
plot.dieharder: no visible global function definition for ‘par’
plot.dieharder: no visible global function definition for ‘hist’
plot.dieharder: no visible global function definition for ‘lines’
plot.dieharder: no visible global function definition for ‘density’
plot.dieharder: no visible global function definition for ‘plot’
plot.dieharder: no visible global function definition for ‘ecdf’
plot.dieharder: no visible global function definition for ‘segments’
plot.dieharder: no visible global function definition for ‘mtext’
plot.dieharder: no visible global function definition for ‘ks.test’
plot.dieharder: no visible global function definition for ‘wilcox.test’
summary.dieharder: no visible global function definition for ‘stem’
summary.dieharder: no visible global function definition for ‘ks.test’
summary.dieharder: no visible global function definition for
  ‘wilcox.test’
Undefined global functions or variables:
  .dieharder.generators .dieharder.tests density ecdf hist ks.test
  lines mtext par plot segments stem wilcox.test
Consider adding
  importFrom("graphics", "hist", "lines", "mtext", "par", "plot",
             "segments", "stem")
  importFrom("stats", "density", "ecdf", "ks.test", "wilcox.test")
to your NAMESPACE file.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘hms’
  All declared Imports should be used.
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)
Error in re-building vignettes:
  ...
Loading required package: REBayes
Loading required package: Matrix
Quitting from lines 291-315 (medde.Rnw) 
Error: processing vignette 'medde.Rnw' failed with diagnostics:
argument is of length zero
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   3.4Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs  11.7Mb
Namespaces in Imports field not imported from:
  ‘igraph’ ‘rJava’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘Rcplex’
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    java   5.8Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/restfulr.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘spatstat’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: GNU Extension: Non-default type object or sequence zz in EQUIVALENCE statement at (1) with objects of different type
  Warning: GNU Extension: Nonstandard type declaration REAL*4 at (1)
  Warning: iteration 7 invokes undefined behavior [-Waggressive-loop-optimizations]
  Warning: GNU Extension: Symbol ‘n’ is used before it is typed at (1)
See ‘/data/gannet/ripley/R/packages/tests-clang/rexpokit.Rcheck/00install.out’ for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    java   5.3Mb
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc     2.0Mb
    fonts   1.5Mb
    libs    2.4Mb
Package unavailable to check Rd xrefs: ‘magick’
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extra   9.4Mb
installed size is 22.0Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    help  10.5Mb
    libs   7.9Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc   9.5Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-clang/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API call to R: ‘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 the system RNG.
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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘crul’
  All declared Imports should be used.
Found the following significant warnings:
  libjson/Source/JSONGlobals.h:43:50: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
  libjson/Source/JSONGlobals.h:44:49: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
  JSONValidator.cpp:394:105: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
  JSONValidator.cpp:397:104: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
See ‘/data/gannet/ripley/R/packages/tests-clang/RJSONIO.Rcheck/00install.out’ for details.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    datasets   8.6Mb
installed size is 45.1Mb
  sub-directories of 1Mb or more:
    exe  45.0Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘arules’ ‘pmml’ ‘rJava’
  All declared Imports should be used.
File ‘rlas/libs/rlas.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Running ‘testthat.R’ [45s/52s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rmapshaper)
  > 
  > test_check("rmapshaper")
  1. Failure: ms_simplify works with lines (@test-simplify.R#442) ----------------
  ms_simplify(line_list) not equal to geojson_list(expected_json).
  Component "features": Component 1: Component 2: Component 2: Component 2: Component 2: Mean relative difference: 1.985531e-08
  
