Package which this enhances but not available for checking: 'gurobi'
print.optimbase: no visible global function definition for 'str'
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
optimx.run: no visible global function definition for 'optim'
optimx.run: no visible global function definition for 'nlminb'
optimx.run: no visible global function definition for 'nlm'
Undefined global functions or variables:
  nlm nlminb optim
Consider adding
  importFrom("stats", "nlm", "nlminb", "optim")
to your NAMESPACE file.
calc.stress: no visible global function definition for 'sd'
opscale: no visible global function definition for 'sd'
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: 'Rmosek'
getMinimumArborescence: no visible global function definition for
  'capture.output'
getMinimumCutTree: no visible global function definition for
  'capture.output'
getMinimumCutTree: no visible global function definition for 'par'
getMinimumSpanningTree: no visible global function definition for
  'capture.output'
getShortestPathTree: no visible global function definition for
  'capture.output'
Undefined global functions or variables:
  capture.output par
Consider adding
  importFrom("graphics", "par")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Package required but not available: 'ROracle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Agrestiind.CI: no visible global function definition for 'qnorm'
BPexact.CI: no visible global function definition for 'uniroot'
BPmidp.CI: no visible global function definition for 'uniroot'
Cornfieldexact.CI: no visible global function definition for 'uniroot'
Cornfieldmidp.CI: no visible global function definition for 'uniroot'
Gart.CI: no visible global function definition for 'qnorm'
Invsinh.CI: no visible global function definition for 'qnorm'
Woolf.CI: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  qnorm uniroot
Consider adding
  importFrom("stats", "qnorm", "uniroot")
to your NAMESPACE file.
BTLboost: no visible global function definition for 'as.formula'
design: no visible global function definition for 'as.formula'
wide2long: no visible global function definition for 'reshape'
Undefined global functions or variables:
  as.formula reshape
Consider adding
  importFrom("stats", "as.formula", "reshape")
to your NAMESPACE file.
'library' or 'require' call to 'psych' which was already attached by Depends.
  Please remove these calls from your code.
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nr' to 'nrow'
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nc' to 'ncol'
bgmm: no visible global function definition for 'ecdf'
bgmm : SplineGMM: no visible global function definition for
  'constrOptim'
blr: no visible global function definition for 'ecdf'
blr: no visible global function definition for 'constrOptim'
blr: no visible global function definition for 'lm'
parentcdf : combinations: no visible global function definition for
  'combn'
parentcdf : solver: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  combn constrOptim ecdf lm uniroot
Consider adding
  importFrom("stats", "constrOptim", "ecdf", "lm", "uniroot")
  importFrom("utils", "combn")
to your NAMESPACE file.
'library' or 'require' call to 'methods' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'grid' 'lattice' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
error.bars: no visible global function definition for 'segments'
lambda.interp: no visible global function definition for 'approx'
orderedLasso: no visible binding for global variable 'sd'
orderedLasso.cv: no visible binding for global variable 'var'
plot.orderedLasso.cv: no visible global function definition for 'par'
plot.orderedLasso.cv: no visible global function definition for 'plot'
plot.orderedLasso.cv: no visible global function definition for 'axis'
plot.orderedLasso.cv: no visible global function definition for 'mtext'
plot.orderedLasso.cv: no visible global function definition for
  'points'
plot.orderedLasso.cv: no visible global function definition for
  'abline'
plot.timeLagLasso.cv: no visible global function definition for 'par'
plot.timeLagLasso.cv: no visible global function definition for 'plot'
plot.timeLagLasso.cv: no visible global function definition for 'axis'
plot.timeLagLasso.cv: no visible global function definition for 'mtext'
plot.timeLagLasso.cv: no visible global function definition for
  'points'
plot.timeLagLasso.cv: no visible global function definition for
  'abline'
timeLagLasso: no visible binding for global variable 'sd'
timeLagLasso.cv: no visible binding for global variable 'sd'
timeLagLasso.cv: no visible binding for global variable 'var'
timeLagLasso.path: no visible binding for global variable 'sd'
Undefined global functions or variables:
  abline approx axis mtext par plot points sd segments var
Consider adding
  importFrom("graphics", "abline", "axis", "mtext", "par", "plot",
             "points", "segments")
  importFrom("stats", "approx", "sd", "var")
to your NAMESPACE file.
Ord.logreg: no visible binding for global variable 'data'
plot.Ord.logreg: no visible global function definition for 'par'
plot.Ord.logreg: no visible global function definition for 'plot'
plot.Ord.logreg: no visible global function definition for 'mtext'
plot.Ord.logreg: no visible global function definition for 'plot.new'
Undefined global functions or variables:
  data mtext par plot plot.new
Consider adding
  importFrom("graphics", "mtext", "par", "plot", "plot.new")
  importFrom("utils", "data")
to your NAMESPACE file.
genRidge: no visible global function definition for 'plogis'
ordGene: no visible global function definition for 'anova'
ordGene: no visible global function definition for 'lm'
ordSelect: no visible binding for global variable 'sd'
ordSmooth: no visible binding for global variable 'sd'
plot.ordPen: no visible global function definition for 'grey'
plot.ordPen: no visible global function definition for 'devAskNewPage'
plot.ordPen: no visible global function definition for 'plot'
plot.ordPen: no visible global function definition for 'lines'
predict.ordPen: no visible global function definition for 'plogis'
Undefined global functions or variables:
  anova devAskNewPage grey lines lm plogis plot sd
Consider adding
  importFrom("grDevices", "devAskNewPage", "grey")
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "anova", "lm", "plogis", "sd")
to your NAMESPACE file.
ORICC1: no visible binding for global variable 'sd'
ORICC1: no visible global function definition for 'write.table'
ORICC1: no visible global function definition for 'postscript'
ORICC1: no visible global function definition for 'jpeg'
ORICC1: no visible global function definition for 'plot'
ORICC1: no visible global function definition for 'points'
ORICC1: no visible global function definition for 'dev.off'
ORICC1: no visible global function definition for 'par'
ORICC2: no visible binding for global variable 'sd'
ORICC2: no visible global function definition for 'write.table'
ORICC2: no visible global function definition for 'postscript'
ORICC2: no visible global function definition for 'jpeg'
ORICC2: no visible global function definition for 'plot'
ORICC2: no visible global function definition for 'points'
ORICC2: no visible global function definition for 'dev.off'
ORICC2: no visible global function definition for 'par'
Undefined global functions or variables:
  dev.off jpeg par plot points postscript sd write.table
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "postscript")
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
boat3d: no visible global function definition for 'rgl.cur'
boat3d: no visible global function definition for 'open3d'
boat3d: no visible global function definition for 'clear3d'
boat3d: no visible global function definition for 'bg3d'
boat3d: no visible global function definition for 'rgl.set'
boat3d: no visible global function definition for 'triangles3d'
boat3d: no visible global function definition for 'quads3d'
boat3d: no visible global function definition for 'decorate3d'
boat3d: no visible global function definition for 'scatterplot3d'
orientlm: no visible global function definition for 'model.matrix'
orientlm: no visible global function definition for 'lm'
Undefined global functions or variables:
  bg3d clear3d decorate3d lm model.matrix open3d quads3d rgl.cur
  rgl.set scatterplot3d triangles3d
Consider adding
  importFrom("stats", "lm", "model.matrix")
to your NAMESPACE file.
File 'OriGen/libs/i386/OriGen.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'OriGen.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'OriGen.o'
File 'OriGen/libs/x64/OriGen.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'OriGen.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'OriGen.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
mdr.c: no visible global function definition for 'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
dicomTable: no visible global function definition for 'txtProgressBar'
dicomTable: no visible global function definition for
  'setTxtProgressBar'
readDICOM: no visible global function definition for 'txtProgressBar'
readDICOM: no visible global function definition for
  'setTxtProgressBar'
writeHeader: no visible global function definition for 'write.table'
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar write.table
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar",
             "write.table")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'Rcpp' 'genefilter' 'gtools' 'nlme'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
est.lme : <anonymous>: warning in rank(iru, ties = "min"): partial
  argument match of 'ties' to 'ties.method'
est.lme : <anonymous>: no visible global function definition for 'lme'
est.lme : <anonymous>: no visible global function definition for
  'VarCorr'
guo: no visible global function definition for 'p.adjust'
guo: no visible global function definition for 'na.omit'
pttest : ptest: no visible global function definition for 'na.omit'
srt : <anonymous>: no visible global function definition for
  'rowttests'
Undefined global functions or variables:
  VarCorr lme na.omit p.adjust rowttests
Consider adding
  importFrom("stats", "na.omit", "p.adjust")
to your NAMESPACE file.
plot.SplineBasis: no visible global function definition for 'matplot'
plot,SplineBasis-matrix: no visible global function definition for
  'matplot'
plot,SplineBasis-missing: no visible global function definition for
  'matplot'
Undefined global functions or variables:
  matplot
Consider adding
  importFrom("graphics", "matplot")
to your NAMESPACE file.
'library' or 'require' call to 'polynom' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'polynom'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
chebyshev.c.polynomials: no visible global function definition for
  'polynomial'
chebyshev.s.polynomials: no visible global function definition for
  'polynomial'
chebyshev.t.polynomials: no visible global function definition for
  'polynomial'
chebyshev.u.polynomials: no visible global function definition for
  'polynomial'
gegenbauer.polynomials: no visible global function definition for
  'polynomial'
ghermite.h.polynomials: no visible global function definition for
  'polynomial'
glaguerre.polynomials: no visible global function definition for
  'polynomial'
hermite.h.polynomials: no visible global function definition for
  'polynomial'
hermite.he.polynomials: no visible global function definition for
  'polynomial'
jacobi.g.polynomials: no visible global function definition for
  'polynomial'
jacobi.p.polynomials: no visible global function definition for
  'polynomial'
legendre.polynomials: no visible global function definition for
  'polynomial'
monic.polynomials: no visible global function definition for
  'polynomial'
orthogonal.polynomials: no visible global function definition for
  'polynomial'
orthonormal.polynomials: no visible global function definition for
  'polynomial'
polynomial.derivatives: no visible global function definition for
  'deriv'
polynomial.integrals: no visible global function definition for
  'integral'
polynomial.values: no visible global function definition for 'predict'
schebyshev.t.polynomials: no visible global function definition for
  'polynomial'
schebyshev.u.polynomials: no visible global function definition for
  'polynomial'
slegendre.polynomials: no visible global function definition for
  'polynomial'
Undefined global functions or variables:
  deriv integral polynomial predict
Consider adding
  importFrom("stats", "deriv", "predict")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'igraph' 'sp'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
as_igraph : <anonymous>: no visible global function definition for
  'distHaversine'
as_igraph: no visible global function definition for 'graph.edgelist'
as_igraph: no visible global function definition for 'E'
as_igraph: no visible global function definition for 'E<-'
as_sp_lines: no visible global function definition for 'Lines'
as_sp_points: no visible global function definition for
  'SpatialPointsDataFrame'
as_sp_polygons: no visible global function definition for 'Polygons'
as_sp_polygons: no visible global function definition for
  'SpatialPolygons'
as_sp_polygons: no visible global function definition for
  'SpatialPolygonsDataFrame'
make_SLDF: no visible global function definition for 'SpatialLines'
make_SLDF: no visible global function definition for
  'SpatialLinesDataFrame'
osm_crs: no visible global function definition for 'CRS'
plot.osmar: no visible global function definition for 'gray'
plot_nodes: no visible global function definition for 'points'
plot_nodes: no visible global function definition for 'plot'
plot_ways: no visible global function definition for 'plot'
plot_ways: no visible global function definition for 'lines'
ways_nodes2Line: no visible global function definition for 'Line'
ways_nodes2Polygon: no visible global function definition for 'Polygon'
Undefined global functions or variables:
  CRS E E<- Line Lines Polygon Polygons SpatialLines
  SpatialLinesDataFrame SpatialPointsDataFrame SpatialPolygons
  SpatialPolygonsDataFrame distHaversine graph.edgelist gray lines plot
  points
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   1.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Package suggested but not available for checking: 'Rcplex'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   1.8Mb
Error in re-building vignettes:
  ...
Warning in .local(x, ...) :
  The following sequence IDs are not in the dataset: 311, 222
Warning in .local(x, ...) :
  The following sequence IDs are not in the dataset: 311, 222
Warning in (if (out_format(c("latex", "sweave", "listings"))) sanitize_fn else paste0)(path,  :
  replaced special characters in figure filename "figs/OutbreakTools-out.width==".8\\textwidth"" -> "figs/OutbreakTools-out.width___.8\\textwidth_"
Warning in (if (out_format(c("latex", "sweave", "listings"))) sanitize_fn else paste0)(path,  :
  dots in figure paths replaced with _ ("figs/OutbreakTools-out_width____8//textwidth_")
Warning: The shape palette can deal with a maximum of 6 discrete values because
more than 6 becomes difficult to discriminate; you have 11. Consider
specifying shapes manually if you must have them.
Warning: Removed 58 rows containing missing values (geom_point).
Warning: `show_guide` has been deprecated. Please use `show.legend` instead.
Warning: `show_guide` has been deprecated. Please use `show.legend` instead.
Warning in download.file(url, destfile = tmp, quiet = !messaging, mode = "wb") :
  cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=51.516439,-0.171146&zoom=14&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false': HTTP status was '403 Forbidden'
Quitting from lines 1022-1023 (OutbreakTools.Rnw) 
Error: processing vignette 'OutbreakTools.Rnw' failed with diagnostics:
cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=51.516439,-0.171146&zoom=14&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false'
Execution halted
odm: no visible binding for global variable 'sd'
odm : <anonymous>: no visible global function definition for 'sd'
odm : <anonymous>: no visible global function definition for 'quantile'
odm: no visible global function definition for 'prcomp'
quant.const: no visible global function definition for 'quantile'
quant.const.D: no visible global function definition for 'reshape'
quant.const.D: no visible global function definition for 'quantile'
quant.linear.D: no visible global function definition for 'reshape'
quant.nonlin : FrankModel: no visible global function definition for
  'qt'
quant.nonlin : FrankModel: no visible global function definition for
  'pt'
quant.nonlin: no visible global function definition for 'predict'
quant.nonlin.D: no visible global function definition for 'reshape'
quant.nonlin.D: no visible global function definition for 'predict'
quant.nonpar.D: no visible global function definition for 'reshape'
rgrubbs.test: no visible global function definition for 'sd'
plot,OutlierDM-missing: no visible binding for global variable 'pch'
summary,OutlierDM: no visible global function definition for 'head'
Undefined global functions or variables:
  head pch prcomp predict pt qt quantile reshape sd
Consider adding
  importFrom("stats", "prcomp", "predict", "pt", "qt", "quantile",
             "reshape", "sd")
  importFrom("utils", "head")
to your NAMESPACE file.
Electre3_AlphaBetaThresholds: no visible global function definition for
  'plot'
Electre3_SimpleThresholds: no visible global function definition for
  'plot'
Electre_1: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
loadCSVtoP2distance: no visible global function definition for
  'read.table'
p2distance : calcularDistancia: no visible binding for global variable
  'sd'
p2distance : ordenarVariables: no visible global function definition
  for 'cor'
p2distance : calculoFactoresPonderacion: no visible global function
  definition for 'lm'
p2distance: no visible global function definition for 'cor'
Undefined global functions or variables:
  cor lm read.table sd
Consider adding
  importFrom("stats", "cor", "lm", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'library' or 'require' call to 'survival' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
p3state: no visible global function definition for 'survfit'
p3state: no visible global function definition for 'terms'
p3state: no visible global function definition for 'as.formula'
p3state: no visible global function definition for 'coxph'
p3state: no visible binding for global variable 'na.exclude'
plot.p3state: no visible global function definition for 'matplot'
plot.p3state: no visible global function definition for 'devAskNewPage'
plot.p3state: no visible global function definition for 'persp'
plot.p3state: no visible global function definition for 'colours'
plot.p3state: no visible global function definition for
  'filled.contour'
Undefined global functions or variables:
  as.formula colours coxph devAskNewPage filled.contour matplot
  na.exclude persp survfit terms
Consider adding
  importFrom("grDevices", "colours", "devAskNewPage")
  importFrom("graphics", "filled.contour", "matplot", "persp")
  importFrom("stats", "as.formula", "na.exclude", "terms")
to your NAMESPACE file.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/PAactivPAL.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
pacbpred : thetaFunc: no visible global function definition for 'lsfit'
pacbpred : thetaFunc: no visible global function definition for 'rnorm'
pacbpred: no visible global function definition for 'var'
pacbpred: no visible global function definition for 'runif'
pacbpred: no visible global function definition for 'rnorm'
pacbpred: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  lsfit rbinom rnorm runif var
Consider adding
  importFrom("stats", "lsfit", "rbinom", "rnorm", "runif", "var")
to your NAMESPACE file.
Running 'testthat.R' [8s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
         week_start = 7L) 
     {
         .Call(`_lubridate_C_update_dt`, dt, year, month, yday, mday, wday, hour, minute, 
             second, tz, roll, week_start)
     })(year = integer(0), month = integer(0), yday = integer(0), mday = c(7, 7, 9, 10
     ), wday = integer(0), hour = c(9, 9, 13, 10), minute = c(11, 46, 25, 45), second = c(21, 
     48, 17, 11), dt = structure(c(1467875481, 1467877608, 1470741917, 1473497111), class = c("POSIXct", 
     "POSIXt"), tzone = ""), roll = FALSE, tz = "", week_start = 7)
  