  
  testthat results ================================================================
  OK: 252 SKIPPED: 0 FAILED: 1
  1. Failure: ms_simplify works with lines (@test-simplify.R#442) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    rmd   6.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    java   4.5Mb
Namespaces in Imports field not imported from:
  ‘mnormt’ ‘pwr’
  All declared Imports should be used.
.onLoad: warning in dir(dll.path, pattern = this.ext, full = FALSE):
  partial argument match of 'full' to 'full.names'
diagnos.envel: warning in apply(jumpDistRes, MARG = 2, FUN = quantile,
  probs = perc[1], na.rm = TRUE): partial argument match of 'MARG' to
  'MARGIN'
diagnos.envel: warning in apply(jumpDistRes, MARG = 2, FUN = quantile,
  probs = perc[2], na.rm = TRUE): partial argument match of 'MARG' to
  'MARGIN'
diagnos.envel: no visible global function definition for ‘quantile’
diagnos.envel: no visible global function definition for ‘qnorm’
diagnos.envel: no visible binding for global variable ‘quantile’
hrplot: no visible global function definition for ‘plot’
hrplot: no visible global function definition for ‘lines’
hrplot: no visible global function definition for ‘abline’
hrplot: no visible global function definition for ‘text’
sim.chain: no visible global function definition for ‘rnorm’
simRandWalk: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline lines plot qnorm quantile rnorm text
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "text")
  importFrom("stats", "qnorm", "quantile", "rnorm")
to your NAMESPACE file.
File ‘RMC/libs/RMC.so’:
  Found ‘_ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
    Objects: ‘RMC.o’, ‘predict.o’
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘ap.o’
File ‘RMC/libs/RMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

It is good practice to use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
mosek: no visible global function definition for ‘help’
mosek_lptoprob: no visible global function definition for ‘is’
mosek_lptoprob: no visible global function definition for ‘as’
mosek_qptoprob: no visible global function definition for ‘is’
mosek_qptoprob: no visible global function definition for ‘as’
mosek_read: no visible global function definition for ‘help’
mosek_write: no visible global function definition for ‘help’
obtain_sparsematrix: no visible global function definition for ‘is’
obtain_sparsematrix: no visible global function definition for ‘as’
Undefined global functions or variables:
  as help is
Consider adding
  importFrom("methods", "as", "is")
  importFrom("utils", "help")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/progress/include/RProgress.h:172:13: warning: variable length arrays are a C99 feature [-Wvla-extension]
  /data/gannet/ripley/R/test-clang/progress/include/RProgress.h:220:16: warning: variable length arrays are a C99 feature [-Wvla-extension]
See ‘/data/gannet/ripley/R/packages/tests-clang/rncl.Rcheck/00install.out’ for details.
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    libs  23.6Mb
installed size is 82.1Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     80.0Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R   9.7Mb
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
See ‘/data/gannet/ripley/R/packages/tests-clang/RobustEM.Rcheck/00install.out’ for details.
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
Found the following significant warnings:
  Warning: control reaches end of non-void function [-Wreturn-type]
See ‘/data/gannet/ripley/R/packages/tests-clang/robust.Rcheck/00install.out’ for details.
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.
Package which this enhances but not available for checking: ‘ROI.plugin.cplex’
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    libs  22.8Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.5Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   3.0Mb
Running examples in ‘rplexos-Ex.R’ failed
The error most likely occurred in:

> ### Name: process_folder
> ### Title: Convert PLEXOS files to SQLite databases
> ### Aliases: process_folder process_input process_solution
> 
> ### ** Examples
> 
> # Process the folder with the solution file provided by rplexos
> location_solution <- location_solution_rplexos()
> process_folder(location_solution)
Error: 'folders' must be a vector of existing folders or the wildcard "*"
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rplexos)
  > 
  > test_check("rplexos")
  Error: 'folders' must be a vector of existing folders or the wildcard "*"
  testthat results ================================================================
  OK: 0 SKIPPED: 6 FAILED: 0
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 44-45 (rplexos.Rmd) 
Error: processing vignette 'rplexos.Rmd' failed with diagnostics:
'folders' must be a vector of existing folders or the wildcard "*"
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Namespaces in Imports field not imported from:
  ‘binman’ ‘httr’
  All declared Imports should be used.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-clang/Rserve.Rcheck/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 the system RNG.
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 use registered native symbols and to disable
symbol search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   9.1Mb
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Error in re-building vignettes:
  ...
Quitting from lines 282-283 (RSNPset.Rnw) 
Error: processing vignette 'RSNPset.Rnw' failed with diagnostics:
ERROR: The estimated pi0 <= 0. Check that you have valid p-values or use a different range of lambda.
Execution halted
installed size is 48.4Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  46.9Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is 58.0Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  54.8Mb
installed size is 242.4Mb
  sub-directories of 1Mb or more:
    libs  240.1Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Namespace in Imports field not imported from: ‘mc2d’
  All declared Imports should be used.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    Lib  11.9Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘stats’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   1.7Mb
installed size is 37.0Mb
  sub-directories of 1Mb or more:
    libs  36.3Mb
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.
Package suggested but not available for checking: ‘gpuR’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    include   5.3Mb
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    test  19.6Mb
Found the following significant warnings:
  Warning: GNU Extension: Different type kinds at (1)
See ‘/data/gannet/ripley/R/packages/tests-clang/rvsel.Rcheck/00install.out’ for details.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.6Mb
Running examples in ‘rwunderground-Ex.R’ failed
The error most likely occurred in:

> ### Name: set_location
> ### Title: Specifies location of request
> ### Aliases: set_location
> 
> ### ** Examples
> 
> set_location(zip_code = "90210")
[1] "90210"
> set_location(territory = "Hawaii", city = "Honolulu")
Error in `[.data.frame`(countrycode::countrycode_data, , c("country.name",  : 
  undefined columns selected
Calls: set_location ... is_valid_territory -> list_countries -> [ -> [.data.frame
Execution halted
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs    6.9Mb
    yacas   1.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    sample_data   3.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Namespace in Imports field not imported from: ‘spanel’
  All declared Imports should be used.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.7Mb
c,scidbdf: warning in build_dim_schema(x, newname = j): partial
  argument match of 'newname' to 'newnames'
.format: no visible global function definition for ‘capture.output’
.scidbstr: no visible global function definition for ‘capture.output’
glm.fit_scidb: no visible global function definition for ‘gaussian’
glm.fit_scidb: no visible global function definition for ‘pnorm’
glm_scidb: no visible global function definition for ‘gaussian’
glm_scidb: no visible global function definition for ‘as.formula’
iqiter : nextEl: no visible global function definition for ‘read.table’
iquery: no visible global function definition for ‘read.table’
model_scidb: no visible global function definition for ‘as.formula’
model_scidb: no visible global function definition for ‘terms’
model_scidb: no visible global function definition for ‘drop.terms’
predict.glm_scidb: no visible global function definition for ‘coef’
print.glm_scidb: no visible global function definition for ‘coef’
summary.glm_scidb: no visible global function definition for ‘coef’
glm.fit,scidb-ANY-MNSN: no visible global function definition for
  ‘gaussian’
glm.fit,scidb-ANY-MNSN: no visible global function definition for
  ‘pnorm’
glm,ANY-ANY-scidbdf: no visible global function definition for
  ‘gaussian’
glm,ANY-ANY-scidbdf: no visible global function definition for
  ‘as.formula’
image,scidb: no visible global function definition for ‘axis’
Undefined global functions or variables:
  as.formula axis capture.output coef drop.terms gaussian pnorm
  read.table terms
Consider adding
  importFrom("graphics", "axis")
  importFrom("stats", "as.formula", "coef", "drop.terms", "gaussian",
             "pnorm", "terms")
  importFrom("utils", "capture.output", "read.table")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   2.0Mb
Namespaces in Imports field not imported from:
  ‘gbm’ ‘graphics’ ‘ncdf4’ ‘rgdal’ ‘sp’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: Integer division truncated to constant ‘67108861’ at (1) [-Winteger-division]
See ‘/data/gannet/ripley/R/packages/tests-clang/seem.Rcheck/00install.out’ for details.
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.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   9.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
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.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Registration problems:
  symbol ‘call_sym’ in the local frame:
   .Call(call_sym, PACKAGE = PACKAGE, args$data, args$block_dim, 
       args$groupWeights, args$parameterWeights, args$alpha, lambda, 
       idx, algorithm.config)
  symbol ‘call_sym’ in the local frame:
   .Call(call_sym, PACKAGE = PACKAGE, args$data, args$block_dim, 
       args$groupWeights, args$parameterWeights, args$alpha, d, 
       lambda.min, lambda.min.rel, algorithm.config)
  symbol ‘call_sym’ in the local frame:
   .Call(call_sym, PACKAGE = PACKAGE, data, beta)
  symbol ‘call_sym’ in the local frame:
   .Call(call_sym, PACKAGE = PACKAGE, args$data, args$test_data, 
       args$block_dim, args$groupWeights, args$parameterWeights, 
       args$alpha, lambda.list[[task]], algorithm.config)
  symbol ‘call_sym’ in the local frame:
   .Call(call_sym, PACKAGE = PACKAGE, args$data, args$test_data, 
       args$block_dim, args$groupWeights, args$parameterWeights, 
       args$alpha, lambda.list[[task]], algorithm.config)
  symbol ‘call_sym’ in the local frame:
   .Call(call_sym, PACKAGE = PACKAGE, args$data, args$block_dim, 
       args$groupWeights, args$parameterWeights, algorithm.config)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   7.7Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    www   9.7Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘gridExtra’ ‘latticeExtra’ ‘msm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘shinyBS’ ‘shinythemes’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    www   6.4Mb
Running ‘testthat.R’ [13s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(simmer.plot)
  Loading required package: simmer
  Loading required package: ggplot2
  > 
  > test_check("simmer.plot")
  1. Failure: a rollback with variable amount is correctly converted to graph (@test-plot-trajectory.R#38) 
  edges_df$to not equal to c(2, 1).
  1/2 mismatches
  [2] 2 - 1 == 1
  
  
  2. Failure: a rollback with variable amount is correctly converted to graph (@test-plot-trajectory.R#39) 
  edges_df$to not equal to c(2, 1).
  1/2 mismatches
  [2] 2 - 1 == 1
  
  
  3. Failure: a complex trajectory is correctly converted to graph (@test-plot-trajectory.R#68) 
  edges_df$to not equal to c(...).
  1/22 mismatches
  [19] 15 - 1 == 14
  
  
  testthat results ================================================================
  OK: 86 SKIPPED: 0 FAILED: 3
  1. Failure: a rollback with variable amount is correctly converted to graph (@test-plot-trajectory.R#38) 
  2. Failure: a rollback with variable amount is correctly converted to graph (@test-plot-trajectory.R#39) 
  3. Failure: a complex trajectory is correctly converted to graph (@test-plot-trajectory.R#68) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
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'
Namespace in Imports field not imported from: ‘pracma’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
Namespace in Imports field not imported from: ‘mcmc’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.5Mb
Note: found 15 marked Latin-1 strings
  Note: found 2 marked UTF-8 strings
Running ‘testthat.R’ [27s/39s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(smapr)
  > 
  > test_check("smapr")
  1. Error: invalid output directories cause errors (@test-download_smap.R#4) ----
  Data are not available for this date. 2015.03.31 does not exist at ftp://n5eil01u.ecs.nsidc.org/SAN/SMAP/SPL3SMP.003/
  1: find_smap(id = "SPL3SMP", dates = "2015-03-31", version = 3) at testthat/test-download_smap.R:4
  2: lapply(dates, find_for_date, id = id, version = version)
  3: FUN(X[[i]], ...)
  4: validate_ftp_request(id, date, version)
  5: validate_date(id, version, date)
  6: stop(paste(prefix, suffix))
  