  == testthat results  ===========================================================
  OK: 572 SKIPPED: 0 FAILED: 1
  1. Error: interval: month (@test_thicken_integration.R#67) 
  
  Error: testthat unit tests failed
  Execution halted
paf: no visible global function definition for 'as.formula'
paf: no visible global function definition for 'model.response'
paf: no visible global function definition for 'model.frame'
paf: no visible global function definition for 'model.matrix'
plot.paf: no visible global function definition for 'plot'
plot.paf: no visible global function definition for 'lines'
Undefined global functions or variables:
  as.formula lines model.frame model.matrix model.response plot
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response")
to your NAMESPACE file.
CalGIF: no visible binding for global variable 'PAGIData'
CalGIF2: no visible binding for global variable 'PAGIData'
PAGI.Main: no visible binding for global variable 'PAGIData'
PAGI.Main: no visible global function definition for 'p.adjust'
PAGI.Main: no visible global function definition for 'pt'
getclass.labels: no visible binding for global variable 'ExampleData'
getdataset: no visible binding for global variable 'ExampleData'
Undefined global functions or variables:
  ExampleData PAGIData p.adjust pt
Consider adding
  importFrom("stats", "p.adjust", "pt")
to your NAMESPACE file.
paired.Loc: no visible global function definition for 'qt'
paired.Loc: no visible global function definition for 'median'
paired.Loc: no visible global function definition for 'qsignrank'
paired.Loc: no visible global function definition for 'qnorm'
paired.Scale: no visible global function definition for 'var'
paired.Scale: no visible global function definition for 'cor'
paired.Scale: no visible global function definition for 'qt'
paired.Scale: no visible global function definition for 'median'
paired.Scale: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  cor median qnorm qsignrank qt var
Consider adding
  importFrom("stats", "cor", "median", "qnorm", "qsignrank", "qt", "var")
to your NAMESPACE file.
pairsD3: no visible global function definition for 'gray.colors'
Undefined global functions or variables:
  gray.colors
Consider adding
  importFrom("grDevices", "gray.colors")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'lattice' 'vegan'
  Please remove these calls from your code.
GOpredict: no visible global function definition for 'fisher.test'
KEGGpredict: no visible global function definition for 'fisher.test'
ProteinCluster: no visible global function definition for 'ecdf'
ProteinCluster: no visible global function definition for 'as.hclust'
ProteinCluster: no visible global function definition for
  'as.dendrogram'
ProteinCluster : addE: no visible global function definition for
  'is.leaf'
ProteinCluster: no visible global function definition for 'plot'
SignificantSubcluster: no visible global function definition for
  'order.dendrogram'
SignificantSubcluster: no visible global function definition for
  'fisher.test'
SignificantSubcluster: no visible global function definition for 'plot'
Undefined global functions or variables:
  as.dendrogram as.hclust ecdf fisher.test is.leaf order.dendrogram
  plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "as.dendrogram", "as.hclust", "ecdf",
             "fisher.test", "is.leaf", "order.dendrogram")
to your NAMESPACE file.
Paneldata.formula: no visible global function definition for
  'model.frame'
Paneldata.formula: no visible global function definition for
  'model.matrix'
Paneldata.formula: no visible global function definition for
  'model.response'
summary.Paneldata: no visible global function definition for 'coef'
summary.Paneldata: no visible global function definition for 'pt'
Undefined global functions or variables:
  coef model.frame model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.frame", "model.matrix",
             "model.response", "pt")
to your NAMESPACE file.
grow.forest: no visible global function definition for 'model.frame'
grow.tree: no visible global function definition for 'model.frame'
predict.forest: no visible global function definition for 'model.frame'
predict.tree: no visible global function definition for 'model.frame'
predict,forest: no visible global function definition for 'model.frame'
predict,tree: no visible global function definition for 'model.frame'
Undefined global functions or variables:
  model.frame
Consider adding
  importFrom("stats", "model.frame")
to your NAMESPACE file.
File 'ParallelForest/libs/i386/ParallelForest.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'random_utils.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'random_utils.o'
File 'ParallelForest/libs/x64/ParallelForest.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'random_utils.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'random_utils.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Warning: no function found corresponding to methods exports from 'parallelize.dynamic' for: 'initialize'

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

Probably some imports need to be declared in the NAMESPACE file.
'library' or 'require' call to 'package' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'methods' 'parallel' 'tools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
parallelExport: no visible global function definition for 'setNames'
parallelGetOptions: no visible global function definition for
  'setNames'
parallelStop: no visible global function definition for
  'getFromNamespace'
stopWithJobErrorMessages: no visible global function definition for
  'head'
Undefined global functions or variables:
  getFromNamespace head setNames
Consider adding
  importFrom("stats", "setNames")
  importFrom("utils", "getFromNamespace", "head")
to your NAMESPACE file.
consensusMCcov: no visible global function definition for 'var'
consensusMCcov: no visible global function definition for 'cov'
consensusMCindep: no visible global function definition for 'var'
semiparamDPE: no visible binding for global variable 'var'
semiparamDPE: no visible global function definition for 'cov'
semiparamDPE: no visible global function definition for 'runif'
Undefined global functions or variables:
  cov runif var
Consider adding
  importFrom("stats", "cov", "runif", "var")
to your NAMESPACE file.
parallelSVM.default: no visible binding for global variable 'na.omit'
parallelSVM.formula: no visible binding for global variable 'na.omit'
predict.parallelSVM: no visible binding for global variable 'predict'
Undefined global functions or variables:
  na.omit predict
Consider adding
  importFrom("stats", "na.omit", "predict")
to your NAMESPACE file.
paran: no visible global function definition for 'cor'
paran: no visible global function definition for 'rnorm'
paran: no visible global function definition for 'quantile'
paran: no visible global function definition for 'par'
paran: no visible global function definition for 'plot.default'
paran: no visible global function definition for 'abline'
paran: no visible global function definition for 'points'
paran: no visible global function definition for 'dev.copy'
paran: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  abline cor dev.copy dev.off par plot.default points quantile rnorm
Consider adding
  importFrom("grDevices", "dev.copy", "dev.off")
  importFrom("graphics", "abline", "par", "plot.default", "points")
  importFrom("stats", "cor", "quantile", "rnorm")
to your NAMESPACE file.
.formula.make: no visible global function definition for 'formula'
regress: no visible global function definition for 'lm'
regress: no visible global function definition for 'model.matrix'
Undefined global functions or variables:
  formula lm model.matrix
Consider adding
  importFrom("stats", "formula", "lm", "model.matrix")
to your NAMESPACE file.
adalasso: no visible global function definition for 'predict'
lm.ridge.univariate: no visible global function definition for 'sd'
mylars: no visible global function definition for 'predict'
mylars: no visible binding for global variable 'var'
performance.pcor: no visible global function definition for
  'ggm.test.edges'
performance.pcor: no visible global function definition for 'var'
ridge.cv: no visible global function definition for 'coef'
ridge.cv: no visible global function definition for 'plot'
Undefined global functions or variables:
  coef ggm.test.edges plot predict sd var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "predict", "sd", "var")
to your NAMESPACE file.
ParentOffspring: no visible global function definition for 'axis'
ParentOffspring: no visible global function definition for 'abline'
ParentOffspring: no visible global function definition for 'title'
ParentOffspring: no visible global function definition for 'box'
Undefined global functions or variables:
  abline axis box title
Consider adding
  importFrom("graphics", "abline", "axis", "box", "title")
to your NAMESPACE file.
par.nmds : nmdscalc: no visible global function definition for 'runif'
par.nmds : nmdscalc: no visible global function definition for 'dist'
par.nmds: no visible binding for global variable 'j'
par.nmds: no visible global function definition for 'cor'
par.nmds: no visible global function definition for 'dist'
par.spp.est: no visible binding for global variable 'i'
par.spp.est: no visible global function definition for 'sd'
Undefined global functions or variables:
  cor dist i j runif sd
Consider adding
  importFrom("stats", "cor", "dist", "runif", "sd")
to your NAMESPACE file.
Package in Depends field not imported from: 'nnet'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fitOR: no visible global function definition for 'multinom'
fitOR: no visible global function definition for 'formula'
fitOR: no visible global function definition for 'coef'
fitOR: no visible global function definition for 'optim'
reportOR: no visible global function definition for 'qnorm'
reportOR: no visible global function definition for 'pchisq'
reportOR: no visible global function definition for 'coef'
simData: no visible global function definition for 'rnorm'
simData: no visible global function definition for 'runif'
Undefined global functions or variables:
  coef formula multinom optim pchisq qnorm rnorm runif
Consider adding
  importFrom("stats", "coef", "formula", "optim", "pchisq", "qnorm",
             "rnorm", "runif")
to your NAMESPACE file.
partitionMap: no visible global function definition for 'predict'
partitionMap: no visible global function definition for 'rnorm'
partitionMap: no visible binding for global variable 'sd'
partitionMap: no visible global function definition for 'sd'
partitionMap: no visible global function definition for 'quantile'
Undefined global functions or variables:
  predict quantile rnorm sd
Consider adding
  importFrom("stats", "predict", "quantile", "rnorm", "sd")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'partsm' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
parviol: no visible global function definition for 'plot.new'
parviol: no visible global function definition for 'plot.window'
parviol: no visible global function definition for 'title'
parviol: no visible global function definition for 'lines'
parviol: no visible global function definition for 'text'
parviol: no visible global function definition for 'rgb'
selecto: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines plot.new plot.window rgb text title
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "plot.new", "plot.window", "text",
             "title")
to your NAMESPACE file.
'library' or 'require' call to 'glmnet' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'glmnet'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cv_nfold: no visible global function definition for 'predict'
cv_nfold: no visible global function definition for 'cv.glmnet'
cv_nfold: no visible global function definition for 'coef'
cv_nfold: no visible global function definition for 'var'
getoptbinsize: no visible global function definition for 'var'
getoptbinsize: no visible global function definition for 'cor'
glmcvbeta: no visible global function definition for 'cv.glmnet'
myhistplot: no visible global function definition for 'par'
myhistplot: no visible global function definition for 'plot'
myhistplot: no visible global function definition for 'axis'
plot.binmod: no visible global function definition for 'par'
plot.binmod: no visible global function definition for 'layout'
plot.binmod: no visible global function definition for 'dev.off'
plot.binmod: no visible binding for global variable 'plot.new'
plot.binmod: no visible global function definition for 'postscript'
plot.binmod: no visible global function definition for 'plot'
plot.binmod: no visible global function definition for 'mtext'
plot.binmod: no visible global function definition for 'legend'
plot.binmod: no visible global function definition for 'arrows'
predict.binmod: no visible global function definition for 'predict'
singlemarkanalysis: no visible global function definition for 'glm'
singlemarkanalysis: no visible global function definition for 'var'
weightedx: no visible global function definition for 'na.exclude'
Undefined global functions or variables:
  arrows axis coef cor cv.glmnet dev.off glm layout legend mtext
  na.exclude par plot plot.new postscript predict var
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "arrows", "axis", "layout", "legend", "mtext",
             "par", "plot", "plot.new")
  importFrom("stats", "coef", "cor", "glm", "na.exclude", "predict",
             "var")
to your NAMESPACE file.
pass: no visible global function definition for 'predict'
plot.pass: no visible global function definition for 'par'
plot.pass: no visible global function definition for 'plot'
Undefined global functions or variables:
  par plot predict
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "predict")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'ape' 'caper'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
conch: no visible global function definition for 'read.tree'
conch: no visible global function definition for 'reorder'
conch: no visible global function definition for 'read.nexus'
conch: no visible global function definition for '.compressTipLabel'
conch: no visible global function definition for 'drop.tip'
conch: no visible global function definition for 'extract.clade'
conch: no visible global function definition for 'which.edge'
conch: no visible global function definition for 'write.tree'
pastis_main: no visible global function definition for 'combn'
read_input: no visible global function definition for 'read.tree'
read_input: no visible global function definition for 'reorder'
read_input: no visible global function definition for 'read.csv'
read_input: no visible global function definition for 'read.dna'
Undefined global functions or variables:
  .compressTipLabel combn drop.tip extract.clade read.csv read.dna
  read.nexus read.tree reorder which.edge write.tree
Consider adding
  importFrom("stats", "reorder")
  importFrom("utils", "combn", "read.csv")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'e1071'
  Please remove these calls from your code.
SweaveAll: no visible global function definition for 'file_test'
texi2dvi: no visible global function definition for 'file_test'
Undefined global functions or variables:
  file_test
Consider adding
  importFrom("utils", "file_test")
to your NAMESPACE file.
Package in Depends field not imported from: 'datautils'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
animatePatches: no visible global function definition for
  'getTimestamp'
animatePatches: no visible global function definition for 'getElapsed'
colorPlot: no visible global function definition for 'layout'
colorPlot: no visible global function definition for 'par'
colorPlot: no visible global function definition for 'image'
colorPlot: no visible global function definition for 'axis'
drawPatches: no visible global function definition for 'rgb'
getInterRGB: no visible global function definition for 'col2rgb'
getInterRGB: no visible global function definition for 'rgb'
plotGmmOverlay: no visible global function definition for 'rgb'
plotGreyPatches : squarepatch: no visible global function definition
  for 'rgb'
plotGreyPatches : trianglepatch: no visible global function definition
  for 'rgb'
Undefined global functions or variables:
  axis col2rgb getElapsed getTimestamp image layout par rgb
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
  importFrom("graphics", "axis", "image", "layout", "par")
to your NAMESPACE file.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
Depends: includes the non-default packages:
  'svmpath' 'kernlab' 'affy' 'Biobase' 'ROCR' 'igraph' 'lpSolve'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' call to 'ROCR' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Biobase' 'ROCR' 'affy' 'igraph' 'kernlab' 'lpSolve' 'svmpath'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'parallel:::detectCores'
  See the note in ?`:::` about the use of this operator.
Package in Depends field not imported from: 'shape'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
arrow: no visible global function definition for 'arrows'
draw: no visible global function definition for 'rect'
draw: no visible global function definition for 'text'
draw: no visible global function definition for 'plotellipse'
wall: no visible global function definition for 'plot.new'
wall: no visible global function definition for 'plot.window'
Undefined global functions or variables:
  arrows plot.new plot.window plotellipse rect text
Consider adding
  importFrom("graphics", "arrows", "plot.new", "plot.window", "rect",
             "text")
to your NAMESPACE file.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    extdata   9.5Mb
Packages in Depends field not imported from:
  'plspm' 'tester'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  -- 2. Failure: standardize_path works with missing files with ./ prefix (@test_s
  standardize_path(x) not equal to `expected`.
  1/2 mismatches
  x[1]: "D:/RCompile/CRANpkg/local/3.5/pathological.Rcheck/tests/testthat/test_dec
  x[1]: ompose_path.R"
  y[1]: "D:/Rcompile/CRANpkg/local/3.5/pathological.Rcheck/tests/testthat/test_dec
  y[1]: ompose_path.R"
  