  2. Error: invalid datasets cause errors (@test-extract_smap.R#4) ---------------
  Data are not available for this date. 2015.03.31 does not exist at ftp://n5eil01u.ecs.nsidc.org/SAN/SMAP/SPL3SMP.003/
  1: find_smap(id = "SPL3SMP", dates = "2015-03-31", version = 3) at testthat/test-extract_smap.R:4
  2: lapply(dates, find_for_date, id = id, version = version)
  3: FUN(X[[i]], ...)
  4: validate_ftp_request(id, date, version)
  5: validate_date(id, version, date)
  6: stop(paste(prefix, suffix))
  
  testthat results ================================================================
  OK: 9 SKIPPED: 14 FAILED: 2
  1. Error: invalid output directories cause errors (@test-download_smap.R#4) 
  2. Error: invalid datasets cause errors (@test-extract_smap.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
Found the following significant warnings:
  Warning: GNU Extension: Symbol ‘ntt’ is used before it is typed at (1)
See ‘/data/gannet/ripley/R/packages/tests-clang/smint.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘compiler’ ‘lmtest’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   3.8Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘nlme’ ‘survival’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gtools’ ‘hashmap’ ‘uuid’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
Found the following significant warnings:
  Warning: GNU Extension: Different type kinds at (1)
See ‘/data/gannet/ripley/R/packages/tests-clang/spanr.Rcheck/00install.out’ for details.
Running ‘testthat.r’
Running the tests in ‘tests/testthat.r’ failed.
Complete output:
  > library(testthat)
  Error in library(testthat) : there is no package called 'testthat'
  Execution halted
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Running examples in ‘spatialEco-Ex.R’ failed
The error most likely occurred in:

> ### Name: trig.trans
> ### Title: Calculates the trigonomic slope and aspect transformation
> ### Aliases: trig.trans
> 
> ### ** Examples
> 
>  trig.trans(slope = 48.146, aspect = 360.000)
[1] -0.2383874
> 
>  library(raster)
Loading required package: sp
>  elev <- getData('alt', country='CHE')
trying URL 'http://biogeo.ucdavis.edu/data/diva/msk_alt/CHE_msk_alt.zip'
Warning in utils::download.file(url = aurl, destfile = fn, method = "auto",  :
  cannot open URL 'http://biogeo.ucdavis.edu/data/diva/msk_alt/CHE_msk_alt.zip': HTTP status was '403 Forbidden'
Error in utils::download.file(url = aurl, destfile = fn, method = "auto",  : 
  cannot open URL 'http://biogeo.ucdavis.edu/data/diva/msk_alt/CHE_msk_alt.zip'
Calls: getData -> .raster -> .download -> <Anonymous>
Execution halted
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Old-style initialization at (1)
  Warning: GNU Extension: Different type kinds at (1)
See ‘/data/gannet/ripley/R/packages/tests-clang/spatialkernel.Rcheck/00install.out’ for details.
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    R      4.9Mb
    data   3.4Mb
    doc    4.6Mb
    help   5.0Mb
    libs   1.7Mb
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  18.4Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    1.5Mb
    etc    1.7Mb
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.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
See ‘/data/gannet/ripley/R/packages/tests-clang/SpherWave.Rcheck/00install.out’ for details.
Running examples in ‘spider-Ex.R’ failed
The error most likely occurred in:

> ### Name: seqStat
> ### Title: Sequence statistics
> ### Aliases: seqStat
> ### Keywords: Barcoding Utilities
> 
> ### ** Examples
> 
> data(anoteropsis)
> seqStat(anoteropsis)
Error in checkDNA(x, gapsAsMissing = TRUE) : object 'output' not found
Calls: seqStat -> sapply -> lapply -> FUN -> checkDNA
Execution halted
sh: -version: command not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
sh: -version: command not found
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
sh: -version: command not found
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
sh: -version: command not found
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
sh: -version: command not found
sh: -version: command not found
sh: -version: command not found
sh: -version: command not found
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Note: found 8 marked Latin-1 strings
  Note: found 83 marked UTF-8 strings
Found the following significant warnings:
  Warning: GNU Extension: Symbol ‘k’ is used before it is typed at (1)
See ‘/data/gannet/ripley/R/packages/tests-clang/spsmooth.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘geoR’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: CHARACTER expression will be truncated in assignment (8/9) at (1) [-Wcharacter-truncation]
See ‘/data/gannet/ripley/R/packages/tests-clang/srd.Rcheck/00install.out’ for details.
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.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    include   8.8Mb
    lib       1.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   4.9Mb
Namespace in Imports field not imported from: ‘MCMCpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘rpart’
  All declared Imports should be used.
Found the following significant warnings:
  decTreeImpFuncCpp.cpp:1677:43: warning: unknown escape sequence '\ ' [-Wunknown-escape-sequence]
See ‘/data/gannet/ripley/R/packages/tests-clang/StatMethRank.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
See ‘/data/gannet/ripley/R/packages/tests-clang/stima.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘tm’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: ‘pi’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-clang/stpp.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Namespaces in Imports field not imported from:
  ‘broom’ ‘car’ ‘lmerTest’ ‘pbkrtest’
  All declared Imports should be used.
Running ‘testthat.R’ [7s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(subprocess)
  > 
  > # See for more details:
  > # https://github.com/hadley/testthat/issues/144
  > # https://github.com/hadley/testthat/issues/86
  > # https://github.com/luckyrandom/cmaker/commit/b85813ac2b7aef69932eca8fbb4fa0ec225e0af0
  > #
  > # When R CMD check runs tests, it sets R_TESTS. When the tests
  > # themeselves run R CMD xxxx, as is the case with the tests in
  > # devtools, having R_TESTS set causes errors because it confuses
  > # the R subprocesses. Unsetting it here avoids those problems.
  > #
  > # We need this because we spawn child R processes and they get very
  > # confused if this variable (R_TESTS) is present in their environment.
  > Sys.setenv("R_TESTS" = "")
  > 
  > test_check("subprocess")
  1. Error: child process is terminated in Linux (@test-termination.R#85) --------
  is_process_handle(handle) is not TRUE
  1: expect_true(wait_until_appears(child_id)) at testthat/test-termination.R:85
  2: expect(identical(as.vector(object), TRUE), sprintf("%s isn't true.", lab), info = info)
  3: as.expectation(exp, ..., srcref = srcref)
  4: identical(as.vector(object), TRUE)
  5: as.vector(object)
  6: wait_until_appears(child_id)
  7: process_wait(handle, TIMEOUT_IMMEDIATE) at /data/gannet/ripley/R/packages/tests-clang/subprocess.Rcheck/tests/testthat/helper-processes.R:56
  8: stopifnot(is_process_handle(handle))
  9: stop(msg, call. = FALSE, domain = NA)
  
  testthat results ================================================================
  OK: 69 SKIPPED: 2 FAILED: 1
  1. Error: child process is terminated in Linux (@test-termination.R#85) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘ISwR’ ‘MASS’ ‘corpcor’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   1.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.5Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
See ‘/data/gannet/ripley/R/packages/tests-clang/survrec.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘graphics’ ‘methods’ ‘stats’
  All declared Imports should be used.
Package in Depends field not imported from: ‘kernlab’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Different type kinds at (1)
  Warning: GNU Extension: initialization of common block variable ‘iset’ in DATA statement at (1)
  Warning: GNU Extension: Variable ‘iset’ at (1) is in COMMON but only in BLOCK DATA initialization is allowed
  Warning: GNU Extension: Missing comma at (1)
  Warning: CHARACTER expression will be truncated in assignment (10/13) at (1) [-Wcharacter-truncation]
  Warning: ‘pst_kg’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘burn_frlb’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘hi_ovr’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘frac_harvk’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘lai_init’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (1/3) at (1) [-Wcharacter-truncation]
  Warning: ‘fr_curb’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-clang/SWATmodel.Rcheck/00install.out’ for details.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/sybilSBML.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘foreach’ ‘parallel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    tklibs   4.9Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    sql   8.7Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.9Mb
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
installed size is 36.6Mb
  sub-directories of 1Mb or more:
    libs  35.4Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
Namespace in Imports field not imported from: ‘modules’
  All declared Imports should be used.
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.5Mb
    libs   6.4Mb
Namespace in Imports field not imported from: ‘irlba’
  All declared Imports should be used.
Note: found 10051 marked UTF-8 strings
  Note: found 10523 strings marked as "bytes"
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    rda    3.8Mb
Running ‘test-all.r’
Running the tests in ‘tests/test-all.r’ failed.
Complete output:
  > library(testthat)
  > test_check("jplyr")
  Loading required package: jplyr
  Error in loadNamespace(name) : there is no package called 'jplyr'
  Calls: test_check ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  In addition: Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'jplyr'
  Execution halted
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Loading required package: lubridate