  == testthat results  ===========================================================
  OK: 186 SKIPPED: 18 FAILED: 2
  1. Failure: decompose_path handles paths with a unicode directory name. (@test_decompose_path.R#466) 
  2. Failure: standardize_path works with missing files with ./ prefix (@test_standardize_path.R#198) 
  
  Error: testthat unit tests failed
  Execution halted
add_noise: no visible global function definition for 'rnorm'
estimate_risk_dream6 : <anonymous>: no visible global function
  definition for 'var'
generate_sample: no visible global function definition for 'rnorm'
generate_sample: no visible global function definition for 'runif'
sample_function: no visible global function definition for 'runif'
sample_function : <anonymous>: no visible global function definition
  for 'var'
sample_function_multi_mod_weight: no visible global function definition
  for 'runif'
sample_function_multi_mod_weight : <anonymous>: no visible global
  function definition for 'var'
sample_function_single_mod: no visible global function definition for
  'runif'
Undefined global functions or variables:
  rnorm runif var
Consider adding
  importFrom("stats", "rnorm", "runif", "var")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'PAWL' for: 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'foreach' 'ggplot2' 'reshape'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'foreach' 'ggplot2' 'methods' 'mvtnorm' 'reshape'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' call to 'rootSolve' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'kinship2' 'tcltk'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'rootSolve' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Not exits: C:/Program Files/netCDF 4.3.2
Not exits: C:/Program Files/netCDF 4.3.2/bin
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/msvcp100.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/msvcr100.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/zlib.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/hdf5.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/hdf5_hl.dll
Not exits: C:/Program Files/netCDF 4.3.2/bin/netcdf.dll
===== WARNING =====
- netCDF 4.3.2 may not install at compile time.
- Environment variables may not be correct at compile and run time.
- pbdNCDF4 binary may not link with netCDF.
- Please consider to rebuild from source.
===================
S3 methods shown with full name in documentation object 'binds':
  'rbind.ddmatrix' 'cbind.ddmatrix'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Not exits: C:/Program Files/netCDF 4.3.2
Not exits: C:/Program Files/netCDF 4.3.2/bin
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/msvcp100.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/msvcr100.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/zlib.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/hdf5.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/hdf5_hl.dll
Not exits: C:/Program Files/netCDF 4.3.2/bin/netcdf.dll
===== WARNING =====
- netCDF 4.3.2 may not install at compile time.
- Environment variables may not be correct at compile and run time.
- pbdNCDF4 binary may not link with netCDF.
- Please consider to rebuild from source.
===================
get.sysenv: no visible global function definition for 'shortPathName'
Undefined global functions or variables:
  shortPathName
Consider adding
  importFrom("utils", "shortPathName")
to your NAMESPACE file.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    lib    6.6Mb
    libs   5.3Mb
dotplot.pbo: no visible global function definition for 'reorder'
pbo: no visible global function definition for '%dopar%'
pbo: no visible global function definition for 'foreach'
pbo: no visible global function definition for 'lm'
xyplot.pbo: no visible global function definition for 'ecdf'
xyplot.pbo: no visible global function definition for 'doubleYScale'
xyplot.pbo: no visible global function definition for 'reorder'
Undefined global functions or variables:
  %dopar% doubleYScale ecdf foreach lm reorder
Consider adding
  importFrom("stats", "ecdf", "lm", "reorder")
to your NAMESPACE file.
a_get_native: no visible global function definition for 'par'
a_get_relative: no visible global function definition for 'par'
brackets: no visible global function definition for 'par'
brackets: no visible global function definition for 'dist'
brackets: no visible global function definition for 'lines'
Undefined global functions or variables:
  dist lines par
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "dist")
to your NAMESPACE file.
.win.appendLog: no visible binding for global variable 'lines'
plotMC : panel: no visible global function definition for 'points'
plotMC: no visible global function definition for 'pairs'
plotMC: no visible global function definition for 'mtext'
plotMC: no visible global function definition for 'axis'
plotMC: no visible global function definition for 'par'
readADpaths: no visible global function definition for 'read.table'
readRep: no visible global function definition for 'read.table'
saveADpaths: no visible global function definition for 'write.table'
Undefined global functions or variables:
  axis lines mtext pairs par points read.table write.table
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "pairs", "par",
             "points")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.4Mb
draw.pcaBootPlot: no visible global function definition for 'plot'
draw.pcaBootPlot: no visible global function definition for 'grid'
draw.pcaBootPlot: no visible global function definition for 'points'
draw.pcaBootPlot: no visible global function definition for 'symbols'
draw.pcaBootPlot: no visible global function definition for 'legend'
pcaBootPlot: no visible global function definition for 'prcomp'
pcaBootPlot: no visible global function definition for 'cor'
pcaBootPlot: no visible global function definition for 'quantile'
pcaBootPlot: no visible global function definition for 'pdf'
pcaBootPlot: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  cor dev.off grid legend pdf plot points prcomp quantile symbols
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "grid", "legend", "plot", "points", "symbols")
  importFrom("stats", "cor", "prcomp", "quantile")
to your NAMESPACE file.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/math/special_functions/detail/bernoulli_details.hpp:72:36: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/math/special_functions/detail/bernoulli_details.hpp:96:9: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.5/pcalg.Rcheck/00install.out' for details.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   2.1Mb
    libs   2.3Mb
PCDReg.wf: no visible global function definition for 'optimize'
Undefined global functions or variables:
  optimize
Consider adding
  importFrom("stats", "optimize")
to your NAMESPACE file.
defineTasks: no visible global function definition for 'par'
defineTasks: no visible global function definition for 'abline'
plotCorCoeff: no visible global function definition for 'hist'
plotCorCoeff: no visible global function definition for 'plot.new'
plotCorCoeff: no visible global function definition for 'plot.window'
plotCorCoeff: no visible global function definition for 'rect'
plotCorCoeff: no visible global function definition for 'axis'
plotCorCoeff: no visible global function definition for 'title'
plotCorCoeff: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline axis hist legend par plot.new plot.window rect title
Consider adding
  importFrom("graphics", "abline", "axis", "hist", "legend", "par",
             "plot.new", "plot.window", "rect", "title")
to your NAMESPACE file.
pcse : extractLMvar: no visible global function definition for
  'model.frame'
pcse: no visible global function definition for 'model.matrix'
pcse: no visible global function definition for 'na.omit'
pcse: no visible global function definition for 'resid'
pcse: no visible global function definition for 'pt'
Undefined global functions or variables:
  model.frame model.matrix na.omit pt resid
Consider adding
  importFrom("stats", "model.frame", "model.matrix", "na.omit", "pt",
             "resid")
to your NAMESPACE file.
PdofCSGt.bootstrap5: no visible global function definition for 'rnorm'
PdofCSGt.bootstrap5: no visible global function definition for 'rt'
PdofCSt.T1or2: no visible global function definition for 'combn'
PofCSGt: no visible global function definition for 'combn'
PofCSLt.bootstrap5: no visible global function definition for 'rnorm'
PofCSLt.bootstrap5: no visible global function definition for 'rt'
PofCSt: no visible global function definition for 'pnorm'
tindep: no visible binding for global variable 'var'
tindep: no visible global function definition for 'pt'
Undefined global functions or variables:
  combn pnorm pt rnorm rt var
Consider adding
  importFrom("stats", "pnorm", "pt", "rnorm", "rt", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    libs   12.1Mb
    share  11.9Mb
pdist: no visible global function definition for 'dist'
pdist: no visible global function definition for 'new'
Undefined global functions or variables:
  dist new
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dist")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/pdolsms.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
band.chol.cv: no visible global function definition for 'cov'
pdsoft.cv: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
peacf: no visible global function definition for 'is.ts'
peacf: no visible global function definition for 'cycle'
peacf: no visible global function definition for 'ts.intersect'
peacf: no visible global function definition for 'lag'
peacf: no visible global function definition for 'ts'
peacf: no visible global function definition for 'pchisq'
peacf.plot: no visible global function definition for 'plot'
peacf.plot: no visible global function definition for 'segments'
peacf.plot: no visible global function definition for 'title'
pear: no visible global function definition for 'cycle'
pear: no visible global function definition for 'pchisq'
peboxplot: no visible global function definition for 'cycle'
peboxplot: no visible global function definition for 'boxplot'
peboxplot: no visible global function definition for 'title'
peplot: no visible global function definition for 'par'
peplot: no visible global function definition for 'cycle'
peplot: no visible global function definition for 'plot'
peplot: no visible global function definition for 'identify'
peplot: no visible global function definition for 'mtext'
Undefined global functions or variables:
  boxplot cycle identify is.ts lag mtext par pchisq plot segments title
  ts ts.intersect
Consider adding
  importFrom("graphics", "boxplot", "identify", "mtext", "par", "plot",
             "segments", "title")
  importFrom("stats", "cycle", "is.ts", "lag", "pchisq", "ts",
             "ts.intersect")
to your NAMESPACE file.
The following files should probably not be installed:
  'addendum.tex', 'slplot.tex', 'table1.tex', 'table3.tex'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
PearsonICA: no visible global function definition for 'rnorm'
PearsonICAdemo: no visible global function definition for 'rnorm'
PearsonICAdemo: no visible global function definition for 'dev.new'
PearsonICAdemo: no visible global function definition for 'par'
PearsonICAdemo: no visible global function definition for 'plot'
PearsonICAdemo: no visible global function definition for 'axis'
PearsonICAdemo: no visible global function definition for 'title'
PearsonICAdemo: no visible global function definition for 'lines'
Undefined global functions or variables:
  axis dev.new lines par plot rnorm title
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "axis", "lines", "par", "plot", "title")
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Malformed Title field: should not end in a period.
'LinkingTo' for 'ggplot2' is unused as it has no 'include' directory
Packages in Depends field not imported from:
  'Rcpp' 'RcppArmadillo' 'ggplot2'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
AssoTestProc: no visible global function definition for 'rbinom'
AssoTestProc: no visible global function definition for 'princomp'
AssoTestProc: no visible global function definition for 'loadings'
AssoTestProc: no visible global function definition for 'lm'
CNVtypeAnay: no visible global function definition for 'cov'
ClusProc: no visible global function definition for 'princomp'
ClusProc: no visible global function definition for 'prcomp'
ClusProc0: no visible global function definition for 'kmeans'
ClusProc0: no visible global function definition for 'cov'
Inde: no visible global function definition for 'lm'
Inde: no visible global function definition for 'var'
STE: no visible global function definition for 'pchisq'
STIM: no visible global function definition for 'cor'
STIM: no visible global function definition for 'pchisq'
plot.clust: no visible global function definition for 'princomp'
plot.clust: no visible global function definition for 'loadings'
plot.clust: no visible global function definition for 'qplot'
plot.clust: no visible global function definition for 'geom_histogram'
plot.clust: no visible global function definition for 'aes_string'
plot.clust: no visible global function definition for 'barplot'
plot.clust: no visible global function definition for 'title'
plot.clust: no visible global function definition for 'mtext'
plot.clust: no visible global function definition for 'text'
Undefined global functions or variables:
  aes_string barplot cor cov geom_histogram kmeans lm loadings mtext
  pchisq prcomp princomp qplot rbinom text title var
Consider adding
  importFrom("graphics", "barplot", "mtext", "text", "title")
  importFrom("stats", "cor", "cov", "kmeans", "lm", "loadings", "pchisq",
             "prcomp", "princomp", "rbinom", "var")
to your NAMESPACE file.
Package in Depends field not imported from: 'reshape'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
blup: no visible global function definition for 'model.matrix'
blup: no visible global function definition for 'model.frame'
blup: no visible global function definition for 'read.table'
calcG: no visible global function definition for 'as'
gblup: no visible global function definition for 'model.matrix'
gblup: no visible global function definition for 'model.frame'
Undefined global functions or variables:
  as model.frame model.matrix read.table
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "model.frame", "model.matrix")
  importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
PEMM_fun : find.lambda: no visible global function definition for
  'optimize'
PEMM_fun: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov optimize
Consider adding
  importFrom("stats", "cov", "optimize")
to your NAMESPACE file.
Depends: includes the non-default packages:
  'e1071' 'MASS' 'corpcor' 'statmod' 'tgp' 'mlegp' 'lhs'
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:
  'MASS' 'corpcor' 'e1071' 'lhs' 'mlegp' 'statmod' 'tgp'
  Please remove these calls from your code.
S3 methods shown with full name in documentation object 'print':
  'print.scad.svm' 'print.1norm.svm'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
grid.points: no visible global function definition for 'quantile'
knots.order: no visible global function definition for 'median'
new.weights: no visible global function definition for 'ecdf'
new.weights: no visible global function definition for 'quantile'
plot.pencopula: no visible global function definition for 'as.formula'
Undefined global functions or variables:
  as.formula ecdf median quantile
Consider adding
  importFrom("stats", "as.formula", "ecdf", "median", "quantile")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/pendensity.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/penRvine.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
create.data: no visible global function definition for 'rexp'
create.data: no visible global function definition for 'runif'
create.data: no visible global function definition for 'rbinom'
opt.splitval: no visible global function definition for 'na.omit'
opt2D : opt.both: no visible global function definition for 'optim'
Undefined global functions or variables:
  na.omit optim rbinom rexp runif
Consider adding
  importFrom("stats", "na.omit", "optim", "rbinom", "rexp", "runif")
to your NAMESPACE file.
'library' or 'require' call to 'survival' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'CoxBoost' 'codetools' 'locfit' 'penalized'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
performance.curves.plot: no visible global function definition for
  'postscript'
performance.curves.plot: no visible global function definition for
  'axis'
performance.curves.plot: no visible global function definition for
  'lines'
performance.curves.plot: no visible global function definition for
  'legend'
performance.curves.plot: no visible global function definition for
  'grid'
performance.curves.plot: no visible global function definition for
  'dev.off'
precision.recall.curves.plot: no visible global function definition for
  'postscript'
precision.recall.curves.plot: no visible global function definition for
  'axis'
precision.recall.curves.plot: no visible global function definition for
  'lines'
precision.recall.curves.plot: no visible global function definition for
  'legend'
precision.recall.curves.plot: no visible global function definition for
  'grid'
precision.recall.curves.plot: no visible global function definition for
  'dev.off'
Undefined global functions or variables:
  axis dev.off grid legend lines postscript
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "axis", "grid", "legend", "lines")
to your NAMESPACE file.
Package suggested but not available for checking: 'dendextendRcpp'
permalgorithm: no visible global function definition for 'is'
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
ksample.pclt: no visible global function definition for 'pchisq'
pCI: no visible global function definition for 'qbeta'
permKS.formula: no visible global function definition for 'terms'
permTREND.default: no visible global function definition for 'cor'
permTREND.formula: no visible global function definition for 'terms'
permTS.formula: no visible global function definition for 'terms'
trend.pclt: no visible global function definition for 'pnorm'
twosample.pclt: no visible global function definition for 'pnorm'
twosample.pclt: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  cor pchisq pnorm qbeta terms
Consider adding
  importFrom("stats", "cor", "pchisq", "pnorm", "qbeta", "terms")
to your NAMESPACE file.
hasMethod: no visible global function definition for 'getS3method'
Undefined global functions or variables:
  getS3method
Consider adding
  importFrom("utils", "getS3method")
to your NAMESPACE file.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
colldiag: no visible global function definition for 'na.omit'
perturb : cutsp: no visible global function definition for 'runif'
perturb: no visible global function definition for 'terms'
perturb: no visible global function definition for 'formula'
perturb: no visible global function definition for 'coefficients'
perturb: no visible global function definition for 'as.formula'
print.reclassify: no visible global function definition for
  'addmargins'
reclassify : best.model: no visible global function definition for
  'glm'
reclassify : best.model: no visible global function definition for
  'as.formula'
reclassify : best.model: no visible global function definition for
  'poisson'
reclassify : best.model: no visible global function definition for
  'coef'
reclassify : best.model: no visible global function definition for
  'model.matrix'
reclassify : assocPat: no visible global function definition for
  'model.matrix'
reclassify : assocPat: no visible global function definition for 'glm'
reclassify : assocPat: no visible global function definition for
  'poisson'
summary.perturb: no visible binding for global variable 'sd'
Undefined global functions or variables:
  addmargins as.formula coef coefficients formula glm model.matrix
  na.omit poisson runif sd terms
Consider adding
  importFrom("stats", "addmargins", "as.formula", "coef", "coefficients",
             "formula", "glm", "model.matrix", "na.omit", "poisson",
             "runif", "sd", "terms")
to your NAMESPACE file.
cdfDist: no visible global function definition for 'tail'
cor2icc: no visible global function definition for 'cor'
plot.cdfDist: no visible global function definition for 'plot'
plot.cdfDist: no visible global function definition for 'lines'
plot.cdfDist: no visible global function definition for 'axis'
plot.cdfDist: no visible global function definition for 'mtext'
plot.cdfDist: no visible global function definition for 'legend'
Undefined global functions or variables:
  axis cor legend lines mtext plot tail
Consider adding
  importFrom("graphics", "axis", "legend", "lines", "mtext", "plot")
  importFrom("stats", "cor")
  importFrom("utils", "tail")
to your NAMESPACE file.
Running examples in 'petro.One-Ex.R' failed
The error most likely occurred in:

> ### Name: get_papers_count
> ### Title: Number of paper for a given query
> ### Aliases: get_papers_count
> 
> ### ** Examples
> 
> # Example 1
> url_1 <- make_search_url(query = "static gradient survey", how = "all")
> get_papers_count(url_1)
Error in open.connection(x, "rb") : 
  SSL certificate problem: unable to get local issuer certificate
Calls: get_papers_count -> <Anonymous> -> read_html.default
Execution halted
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  OK: 33 SKIPPED: 0 FAILED: 28
  1. Error: (unknown) (@test_GTE-summary_by.R#7) 
  2. Error: all queries match expected values (@test_GTE_paper_count.R#132) 
  3. Error: document type = *journal-paper* matches (@test_document_type.R#11) 
  4. Error: document type = *conference-paper* matches (@test_document_type.R#22) 
  5. Error: make_search_url matches number of papers from_year to_year (@test_from_year_to_year.R#12) 
  6. Error: is_dctype_enabled = FALSE (@test_is_dctype_enabled.R#8) 
  7. Error: is_dctype_enabled = TRUE (@test_is_dctype_enabled.R#21) 
  8. Error: both dataframes return rows - test #5 (@test_joining.R#11) 
  9. Error: both dataframes return rows - test #3 (@test_joining.R#25) 
  1. ...
  
  Error: testthat unit tests failed
  In addition: There were 16 warnings (use warnings() to see them)
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 31-37 (document_types_of_papers.Rmd) 
Error: processing vignette 'document_types_of_papers.Rmd' failed with diagnostics:
SSL certificate problem: unable to get local issuer certificate
Execution halted
pGLS: no visible global function definition for 'model.response'
pGLS: no visible global function definition for 'model.matrix'
pGLS: no visible global function definition for 'pt'
Undefined global functions or variables:
  model.matrix model.response pt
Consider adding
  importFrom("stats", "model.matrix", "model.response", "pt")
to your NAMESPACE file.
dvol.mse.est: no visible global function definition for 'optim'
ellipsoidSurface: no visible global function definition for 'integrate'
latscale: no visible global function definition for 'uniroot'
covariogram,Segment-function: no visible global function definition for
  'integrate'
plot,FigLat-missing: no visible global function definition for 'par'
plot,PointPattern-matrix: no visible global function definition for
  'par'
plot,PointPattern-matrix: no visible global function definition for
  'lines'
plot,PointPattern-missing: no visible global function definition for
  'points'
plot,Quadrat-missing: no visible global function definition for 'lines'
plot,Segment-matrix: no visible global function definition for 'par'
plot,Segment-matrix: no visible global function definition for
  'polygon'
plot,Segment-missing: no visible global function definition for 'lines'
Undefined global functions or variables:
  integrate lines optim par points polygon uniroot
Consider adding
  importFrom("graphics", "lines", "par", "points", "polygon")
  importFrom("stats", "integrate", "optim", "uniroot")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/phalen.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
PharmPow_crossover: no visible global function definition for
  'read.table'
PharmPow_crossover: no visible global function definition for
  'write.csv'
PharmPow_crossover: no visible global function definition for 'pdf'
PharmPow_crossover: no visible global function definition for 'dev.off'
PharmPow_parallel: no visible global function definition for
  'read.table'
PharmPow_parallel: no visible global function definition for
  'write.csv'
PharmPow_parallel: no visible global function definition for 'pdf'
PharmPow_parallel: no visible global function definition for 'dev.off'
fig_PharmPow_crossover: no visible global function definition for
  'read.csv'
fig_PharmPow_parallel: no visible global function definition for
  'read.csv'
Undefined global functions or variables:
  dev.off pdf read.csv read.table write.csv
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "read.csv", "read.table", "write.csv")
to your NAMESPACE file.
flowField: no visible global function definition for 'plot'
flowField: no visible global function definition for 'arrows'
nullclines: no visible global function definition for 'contour'
numericalSolution: no visible global function definition for 'locator'
numericalSolution: no visible global function definition for 'plot'
numericalSolution: no visible global function definition for 'lines'
phasePortrait: no visible global function definition for 'plot'
phasePortrait: no visible global function definition for 'arrows'
stability: no visible global function definition for 'locator'
trajectory: no visible global function definition for 'locator'
trajectory: no visible global function definition for 'plot'
trajectory: no visible global function definition for 'lines'
trajectory: no visible global function definition for 'points'
Undefined global functions or variables:
  arrows contour lines locator plot points
Consider adding
  importFrom("graphics", "arrows", "contour", "lines", "locator", "plot",
             "points")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'ggplot2' 'reshape'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plot.phtMCMC: no visible global function definition for 'ggplot'
plot.phtMCMC: no visible global function definition for 'melt'
plot.phtMCMC: no visible global function definition for 'geom_line'
plot.phtMCMC: no visible global function definition for 'aes_string'
plot.phtMCMC: no visible global function definition for 'geom_smooth'
plot.phtMCMC: no visible global function definition for 'facet_wrap'
plot.phtMCMC: no visible global function definition for 'ggtitle'
plot.phtMCMC: no visible global function definition for 'xlab'
plot.phtMCMC: no visible global function definition for 'ylab'
plot.phtMCMC: no visible global function definition for 'geom_density'
Undefined global functions or variables:
  aes_string facet_wrap geom_density geom_line geom_smooth ggplot
  ggtitle melt xlab ylab
File 'PhaseType/libs/i386/PhaseType.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'LJMA_arms.o'
File 'PhaseType/libs/x64/PhaseType.dll':
  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 use Fortran I/O
nor system RNGs.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
deforestation: no visible global function definition for 'model.frame'
deforestation: no visible global function definition for 'model.matrix'
deforestation: no visible global function definition for
  'model.response'
deforestation: no visible global function definition for 'vcov'
deforestation: no visible global function definition for 'glm'
demography: no visible global function definition for 'model.frame'
demography: no visible global function definition for 'model.matrix'
demography: no visible global function definition for 'model.response'
form.beta.start: no visible global function definition for 'coef'
form.beta.start: no visible global function definition for 'glm'
form.sigma2.start: no visible global function definition for 'var'
form.sigma2.start: no visible global function definition for
  'residuals'
form.sigma2.start: no visible global function definition for 'glm'
rinvgamma: no visible global function definition for 'rgamma'
rwish: no visible global function definition for 'rchisq'
rwish: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  coef glm model.frame model.matrix model.response rchisq residuals
  rgamma rnorm var vcov
Consider adding
  importFrom("stats", "coef", "glm", "model.frame", "model.matrix",
             "model.response", "rchisq", "residuals", "rgamma", "rnorm",
             "var", "vcov")
to your NAMESPACE file.
Package has both 'src/Makevars.in' and 'src/Makevars'.
Installation with --no-configure' is unlikely to work.  If you intended
'src/Makevars' to be used on Windows, rename it to 'src/Makevars.win'
otherwise remove it.  If 'configure' created 'src/Makevars', you need a
'cleanup' script.
fox: no visible binding for global variable 'sd'
fox: no visible global function definition for 'cor'
fox: no visible global function definition for 'interaction.plot'
fox: no visible global function definition for 'reorder'
fox: no visible global function definition for 'plot'
kang: no visible global function definition for 'var'
kang: no visible binding for global variable 'sd'
kang: no visible global function definition for 'cor'
kang: no visible global function definition for 'interaction.plot'
kang: no visible global function definition for 'reorder'
kang: no visible global function definition for 'plot'
nahu: no visible global function definition for 'interaction.plot'
nahu: no visible global function definition for 'reorder'
nahu: no visible global function definition for 'plot'
thsu: no visible global function definition for 'median'
thsu: no visible binding for global variable 'sd'
thsu: no visible global function definition for 'cor'
thsu: no visible global function definition for 'interaction.plot'
thsu: no visible global function definition for 'reorder'
thsu: no visible global function definition for 'plot'
Undefined global functions or variables:
  cor interaction.plot median plot reorder sd var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "cor", "interaction.plot", "median", "reorder",
             "sd", "var")
to your NAMESPACE file.
pheno.ddm: no visible global function definition for 'new'
pheno.flm.fit: no visible binding for global variable 'na.exclude'
pheno.flm.fit: no visible global function definition for 'terms'
pheno.flm.fit: no visible global function definition for 'residuals'
pheno.flm.fit: no visible global function definition for 'qt'
pheno.lad.fit: no visible binding for global variable 'na.exclude'
pheno.mlm.fit: no visible binding for global variable 'na.exclude'
pheno.mlm.fit: no visible global function definition for 'residuals'
Undefined global functions or variables:
  na.exclude new qt residuals terms
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "na.exclude", "qt", "residuals", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in 'phuse-Ex.R' failed
The error most likely occurred in:

> ### Name: cvt_list2df
> ### Title: Convert list to data frame
> ### Aliases: cvt_list2df
> 
> ### ** Examples
> 
>   a <- "https://github.com/phuse-org/phuse-scripts/raw/master"
>   b <- "development/R/scripts"
>   c <- "Draw_Dist2_R.yml"
>   f1 <- paste(a,b,c, sep = '/')
>   r1 <- read_yml(f1)
>   r2 <- cvt_list2df(r1)
Error in a[[k1]] : subscript out of bounds
Calls: cvt_list2df
Execution halted
Package in Depends field not imported from: 'raster'
  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:
  Note: possible error in 'try(xtriple, ftriple, ': unused arguments (lfmid, 1, 2) 
  Note: possible error in 'try(xtriple, ftriple, ': unused arguments (rfmid, 2, 3) 
See 'd:/Rcompile/CRANpkg/local/3.5/phyreg.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
inf: no visible global function definition for 'tail'
phyfromnewick: no visible global function definition for 'head'
phyreg : inphyreg : merge.formulae.ag: no visible global function
  definition for 'update'
phyreg : inphyreg : merge.formula.test.ag: no visible global function
  definition for 'reformulate'
phyreg : inphyreg: no visible global function definition for
  'as.formula'
phyreg : inphyreg: no visible global function definition for
  'model.frame'
phyreg : inphyreg: no visible binding for global variable 'na.omit'
phyreg : inphyreg: no visible global function definition for
  'model.matrix'
phyreg : inphyreg: no visible global function definition for 'lm'
phyreg : inphyreg: no visible global function definition for 'lm.wfit'
phyreg : inphyreg: no visible global function definition for 'pf'
phyreg : inphyreg: no visible global function definition for 'coef'
Undefined global functions or variables:
  as.formula coef head lm lm.wfit model.frame model.matrix na.omit pf
  reformulate tail update
Consider adding
  importFrom("stats", "as.formula", "coef", "lm", "lm.wfit",
             "model.frame", "model.matrix", "na.omit", "pf",
             "reformulate", "update")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Found the following hidden files and directories:
  data/.Rhistory
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
plotData: no visible global function definition for 'plot'
plotData: no visible global function definition for 'abline'
plotData: no visible global function definition for 'text'
Undefined global functions or variables:
  abline plot text
Consider adding
  importFrom("graphics", "abline", "plot", "text")
to your NAMESPACE file.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/PhySortR.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
incident: no visible global function definition for 'splinefun'
incident: no visible global function definition for 'integrate'
phytoprod: no visible global function definition for 'approx'
phytoprod: no visible global function definition for 'splinefun'
phytoprod: no visible global function definition for 'integrate'
reflectance: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx integrate splinefun
Consider adding
  importFrom("stats", "approx", "integrate", "splinefun")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/picante.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
'library' or 'require' calls in package code:
  'brglm' 'quantreg'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
File which contains pragma(s) suppressing diagnostics:
  'src/pijavski.cpp'
plot.pred.int: no visible global function definition for 'plot.default'
plot.pred.int: no visible global function definition for 'axis'
plot.pred.int: no visible global function definition for 'box'
plot.pred.int : cidist: no visible global function definition for
  'ecdf'
plot.pred.int : negcidist: no visible global function definition for
  'ecdf'
plot.pred.int : pi.col.fun: no visible global function definition for
  'gray'
plot.pred.int: no visible global function definition for 'segments'
plot.pred.int: no visible global function definition for 'points'
plot.pred.int: no visible global function definition for 'abline'
pred.int: no visible binding for global variable 'sd'
prop.test.mult: no visible global function definition for 'qnorm'
sim.basic: no visible global function definition for 'rbinom'
sim.basic: no visible global function definition for 'rnorm'
t.test.mult: no visible global function definition for 'qt'
Undefined global functions or variables:
  abline axis box ecdf gray plot.default points qnorm qt rbinom rnorm
  sd segments
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "box", "plot.default",
             "points", "segments")
  importFrom("stats", "ecdf", "qnorm", "qt", "rbinom", "rnorm", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: 'ggsubplot'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.4Mb
'library' or 'require' calls in package code:
  'argparse' 'devtools' 'knitr'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Depends: includes the non-default packages:
  'RGtk2' 'gWidgetsRGtk2' 'cairoDevice' 'lattice' 'rggobi' 'ggplot2'
  'proto'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'RGtk2' 'gWidgetsRGtk2'
A package should be listed in only one of these fields.
Package in Depends field not imported from: 'cairoDevice'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
PKmod: no visible global function definition for 'deriv'
Undefined global functions or variables:
  deriv
Consider adding
  importFrom("stats", "deriv")
to your NAMESPACE file.
PKadjust: no visible binding for global variable 'jpeg'
PKadjust: no visible binding for global variable 'bmp'
PKadjust: no visible binding for global variable 'png'
PKadjust: no visible binding for global variable 'tiff'
PKadjust: no visible binding for global variable 'dev.new'
PKadjust: no visible global function definition for 'dev.off'
PKfigure: no visible global function definition for 'dev.cur'
PKfigure: no visible global function definition for 'dev.off'
PKoutput: no visible global function definition for 'heatmap'
PKoutput: no visible global function definition for
  'packageDescription'
PKshow: no visible global function definition for 'browseURL'
addList1: no visible global function definition for 'formula'
addList1.old: no visible global function definition for 'formula'
addList2: no visible global function definition for 'formula'
generate.plot: no visible global function definition for 'dev.off'
writeHTML: no visible global function definition for
  'packageDescription'
writeLst: no visible global function definition for
  'packageDescription'
writeLst.tab: no visible global function definition for
  'packageDescription'
writeTable: no visible global function definition for
  'packageDescription'
writeTable: no visible global function definition for 'quantile'
initialize,nonmem: no visible global function definition for
  'read.table'
Undefined global functions or variables:
  bmp browseURL dev.cur dev.new dev.off formula heatmap jpeg
  packageDescription png quantile read.table tiff
Consider adding
  importFrom("grDevices", "bmp", "dev.cur", "dev.new", "dev.off", "jpeg",
             "png", "tiff")
  importFrom("stats", "formula", "heatmap", "quantile")
  importFrom("utils", "browseURL", "packageDescription", "read.table")
to your NAMESPACE file.
plot.burndown: no visible global function definition for 'par'
plot.burndown: no visible global function definition for 'hcl'
plot.burndown: no visible global function definition for 'plot'
plot.burndown: no visible global function definition for 'polygon'
plot.burndown: no visible global function definition for 'lm'
plot.burndown: no visible global function definition for 'abline'
plot.burndown: no visible global function definition for 'lines'
plot.burndown: no visible global function definition for 'points'
plot.burndown: no visible global function definition for 'legend'
plot.burndown: no visible global function definition for 'mtext'
plot.gantt: no visible global function definition for 'gray'
plot.gantt: no visible global function definition for 'par'
plot.gantt: no visible global function definition for 'strheight'
plot.gantt: no visible global function definition for 'strwidth'
plot.gantt: no visible global function definition for 'plot'
plot.gantt: no visible global function definition for 'box'
plot.gantt: no visible global function definition for 'mtext'
plot.gantt: no visible global function definition for 'axis.POSIXct'
plot.gantt: no visible global function definition for 'rug'
plot.gantt: no visible global function definition for 'abline'
plot.gantt: no visible global function definition for 'axis'
plot.gantt: no visible global function definition for 'lines'
plot.gantt: no visible global function definition for 'rect'
Undefined global functions or variables:
  abline axis axis.POSIXct box gray hcl legend lines lm mtext par plot
  points polygon rect rug strheight strwidth
Consider adding
  importFrom("grDevices", "gray", "hcl")
  importFrom("graphics", "abline", "axis", "axis.POSIXct", "box",
             "legend", "lines", "mtext", "par", "plot", "points",
             "polygon", "rect", "rug", "strheight", "strwidth")
  importFrom("stats", "lm")
to your NAMESPACE file.
Package suggested but not available for checking: 'latticist'
'library' or 'require' call to 'lattice' which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to 'latticist' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'cairoDevice' 'gWidgetsRGtk2' 'grid' 'lattice'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  'lattice:::lattice.getStatus' 'stats:::biplot.prcomp'
  See the note in ?`:::` about the use of this operator.
S3 methods shown with full name in documentation object 'plotCoords':
  'plotCoords.plot' 'plotCoords.biplot'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
bwfw.hmm: no visible global function definition for 'dnorm'
bwfw1.hmm: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'R.oo' 'limma' 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fitBspline: no visible global function definition for 'median'
fitBspline: no visible global function definition for 'quantile'
fitGAPLM: no visible global function definition for 'poisson'
fitGAPLM: no visible global function definition for 'quantile'
fitGAPLM: no visible global function definition for 'anova'
fitGAPLM: no visible global function definition for 'as.formula'
fitGAPLM: no visible global function definition for 'glm'
fitGAPLM: no visible global function definition for 'pf'
fitGAPLM: no visible global function definition for 'lm'
fitGAPLM: no visible global function definition for 'p.adjust'
head.DEresults: no visible global function definition for 'head'
head.plmDE: no visible global function definition for 'head'
hist.DEresults: no visible global function definition for 'hist'
hist.DEresults: no visible global function definition for 'colors'
hist.DEresults: no visible global function definition for 'box'
limmaPLM: no visible global function definition for 'quantile'
plot.DEresults: no visible global function definition for 'as.formula'
plot.DEresults: no visible global function definition for 'lm'
plot.DEresults: no visible global function definition for 'glm'
plot.DEresults: no visible global function definition for 'plot'
plot.DEresults: no visible global function definition for 'lines'
plot.DEresults: no visible global function definition for 'points'
plot.DEresults: no visible global function definition for 'predict'
Undefined global functions or variables:
  anova as.formula box colors glm head hist lines lm median p.adjust pf
  plot points poisson predict quantile
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "box", "hist", "lines", "plot", "points")
  importFrom("stats", "anova", "as.formula", "glm", "lm", "median",
             "p.adjust", "pf", "poisson", "predict", "quantile")
  importFrom("utils", "head")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'Formula' 'sm'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
nrmlepln: no visible global function definition for 'pchisq'
nrmlerasch: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
Running examples in 'plotKML-Ex.R' failed
The error most likely occurred in:

> ### Name: plotKML-method
> ### Title: Methods for plotting results of spatial analysis in Google Earth
> ### Aliases: plotKML-method plotKML plotKML,SpatialPointsDataFrame-method
> ###   plotKML,SpatialLinesDataFrame-method
> ###   plotKML,SpatialPolygonsDataFrame-method
> ###   plotKML,SoilProfileCollection-method
> ###   plotKML,SpatialGridDataFrame-method
> ###   plotKML,SpatialPixelsDataFrame-method plotKML,RasterLayer-method
> ###   plotKML,SpatialPhotoOverlay-method plotKML,STIDF-method
> ###   plotKML,STFDF-method plotKML,STSDF-method plotKML,STTDF-method
> ###   plotKML,SpatialPredictions-method
> ###   plotKML,RasterBrickSimulations-method
> ###   plotKML,SpatialVectorsSimulations-method
> ###   plotKML,SpatialMaxEntOutput-method
> ###   plotKML,RasterBrickTimeSeries-method
> ###   plotKML,SpatialSamplingPattern-method plotKML,list-method
> ### Keywords: spatial methods
> 
> ### ** Examples
> 
> plotKML.env(silent = FALSE, kmz = FALSE)
Search for SAGA command line program and modules... 
SAGA command line program not found in the following default paths:
C:/Progra~1/SAGA-GIS
C:/SAGA-GIS
C:/OSGeo4W64/apps/saga
C:/OSGeo4W64/apps/saga-ltr
Search on the entire hard drive...
Error in paths(show.paths = TRUE) : object 'saga.version' not found
Calls: plotKML.env -> paths
Execution halted
Error in re-building vignettes:
  ...
URL: http://plotkml.r-forge.r-project.org/
Loading required package: GSIF
GSIF version 0.5-4 (2017-04-25)
URL: http://gsif.r-forge.r-project.org/

Attaching package: 'XML'

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

    toHTML

Reprojecting to +proj=longlat +datum=WGS84 ...
KML file opened for writing...
Writing to KML...
Closing  eberg.ll__CLYMHT_A__.kml
KML file opened for writing...
Writing to KML...
Closing  eberg.ll.kml
KML file opened for writing...
Reprojecting to +proj=longlat +datum=WGS84 ...

Error: processing vignette 'jss1079.Rnw' failed with diagnostics:
 chunk 12 
Error in paths(show.paths = TRUE) : object 'saga.version' not found
Execution halted
plotAuto: no visible global function definition for 'window'
plotAuto: no visible global function definition for 'title'
plotAuto: no visible global function definition for 'axis'
plotAuto: no visible global function definition for 'box'
plotCumu: no visible global function definition for 'title'
plotCumu: no visible global function definition for 'axis'
plotCumu: no visible global function definition for 'box'
plotDens : panel.dens: no visible global function definition for 'var'
plotDens : panel.dens: no visible global function definition for
  'quantile'
plotDens : panel.dens: no visible global function definition for
  'median'
plotDens: no visible global function definition for 'tail'
plotQuant: no visible global function definition for 'par'
plotQuant: no visible binding for global variable 'quantile'
plotQuant: no visible global function definition for 'plot'
plotQuant: no visible global function definition for 'lines'
plotQuant: no visible global function definition for 'bxp'
plotQuant: no visible global function definition for 'matplot'
plotQuant: no visible global function definition for 'axis'
plotQuant: no visible global function definition for 'box'
plotQuant: no visible global function definition for 'title'
plotSplom: no visible global function definition for 'pairs'
plotTrace : panel.trace: no visible global function definition for
  'var'
plotTrace : panel.trace: no visible global function definition for
  'median'
plotTrace: no visible global function definition for 'tail'
Undefined global functions or variables:
  axis box bxp lines matplot median pairs par plot quantile tail title
  var window
Consider adding
  importFrom("graphics", "axis", "box", "bxp", "lines", "matplot",
             "pairs", "par", "plot", "title")
  importFrom("stats", "median", "quantile", "var", "window")
  importFrom("utils", "tail")
to your NAMESPACE file.
generateEnvelope: no visible global function definition for 'tail'
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
llla.bi: no visible global function definition for 'as.formula'
llla.bi: no visible global function definition for 'glm'
llla.bi: no visible global function definition for 'binomial'
llla.bi: no visible binding for global variable 'logit'
llla.bi: no visible global function definition for 'vcov'
llla.bi: no visible global function definition for 'coef'
llla.mc: no visible global function definition for 'model.matrix'
llla.mc: no visible global function definition for 'as.formula'
llla.mc: no visible global function definition for 'coxph'
llla.mc: no visible global function definition for 'vcov'
llla.mc: no visible global function definition for 'coef'
llla.mle: no visible global function definition for 'as.formula'
llla.mle: no visible global function definition for 'glm'
llla.mle: no visible global function definition for 'poisson'
llla.mle: no visible global function definition for 'coef'
llla.mle: no visible global function definition for 'vcov'
mclgen: no visible global function definition for 'reshape'
simRasch.1D: no visible global function definition for 'rnorm'
simRasch.1D: no visible global function definition for 'runif'
vcov.sandwich.glm: no visible global function definition for
  'model.matrix'
vcov.sandwich.glm: no visible global function definition for 'weights'
vcov.sandwich.glm: no visible global function definition for
  'residuals'
vcov.sandwich.glm: no visible global function definition for 'vcov'
Undefined global functions or variables:
  as.formula binomial coef coxph glm logit model.matrix poisson reshape
  residuals rnorm runif vcov weights
Consider adding
  importFrom("stats", "as.formula", "binomial", "coef", "glm",
             "model.matrix", "poisson", "reshape", "residuals", "rnorm",
             "runif", "vcov", "weights")
to your NAMESPACE file.
compute.lower.bound: no visible global function definition for 'cor'
kernel.pls.fit: no visible binding for global variable 'sd'
linear.pls.fit: no visible binding for global variable 'sd'
pcr: no visible binding for global variable 'sd'
pcr: no visible global function definition for 'cor'
pcr.cv: no visible global function definition for 'cor'
pcr.cv: no visible global function definition for 'plot'
pls.model: no visible binding for global variable 'sd'
ridge.cv: no visible global function definition for 'coef'
ridge.cv: no visible global function definition for 'cor'
ridge.cv: no visible global function definition for 'plot'
Undefined global functions or variables:
  coef cor plot sd
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "cor", "sd")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/plsRglm.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
'library' or 'require' calls in package code:
  'MASS' 'plsdof'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
print.densityEHpi: no visible global function definition for 'str'
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'rbind.fill':
  'rbind.fill'

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   1.6Mb
Packages in Depends field not imported from:
  'impute' 'plyr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.MCM: no visible global function definition for 'runif'
.MCM: no visible global function definition for 'rmultinom'
.MCM: no visible global function definition for 'mahalanobis'
.MCM: no visible global function definition for 'optimize'
.MCM : f: no visible global function definition for 'mahalanobis'
.MCM: no visible global function definition for 'alarm'
.igpark: no visible global function definition for 'kmeans'
.loglik: no visible global function definition for 'mahalanobis'
.plot.gpcm: no visible global function definition for 'plot'
.plot.gpcm: no visible global function definition for 'lines'
.plot.gpcm: no visible global function definition for 'legend'
.rwgpar: no visible global function definition for 'rexp'
.weights: no visible global function definition for 'mahalanobis'
Undefined global functions or variables:
  alarm kmeans legend lines mahalanobis optimize plot rexp rmultinom
  runif
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "kmeans", "mahalanobis", "optimize", "rexp",
             "rmultinom", "runif")
  importFrom("utils", "alarm")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/pmlr.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
pmlr: no visible global function definition for 'model.response'
pmlr: no visible global function definition for 'model.matrix'
pmlr: no visible global function definition for 'model.weights'
pmlr: no visible global function definition for 'pchisq'
pmlr: no visible global function definition for 'qnorm'
profileCIs: no visible global function definition for 'qchisq'
test.LR: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  model.matrix model.response model.weights pchisq qchisq qnorm
Consider adding
  importFrom("stats", "model.matrix", "model.response", "model.weights",
             "pchisq", "qchisq", "qnorm")
to your NAMESPACE file.
dbm: no visible global function definition for 'optim'
dbm: no visible global function definition for 'new'
destat: no visible global function definition for 'weighted.mean'
local.knn: no visible global function definition for 'sd'
local.knn: no visible global function definition for 'optim'
mdpref: no visible global function definition for 'sd'
mdpref: no visible global function definition for 'text'
mdpref: no visible global function definition for 'lines'
phicom: no visible global function definition for 'optim'
phicom: no visible global function definition for 'new'
pl: no visible global function definition for 'optim'
pl: no visible global function definition for 'new'
rol: no visible global function definition for 'nlm'
rol: no visible global function definition for 'new'
wdbm: no visible global function definition for 'optim'
wdbm: no visible global function definition for 'new'
Undefined global functions or variables:
  lines new nlm optim sd text weighted.mean
Consider adding
  importFrom("graphics", "lines", "text")
  importFrom("methods", "new")
  importFrom("stats", "nlm", "optim", "sd", "weighted.mean")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' call to 'MASS' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'MASS'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pnmtrem1: no visible global function definition for 'pnorm'
pnmtrem1: no visible global function definition for 'dnorm'
pnmtrem1: no visible global function definition for 'ginv'
pnmtrem1 : fun: no visible global function definition for 'pnorm'
pnmtrem1 : derf: no visible global function definition for 'dnorm'
pnmtrem1 : derf: no visible global function definition for 'pnorm'
pnmtrem1 : fun: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm ginv pnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm")
to your NAMESPACE file.
'library' or 'require' call to 'rgenoud' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.sigma: no visible global function definition for 'plot'
smooth: no visible global function definition for 'genoud'
Undefined global functions or variables:
  genoud plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
ppoibin: no visible global function definition for 'pnorm'
ppoibin: no visible global function definition for 'dnorm'
rpoibin: no visible global function definition for 'runif'
Undefined global functions or variables:
  dnorm pnorm runif
Consider adding
  importFrom("stats", "dnorm", "pnorm", "runif")
to your NAMESPACE file.
ColorDendrogram: no visible global function definition for 'plot'
ColorDendrogram: no visible global function definition for 'segments'
CountDataSet: no visible global function definition for 'rexp'
CountDataSet: no visible global function definition for 'runif'
CountDataSet: no visible global function definition for 'rnorm'
CountDataSet: no visible global function definition for 'rnbinom'
NullModel: no visible binding for global variable 'quantile'
NullModel : <anonymous>: no visible global function definition for
  'median'
NullModelTest: no visible binding for global variable 'quantile'
NullModelTest : <anonymous>: no visible global function definition for
  'median'
PoissonDistance: no visible global function definition for 'as.dist'
permute.rows: no visible global function definition for 'runif'
print.poiclacv: no visible global function definition for 'write.table'
se: no visible global function definition for 'sd'
Undefined global functions or variables:
  as.dist median plot quantile rexp rnbinom rnorm runif sd segments
  write.table
Consider adding
  importFrom("graphics", "plot", "segments")
  importFrom("stats", "as.dist", "median", "quantile", "rexp", "rnbinom",
             "rnorm", "runif", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
bipoilogMLE: no visible global function definition for 'optim'
bipoilogMLE: no visible global function definition for 'write.table'
poilogMLE: no visible global function definition for 'optim'
rbipoilog : sim: no visible global function definition for 'rnorm'
rbipoilog : sim: no visible global function definition for 'rpois'
rpoilog : sim: no visible global function definition for 'rnorm'
rpoilog : sim: no visible global function definition for 'rpois'
Undefined global functions or variables:
  optim rnorm rpois write.table
Consider adding
  importFrom("stats", "optim", "rnorm", "rpois")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Running examples in 'pointblank-Ex.R' failed
The error most likely occurred in:

> ### Name: col_exists
> ### Title: Verify that one or more columns exist
> ### Aliases: col_exists
> 
> ### ** Examples
> 
> # Validate that column `a` exists in
> # the `small_table` CSV file; do this
> # by creating an agent, focussing on
> # that table, creating a `col_exists()`
> # step, and then interrogating the table
> agent <-
+   create_agent() %>%
+   focus_on(
+     file_name = 
+       system.file(
+         "extdata", "small_table.csv",
+         package = "pointblank"),
+     col_types = "TDicidlc") %>%
+   col_exists(column = a) %>%
+   interrogate()
Error: `UQ()` can only be used within a quasiquoted argument
Execution halted
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  OK: 53 SKIPPED: 0 FAILED: 24
  1. Error: Creating a `col_is_character()` step is possible (@test-create_validation_steps.R#10) 
  2. Error: Creating a `col_is_date()` step is possible (@test-create_validation_steps.R#74) 
  3. Error: Creating a `col_is_factor()` step is possible (@test-create_validation_steps.R#138) 
  4. Error: Creating a `col_is_integer()` step is possible (@test-create_validation_steps.R#202) 
  5. Error: Creating a `col_is_logical()` step is possible (@test-create_validation_steps.R#266) 
  6. Error: Creating a `col_is_numeric()` step is possible (@test-create_validation_steps.R#330) 
  7. Error: Creating a `col_is_posix()` step is possible (@test-create_validation_steps.R#394) 
  8. Error: Creating a `col_vals_between()` step is possible (@test-create_validation_steps.R#458) 
  9. Error: Creating a `col_vals_not_between()` step is possible (@test-create_validation_steps.R#530) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
approxMargMLE: no visible global function definition for 'optim'
approxMargMLECI : ciFunction: no visible global function definition for
  'qchisq'
approxMargMLECI: no visible global function definition for 'uniroot'
margMLE: no visible global function definition for 'optim'
margMLECI: no visible global function definition for 'optim'
margMLECI : unNormLikeMinusVal: no visible global function definition
  for 'qchisq'
margMLECI: no visible global function definition for 'uniroot'
profMLECI : ciFunction: no visible global function definition for
  'qchisq'
profMLECI: no visible global function definition for 'uniroot'
rtbinom: no visible global function definition for 'rbinom'
rtpois: no visible global function definition for 'rpois'
waldCI: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  optim qchisq qnorm rbinom rpois uniroot
Consider adding
  importFrom("stats", "optim", "qchisq", "qnorm", "rbinom", "rpois",
             "uniroot")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'combinat' 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Est.Depth: no visible global function definition for 'quantile'
PS.FDR: no visible global function definition for 'quantile'
Permu.Ind: no visible global function definition for 'permn'
Permu.Ind: no visible global function definition for 'hcube'
Trans.Data: no visible global function definition for 'write.table'
Trans.Data: no visible global function definition for 'predict'
Trans.Data: no visible global function definition for 'lm'
Undefined global functions or variables:
  hcube lm permn predict quantile write.table
Consider adding
  importFrom("stats", "lm", "predict", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
rpoistweedie: no visible global function definition for 'runif'
testOmegaPT: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'MASS' 'scatterplot3d'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plot.poLCA: no visible global function definition for 'layout'
plot.poLCA: no visible global function definition for 'par'
poLCA: no visible global function definition for 'model.frame'
poLCA: no visible global function definition for 'model.response'
poLCA: no visible global function definition for 'model.matrix'
poLCA: no visible global function definition for 'runif'
poLCA: no visible global function definition for 'ginv'
poLCA: no visible global function definition for 'flush.console'
poLCA.makeplot.dich: no visible global function definition for
  'scatterplot3d'
poLCA.makeplot.poly: no visible global function definition for
  'scatterplot3d'
poLCA.se: no visible global function definition for 'ginv'
poLCA.simdata: no visible global function definition for 'runif'
poLCA.simdata: no visible global function definition for 'rnorm'
poLCA.table: no visible global function definition for 'model.frame'
print.poLCA: no visible global function definition for 'pt'
print.poLCA: no visible global function definition for 'flush.console'
rmulti: no visible global function definition for 'runif'
Undefined global functions or variables:
  flush.console ginv layout model.frame model.matrix model.response par
  pt rnorm runif scatterplot3d
Consider adding
  importFrom("graphics", "layout", "par")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "pt", "rnorm", "runif")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Packages suggested but not available for checking:
  'polmineR.Rcpp' 'europarl.en' 'rcqp'
qPolyaAeppliSingle: no visible global function definition for 'qgamma'
rPolyaAeppli: no visible global function definition for 'rpois'
rPolyaAeppli: no visible global function definition for 'rgeom'
Undefined global functions or variables:
  qgamma rgeom rpois
Consider adding
  importFrom("stats", "qgamma", "rgeom", "rpois")
to your NAMESPACE file.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      6.4Mb
    data   2.5Mb
DistributionPlotBinomial: no visible global function definition for
  'qbinom'
DistributionPlotBinomial: no visible global function definition for
  'plot'
DistributionPlotBinomial: no visible global function definition for
  'dbinom'
DistributionPlotBinomial: no visible global function definition for
  'points'
DistributionPlotBinomial: no visible global function definition for
  'abline'
DistributionPlotGamma: no visible global function definition for
  'qgamma'
DistributionPlotGamma: no visible global function definition for 'plot'
DistributionPlotGamma: no visible global function definition for
  'dgamma'
DistributionPlotGamma: no visible global function definition for
  'abline'
DistributionPlotNorm: no visible global function definition for 'qnorm'
DistributionPlotNorm: no visible global function definition for 'plot'
DistributionPlotNorm: no visible global function definition for 'dnorm'
DistributionPlotNorm: no visible global function definition for
  'abline'
calculateDIC: no visible global function definition for 'pnorm'
plot.segratioMCMC: no visible global function definition for 'plot'
plotFitted: no visible global function definition for 'nclass.Sturges'
plotFitted : totalCurve: no visible global function definition for
  'dnorm'
plotFitted : <anonymous>: no visible global function definition for
  'dnorm'
plotTheoretical: no visible global function definition for
  'nclass.Sturges'
plotTheoretical: no visible global function definition for 'dbinom'
setPriors: no visible global function definition for 'qbinom'
Undefined global functions or variables:
  abline dbinom dgamma dnorm nclass.Sturges plot pnorm points qbinom
  qgamma qnorm
Consider adding
  importFrom("grDevices", "nclass.Sturges")
  importFrom("graphics", "abline", "plot", "points")
  importFrom("stats", "dbinom", "dgamma", "dnorm", "pnorm", "qbinom",
             "qgamma", "qnorm")
to your NAMESPACE file.
plot.segRatio: no visible global function definition for 'hist'
plot.segRatio: no visible global function definition for 'par'
plot.segRatio: no visible global function definition for 'layout'
plot.simAutoCross: no visible global function definition for 'plot'
plot.simAutoMarkers: no visible global function definition for 'plot'
sim.autoCross: no visible global function definition for 'rmultinom'
sim.autoMarkers: no visible global function definition for 'rmultinom'
sim.autoMarkers: no visible global function definition for 'rbinom'
sim.autoMarkers: no visible global function definition for 'rbeta'
test.segRatio: no visible global function definition for 'chisq.test'
test.segRatio: no visible global function definition for 'pbinom'
Undefined global functions or variables:
  chisq.test hist layout par pbinom plot rbeta rbinom rmultinom
Consider adding
  importFrom("graphics", "hist", "layout", "par", "plot")
  importFrom("stats", "chisq.test", "pbinom", "rbeta", "rbinom",
             "rmultinom")
to your NAMESPACE file.
'library' or 'require' call to 'matrixcalc' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'matrixcalc'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
print.mixed.pom: no visible global function definition for 'pnorm'
print.pom: no visible global function definition for 'pnorm'
siteocc : get.mod.matrix: no visible binding for global variable
  'na.pass'
siteocc : get.mod.matrix: no visible global function definition for
  'formula'
siteocc : get.mod.matrix: no visible global function definition for
  'model.matrix'
siteocc: no visible global function definition for 'nlminb'
siteocc: no visible global function definition for
  'is.positive.definite'
Undefined global functions or variables:
  formula is.positive.definite model.matrix na.pass nlminb pnorm
Consider adding
  importFrom("stats", "formula", "model.matrix", "na.pass", "nlminb",
             "pnorm")
to your NAMESPACE file.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/PopGenome.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
asymmetricIntervals: no visible global function definition for 'stack'
bonferroniIntervals: no visible global function definition for 'stack'
bonferroniIntervals: no visible global function definition for 'lm'
bonferroniIntervals: no visible global function definition for
  'predict'
bootstrapIntervals: no visible global function definition for 'stack'
component1a: no visible global function definition for 'pnorm'
component1b: no visible global function definition for 'pnorm'
component2: no visible global function definition for 'dgamma'
eqnForMin: no visible global function definition for 'pnorm'
eqnForMin: no visible global function definition for 'integrate'
integrand : <anonymous>: no visible global function definition for
  'pnorm'
integrand: no visible global function definition for 'dnorm'
integrate2: no visible global function definition for 'integrate'
integrate2a: no visible global function definition for 'integrate'
integrate2b: no visible global function definition for 'integrate'
integrate4a: no visible global function definition for 'integrate'
integrate4b: no visible global function definition for 'integrate'
optimalCScalar2: no visible global function definition for 'uniroot'
optimalLambda: no visible global function definition for 'optimise'
optimalLambdaC: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dgamma dnorm integrate lm optimise pnorm predict stack uniroot
Consider adding
  importFrom("stats", "dgamma", "dnorm", "integrate", "lm", "optimise",
             "pnorm", "predict", "uniroot")
  importFrom("utils", "stack")
to your NAMESPACE file.
popRangeSim: no visible global function definition for 'write.table'
Undefined global functions or variables:
  write.table
Consider adding
  importFrom("utils", "write.table")
to your NAMESPACE file.
Running examples in 'popRange-Ex.R' failed
The error most likely occurred in:

> ### Name: popRangeSim
> ### Title: popRangeSim
> ### Aliases: popRangeSim
> 
> ### ** Examples
>  
> ## Example: In this scenario, we are simulating a 3x3 grid of populations for 50 
> ## generations. Each population starts with 100 diploid individuals. Each individual 
> ## has a 0.01 probability of migrating away from their populations. There are 100 
> ## SNPs that all have a starting frequency of 0.5, and the program outputs the standard 
> ## "results" file, as well as a PLINK file. 
> 
> ## Commands
> 
> mat = matrix(1,nrow=3,ncol=3) 
> popRangeSim(world = mat, popSize = 100, diploid = TRUE, nGens = 50,
+               mig = 0.01, SNP_model = 0, nSNPs = 100, SNPs_starting_freq = 0.5, 
+               outfile= "outFile1", PLINK=TRUE)
Error in loadNamespace(name) : there is no package called 'reticulate'
[1] "Could not find an acceptable version of python with numpy installed. This should be able to locate python \n      anywhere on your computer, but perhaps try adding python to your PATH if you think this message is an error."
Error in popRangeSim(world = mat, popSize = 100, diploid = TRUE, nGens = 50,  : 
  
Execution halted
estMod.rinvGamma.mar29: no visible global function definition for
  'rgamma'
life.expectancy.stationary: no visible global function definition for
  'head'
life.expectancy.stationary: no visible global function definition for
  'tail'
log.lhood.mar29: no visible global function definition for 'dnorm'
log.post.mar29: no visible global function definition for 'dnorm'
popRecon.sampler: no visible global function definition for 'rnorm'
popRecon.sampler: no visible global function definition for 'runif'
Undefined global functions or variables:
  dnorm head rgamma rnorm runif tail
Consider adding
  importFrom("stats", "dnorm", "rgamma", "rnorm", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Missing or unexported object: 'forecast::simulate.Arima'
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/PortfolioAnalytics.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
'library' or 'require' call to 'methods' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'lattice' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File 'portfolioSim/R/AllClasses.R':
  .onLoad calls:
    require(methods)

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

contributionSummaryDf,simResult : <anonymous>: no visible global
  function definition for 'aggregate'
getSimTrades,stiFromSignal-orderable-portfolio-simData-logical: no
  visible binding for global variable 'shares'
loadIn,simResult-character-missing: no visible binding for global
  variable 'master.freq'
loadIn,simResult-character-missing: no visible binding for global
  variable 'master.errors'
loadIn,simResult-character-missing: no visible binding for global
  variable 'master.type'
loadIn,simResult-character-missing: no visible binding for global
  variable 'master.summary.interface'
loadIn,simResultSinglePeriod-character-missing: no visible binding for
  global variable 'x'
plot,simResult-missing: no visible global function definition for
  'xyplot'
runSim,portfolioSim-logical: no visible binding for global variable
  'id'
runSim,portfolioSim-logical: no visible global function definition for
  'updateSummary'
securityPerfSummaryDf,simResult: no visible global function definition
  for 'aggregate'
summary,simResult: no visible global function definition for 'sd'
summary,simResult: no visible global function definition for 'head'
summary,simResult: no visible global function definition for 'tail'
Undefined global functions or variables:
  aggregate head id master.errors master.freq master.summary.interface
  master.type sd shares tail updateSummary x xyplot
Consider adding
  importFrom("stats", "aggregate", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

powell: no visible global function definition for 'Quote'
Undefined global functions or variables:
  Quote
Consider adding
  importFrom("methods", "Quote")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File 'powell/libs/i386/powell.dll':
  Found 'printf', possibly from 'printf' (C)
    Object: 'powell.o'
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
    Object: 'powell.o'
File 'powell/libs/x64/powell.dll':
  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 use Fortran I/O
nor system RNGs.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/powerCompRisk.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
fnfam: no visible global function definition for 'qnorm'
fx: no visible global function definition for 'qnorm'
normplot : <local> : replot: no visible global function definition for
  'qnorm'
normplot : <local> : replot: no visible global function definition for
  'pnorm'
normplot : <local> : replot: no visible global function definition for
  'plot'
normplot : <local> : replot: no visible global function definition for
  'dnorm'
normplot : <local> : replot: no visible global function definition for
  'points'
normplot : <local> : replot: no visible global function definition for
  'lines'
normplot : <local> : regen: no visible global function definition for
  'rnorm'
normplot : <local> : regen: no visible global function definition for
  'rexp'
nsibs: no visible global function definition for 'qnorm'
ntdt: no visible global function definition for 'uniroot'
plotDom: no visible global function definition for 'plot'
plotNsibs: no visible global function definition for 'plot'
plotNtdt: no visible global function definition for 'plot'
plotNtdt: no visible global function definition for 'lines'
plotNtdt: no visible global function definition for 'legend'
ptdt: no visible global function definition for 'optimize'
ptdt: no visible global function definition for 'uniroot'
ptdt: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dnorm legend lines optimize plot pnorm points qnorm rexp rnorm
  uniroot
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("stats", "dnorm", "optimize", "pnorm", "qnorm", "rexp",
             "rnorm", "uniroot")
to your NAMESPACE file.
Packages which this enhances but not available for checking:
  'org.EcSakai.eg.db' 'org.Pf.plasmo.db'
Found the following significant warnings:
  Note: possible error in 'geneSim(as.character(Sims[[1]][i]), ': unused arguments (ont = "BP", organism = wh_organism) 
  Note: possible error in 'geneSim(as.character(Sims[[1]][i]), ': unused arguments (ont = "MF", organism = wh_organism) 
  Note: possible error in 'geneSim(as.character(Sims[[1]][i]), ': unused arguments (ont = "CC", organism = wh_organism) 
See 'd:/Rcompile/CRANpkg/local/3.5/ppiPre.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
graphic.ppls.splines: no visible global function definition for 'par'
graphic.ppls.splines: no visible global function definition for 'plot'
graphic.ppls.splines: no visible global function definition for 'lines'
jack.ppls: no visible global function definition for 'cov'
penalized.pls: no visible binding for global variable 'var'
penalized.pls.default: no visible global function definition for 'var'
penalized.pls.kernel: no visible global function definition for 'var'
penalized.pls.select: no visible global function definition for 'var'
sim.data.ppls: no visible global function definition for 'runif'
sim.data.ppls: no visible global function definition for 'var'
sim.data.ppls: no visible global function definition for 'rnorm'
ttest.ppls: no visible global function definition for 'coef'
ttest.ppls: no visible global function definition for 'vcov'
ttest.ppls: no visible global function definition for 'pt'
Undefined global functions or variables:
  coef cov lines par plot pt rnorm runif var vcov
Consider adding
  importFrom("graphics", "lines", "par", "plot")
  importFrom("stats", "coef", "cov", "pt", "rnorm", "runif", "var",
             "vcov")
to your NAMESPACE file.
pps1: no visible global function definition for 'runif'
ppss: no visible global function definition for 'runif'
ppswr: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
LDA.Tree : Find.proj: no visible binding for global variable 'var'
LDA.Tree : Find.proj: no visible binding for global variable 'IQR'
LDA.Tree : Find.proj: no visible binding for global variable 'median'
PDA.Tree : Find.proj: no visible binding for global variable 'var'
PDA.Tree : Find.proj: no visible binding for global variable 'median'
PDA.Tree : Find.proj: no visible binding for global variable 'IQR'
PP.Tree : Find.proj: no visible binding for global variable 'var'
PP.Tree : Find.proj: no visible binding for global variable 'median'
PP.Tree : Find.proj: no visible binding for global variable 'IQR'
PP.optimize.Huber: no visible binding for global variable 'sd'
PP.optimize.anneal: no visible binding for global variable 'sd'
PP.optimize.plot: no visible binding for global variable 'sd'
PP.optimize.plot: no visible global function definition for 'hist'
PP.optimize.plot: no visible global function definition for 'text'
PP.optimize.plot: no visible global function definition for 'par'
PP.optimize.plot: no visible global function definition for 'plot'
PP.optimize.plot: no visible global function definition for 'colors'
PP.optimize.plot: no visible global function definition for 'pairs'
PP.optimize.random: no visible binding for global variable 'sd'
Undefined global functions or variables:
  IQR colors hist median pairs par plot sd text var
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "hist", "pairs", "par", "plot", "text")
  importFrom("stats", "IQR", "median", "sd", "var")
to your NAMESPACE file.
prais.winsten: no visible global function definition for 'model.frame'
prais.winsten: no visible global function definition for 'as.formula'
prais.winsten: no visible global function definition for 'tail'
Undefined global functions or variables:
  as.formula model.frame tail
Consider adding
  importFrom("stats", "as.formula", "model.frame")
  importFrom("utils", "tail")
to your NAMESPACE file.
TT.test : <anonymous>: no visible global function definition for
  't.test'
TT.test: no visible binding for global variable 'sd'
TT.test: no visible global function definition for 'setNames'
kirjelda : combo: no visible binding for global variable 'sd'
kor.tabel: no visible binding for global variable 'cor.test'
Undefined global functions or variables:
  cor.test sd setNames t.test
Consider adding
  importFrom("stats", "cor.test", "sd", "setNames", "t.test")
to your NAMESPACE file.
gausspred: no visible global function definition for 'qt'
mvapred: no visible global function definition for 'qt'
Undefined global functions or variables:
  qt
Consider adding
  importFrom("stats", "qt")
to your NAMESPACE file.
Found the following significant warnings:
  Note: possible error in 'psf(data = dataIn1, n.ahead = nextVal)': unused argument (n.ahead = nextVal) 
See 'd:/Rcompile/CRANpkg/local/3.5/PredictTestbench.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'predmixcor/R/firstlib.r':
  .First.lib calls:
    cat("predmixcor loaded\n", "COPY RIGHT: Longhai Li\n", "http://math.usask.ca/~longhai\n",     "Type ?begin.predmixcor for help\n", sep = "")