Attaching package: 'lubridate'

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

    date

Loading required package: quantmod
Loading required package: xts
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: TTR
Version 0.4-0 included new data defaults. See ?getSymbols.
Loading required package: tidyverse
Loading tidyverse: ggplot2
Loading tidyverse: tibble
Loading tidyverse: tidyr
Loading tidyverse: readr
Loading tidyverse: purrr
Loading tidyverse: dplyr
Conflicts with tidy packages ----------------------------------------------
as.difftime(): lubridate, base
date():        lubridate, base
filter():      dplyr, stats
first():       dplyr, xts
intersect():   lubridate, base
lag():         dplyr, stats
last():        dplyr, xts
setdiff():     lubridate, base
union():       lubridate, base

Attaching package: 'tidyquant'

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

    as_tibble

Warning: Removed 4160 rows containing non-finite values (stat_smooth).
Warning: Removed 4160 rows containing missing values (position_stack).
Getting data...

Quitting from lines 202-205 (tidyquant.Rmd) 
Error: processing vignette 'tidyquant.Rmd' failed with diagnostics:
Can not automatically convert from character to integer in column "Last.Trade.Size".
Execution halted
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    examples  11.7Mb
    include    3.0Mb
File ‘tpr/libs/tpr.so’:
  Found ‘_ZNSt3__14cerrE’, 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 the system RNG.
It is good practice to use registered native symbols and to disable
symbol search.

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

> ### Name: tranSurvfit
> ### Title: This function creates survival curves under dependent truncation
> ###   and independent censoring via a structural transformation model.
> ### Aliases: tranSurvfit
> 
> ### ** Examples
> 
> ## Generate simulated data from a transformation model
> datgen <- function(n) {
+     a <- -0.3
+     X <- rweibull(n, 2, 4) ## failure times
+     U <- rweibull(n, 2, 1) ## latent truncation time
+     T <- (1 + a) * U - a * X ## apply transformation
+     C <- rlnorm(n, .8, 1) ## censoring
+     dat <- data.frame(trun = T, obs = pmin(X, C), delta = 1 * (X <= C))
+     return(subset(dat, trun <= obs))
+ }
> 
> set.seed(123)
> dat <- datgen(300)
> fit <- with(dat, tranSurvfit(trun, obs, delta))
Error in if (abs(byTau$obj[1]) > 0.1 || byP$obj < 0.6) warning("Best estimate does not achieve tau_c = 0. This model may not be appropriate.",  : 
  missing value where TRUE/FALSE needed
Calls: with -> with.default -> eval -> eval -> tranSurvfit
Execution halted
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
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.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ubeR)
  > 
  > test_check("ubeR")
  1. Failure: raise error on fail to geocode (@test_utils.R#4) -------------------
  geocode("The Old Biscuit Mill") did not throw an error.
  
  
  testthat results ================================================================
  OK: 8 SKIPPED: 0 FAILED: 1
  1. Failure: raise error on fail to geocode (@test_utils.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.2Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    data  26.4Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   6.2Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   3.7Mb
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'
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.2Mb
    help   2.6Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc           3.6Mb
    htmlwidgets   3.6Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    extdata  10.8Mb
Error in re-building vignettes:
  ...
Loading required package: ggplot2
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'walkr.tex' failed.
LaTeX errors:
! Undefined control sequence.
T1+zi4 ->zifour@spc 
                    
l.879 \section{Using \texttt{walkr}}
                                    
! Undefined control sequence.
T1+zi4 ->zifour@spc 
                    
l.910 \hlstd{A} \hlkwb{<-} \hlkwd{matrix}
                                         \hlstd{(}\hlnum{1}\hlstd{,} \hlkwc{...
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Namespaces in Imports field not imported from:
  ‘DT’ ‘ENMeval’ ‘RColorBrewer’ ‘devtools’ ‘dismo’ ‘dplyr’ ‘maptools’
  ‘raster’ ‘rgdal’ ‘rgeos’ ‘rmarkdown’ ‘shinyBS’ ‘shinyjs’
  ‘shinythemes’ ‘spThin’ ‘spocc’
  All declared Imports should be used.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    doc  12.1Mb
Running examples in ‘WhopGenome-Ex.R’ failed
The error most likely occurred in:

> ### Name: fai_close
> ### Title: Closes a file previously opened with fai_open
> ### Aliases: fai_close
> 
> ### ** Examples
> 
> 
> ##
> ##	Example :
> ##
> faifile  <- system.file("extdata", "ex.fasta", package = "WhopGenome")
> faifh <- fai_open( faifile )
> stopifnot( faifh != NULL )
Error in faifh != NULL : 
  comparison (2) is possible only for atomic and list types
Calls: stopifnot
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Namespace in Imports field not imported from: ‘RMySQL’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.7Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
Error in re-building vignettes:
  ...
Loading required package: WRS2
Loading required package: beanplot
Loading required package: car
Loading required package: MASS
Loading required package: colorspace
Loading required package: reshape
Loading required package: ez
Loading required package: MBESS
Warning: Converting "id" to factor for ANOVA.
Warning in Qanova(GoalsGame ~ League, data = eurosoccer, q = c(0.25, 0.5,  :
  Cardinality of sample space is less than 20 for one more groups. Type I error might not be controlled!
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'WRS2.tex' failed.
LaTeX errors:
! Dimension too large.
\fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa 
                                                  \fb@putboxa #1\fb@afterfra...
l.2320 ...() or as.vector() instead.}}\end{kframe}
                                                  
! Dimension too large.
\fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa 
                                                  \fb@putboxa #1\fb@afterfra...
l.2320 ...() or as.vector() instead.}}\end{kframe}
                                                  
! Dimension too large.
\fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa 
                                                  \fb@putboxa #1\fb@afterfra...
l.2320 ...() or as.vector() instead.}}\end{kframe}
                                                  
! Dimension too large.
\fb@put@frame ...p \ifdim \dimen@ >\ht \@tempboxa 
                                                  \fb@putboxa #1\fb@afterfra...
l.2320 ...() 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    data  14.1Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    java  17.4Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    java        4.6Mb
    unitTests   1.1Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    exampleData   1.6Mb
    examples      4.6Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘ggplot2’ ‘quantmod’ ‘sde’ ‘shinyBS’ ‘shinydashboard’ ‘shinyjs’
  ‘yuima’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘lubridate’
  All declared Imports should be used.
File ‘ABCoptim/libs/ABCoptim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
File ‘ACEt/libs/ACEt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
File ‘acrt/libs/acrt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data       2.8Mb
    pictures   2.1Mb
File ‘ade4/libs/ade4.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ADM3/libs/ADM3.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘allelic/libs/allelic.so’:
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Object: ‘newallelic.o’
File ‘allelic/libs/allelic.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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