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

Predict.mix: no visible global function definition for 'dbinom'
abs_cor: no visible global function definition for 'cor'
gen.alpha.IGamma: no visible global function definition for 'qgamma'
gendata.mix: no visible global function definition for 'runif'
gendata.mix: no visible global function definition for 'rbeta'
mh1.unif: no visible global function definition for 'runif'
train_predict_mix: no visible global function definition for 'dbinom'
training: no visible global function definition for 'runif'
training: no visible global function definition for 'dbinom'
Undefined global functions or variables:
  cor dbinom qgamma rbeta runif
Consider adding
  importFrom("stats", "cor", "dbinom", "qgamma", "rbeta", "runif")
to your NAMESPACE file.
Found the following hidden files and directories:
  data/.Rapp.history
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
'library' or 'require' call to 'deSolve' which was already attached by Depends.
  Please remove these calls from your code.
LVCompGames: no visible global function definition for 'runif'
LVCompGames: no visible global function definition for 'plot'
LVCompGames: no visible global function definition for 'axis'
LVCompGames: no visible global function definition for 'box'
LVCompGames: no visible global function definition for 'lines'
LVCompGames: no visible global function definition for 'points'
MetaSim: no visible global function definition for 'runif'
chesson: no visible global function definition for 'rbeta'
chesson: no visible global function definition for 'dbeta'
chesson : rhof: no visible global function definition for 'dbeta'
chesson: no visible global function definition for 'integrate'
pimmlawton: no visible global function definition for 'runif'
Undefined global functions or variables:
  axis box dbeta integrate lines plot points rbeta runif
Consider adding
  importFrom("graphics", "axis", "box", "lines", "plot", "points")
  importFrom("stats", "dbeta", "integrate", "rbeta", "runif")
to your NAMESPACE file.
bias.correct.curve: no visible global function definition for 'approx'
lines.principal.curve: no visible global function definition for
  'lines'
periodic.lowess: no visible global function definition for 'lowess'
periodic.lowess: no visible global function definition for 'approx'
plot.principal.curve: no visible global function definition for 'plot'
points.principal.curve: no visible global function definition for
  'points'
principal.curve : <anonymous>: no visible global function definition
  for 'lowess'
principal.curve : <anonymous>: no visible global function definition
  for 'smooth.spline'
principal.curve : <anonymous>: no visible global function definition
  for 'predict'
principal.curve: no visible global function definition for 'var'
principal.curve: no visible global function definition for 'plot'
principal.curve: no visible global function definition for 'lines'
Undefined global functions or variables:
  approx lines lowess plot points predict smooth.spline var
Consider adding
  importFrom("graphics", "lines", "plot", "points")
  importFrom("stats", "approx", "lowess", "predict", "smooth.spline",
             "var")
to your NAMESPACE file.
basisplot: no visible global function definition for 'plot'
basisplot: no visible global function definition for 'abline'
basisplot: no visible global function definition for 'text'
basisplot: no visible global function definition for 'par'
plot.prinsimp: no visible global function definition for 'screeplot'
plot.simpart: no visible global function definition for 'par'
position_text: no visible global function definition for 'par'
position_text: no visible global function definition for 'strwidth'
simpart.formula: no visible global function definition for 'terms'
simpart.formula: no visible global function definition for
  'model.matrix'
varperc: no visible global function definition for 'plot'
varperc: no visible global function definition for 'lines'
varperc: no visible global function definition for 'text'
varsimp: no visible global function definition for 'plot'
varsimp: no visible global function definition for 'points'
varsimp: no visible global function definition for 'text'
varsimp: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline lines model.matrix par plot points screeplot strwidth terms
  text
Consider adding
  importFrom("graphics", "abline", "lines", "par", "plot", "points",
             "strwidth", "text")
  importFrom("stats", "model.matrix", "screeplot", "terms")
to your NAMESPACE file.
Package suggested but not available for checking: 'gurobi'
dplr.data.frame: no visible global function definition for 'as.formula'
dplr.fit : do.output: no visible global function definition for 'optim'
dplr.fit : do.perturb: no visible global function definition for
  'optim'
dplr.formula: no visible global function definition for 'model.frame'
dplr.formula: no visible global function definition for 'model.matrix'
dplr.formula: no visible global function definition for 'terms'
dplr.formula: no visible global function definition for
  'model.response'
dplr.formula: no visible global function definition for 'formula'
dplr.formula : <anonymous>: no visible global function definition for
  'predict'
dplr.formula: no visible global function definition for 'predict'
logreg.w : do.output: no visible global function definition for 'optim'
logreg.w : do.perturb: no visible global function definition for
  'optim'
predict.dplr: no visible global function definition for
  'delete.response'
predict.dplr: no visible global function definition for 'model.matrix'
rerlang: no visible global function definition for 'rexp'
sampleR: no visible global function definition for 'rnorm'
scaled: no visible global function definition for 'model.frame'
scaled: no visible global function definition for 'model.matrix'
scaled: no visible global function definition for 'terms'
scaled: no visible global function definition for 'model.response'
Undefined global functions or variables:
  as.formula delete.response formula model.frame model.matrix
  model.response optim predict rexp rnorm terms
Consider adding
  importFrom("stats", "as.formula", "delete.response", "formula",
             "model.frame", "model.matrix", "model.response", "optim",
             "predict", "rexp", "rnorm", "terms")
to your NAMESPACE file.
pr.conditional: no visible global function definition for 'qnorm'
pr.marginal: no visible global function definition for 'qnorm'
prLogisticDelta: no visible global function definition for 'glm'
prLogisticDelta: no visible binding for global variable 'binomial'
Undefined global functions or variables:
  binomial glm qnorm
Consider adding
  importFrom("stats", "binomial", "glm", "qnorm")
to your NAMESPACE file.
.pfda.fstep: no visible global function definition for 'dist'
.pfda.main: no visible global function definition for 'plot'
.pfda.mstep: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov dist plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "cov", "dist")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/processmapR.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
process_map: no visible global function definition for
  'set_global_graph_attrs'
Undefined global functions or variables:
  set_global_graph_attrs
File 'processx/libs/i386/processx.dll':
  Found non-API call to R: 'R_new_custom_connection'
File 'processx/libs/x64/processx.dll':
  Found non-API call to R: 'R_new_custom_connection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
GPois: no visible global function definition for 'dnorm'
GPois: no visible binding for global variable 'poisson'
GPois: no visible global function definition for 'predict'
GPois: no visible global function definition for 'fitted'
GPois: no visible global function definition for 'residuals'
GPois: no visible global function definition for 'smooth.spline'
ProDenICA: no visible global function definition for 'rnorm'
d.gaussmix: no visible global function definition for 'dnorm'
djordan: no visible global function definition for 'dt'
djordan: no visible global function definition for 'dunif'
mixmat: no visible global function definition for 'rnorm'
mixmat: no visible global function definition for 'runif'
plot.ProDenICA: no visible global function definition for 'plot'
r.gaussmix: no visible global function definition for 'rmultinom'
r.gaussmix: no visible global function definition for 'rnorm'
rjordan: no visible global function definition for 'rt'
rjordan: no visible global function definition for 'runif'
rmix.dexp: no visible global function definition for 'runif'
Undefined global functions or variables:
  dnorm dt dunif fitted plot poisson predict residuals rmultinom rnorm
  rt runif smooth.spline
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dnorm", "dt", "dunif", "fitted", "poisson",
             "predict", "residuals", "rmultinom", "rnorm", "rt", "runif",
             "smooth.spline")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/PROFANCY.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
getCandidates: no visible binding for global variable 'envData'
getGraph: no visible binding for global variable 'envData'
getProvidedDiseaseName: no visible binding for global variable
  'envData'
getSeed: no visible binding for global variable 'envData'
getTopDiseaseMetabolites: no visible binding for global variable
  'envData'
Undefined global functions or variables:
  envData
profBinary: no visible global function definition for 'model.frame'
profBinary: no visible global function definition for 'model.matrix'
profLinear: no visible global function definition for 'model.frame'
profLinear: no visible global function definition for 'model.matrix'
profLinear: no visible global function definition for 'model.response'
profLinear: no visible global function definition for 'model.extract'
summary.profBinary: no visible global function definition for 'terms'
summary.profBinary: no visible global function definition for 'qbeta'
summary.profLinear: no visible global function definition for 'terms'
Undefined global functions or variables:
  model.extract model.frame model.matrix model.response qbeta terms
Consider adding
  importFrom("stats", "model.extract", "model.frame", "model.matrix",
             "model.response", "qbeta", "terms")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/profileR.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   6.4Mb
    libs      1.7Mb
.simplify : <anonymous>: no visible binding for global variable 'hist'
.simplify : <anonymous>: no visible binding for global variable 'start'
.simplify: no visible binding for global variable 'start'
.simplify: no visible binding for global variable 'end'
ggplot.profr: no visible global function definition for 'ggplot'
ggplot.profr: no visible global function definition for 'geom_rect'
ggplot.profr: no visible global function definition for 'aes'
ggplot.profr: no visible binding for global variable 'start'
ggplot.profr: no visible binding for global variable 'end'
ggplot.profr: no visible global function definition for 'geom_text'
ggplot.profr: no visible binding for global variable 'time'
ggplot.profr: no visible global function definition for
  'scale_y_continuous'
ggplot.profr: no visible global function definition for
  'scale_x_continuous'
plot.profr: no visible global function definition for 'plot'
plot.profr: no visible global function definition for 'rect'
plot.profr: no visible binding for global variable 'time'
plot.profr: no visible global function definition for 'text'
profr: no visible global function definition for 'Rprof'
Undefined global functions or variables:
  Rprof aes end geom_rect geom_text ggplot hist plot rect
  scale_x_continuous scale_y_continuous start text time
Consider adding
  importFrom("graphics", "hist", "plot", "rect", "text")
  importFrom("stats", "end", "start", "time")
  importFrom("utils", "Rprof")
to your NAMESPACE file.
Package suggested but not available for checking: 'qtbase'
Packages in Depends field not imported from:
  'splines' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
IndividualPROC: no visible global function definition for 'survfit'
IndividualPROC: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile survfit
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
addpi: no visible global function definition for 'lines'
genPerms: no visible global function definition for 'combn'
getVar: no visible global function definition for 'glm'
getVar: no visible global function definition for 'binomial'
getVar: no visible global function definition for 'var'
pba: no visible global function definition for 'glm'
pba: no visible global function definition for 'binomial'
pba: no visible global function definition for 'predict'
pba: no visible global function definition for 'rbinom'
pcr: no visible global function definition for 'quantile'
plotpi: no visible global function definition for 'plot'
plotpi: no visible global function definition for 'axis'
plotpi: no visible global function definition for 'abline'
plotpi: no visible global function definition for 'lines'
Undefined global functions or variables:
  abline axis binomial combn glm lines plot predict quantile rbinom var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "plot")
  importFrom("stats", "binomial", "glm", "predict", "quantile", "rbinom",
             "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
Cul: no visible global function definition for 'qf'
blockScale: no visible binding for global variable 'sd'
cochranTest: no visible global function definition for 'prcomp'
cochranTest: no visible binding for global variable 'var'
cochranTest: no visible global function definition for 'matplot'
cochranTest: no visible global function definition for 'legend'
continuumRemoval : crfun: no visible global function definition for
  'chull'
continuumRemoval : crfun: no visible global function definition for
  'approx'
continuumRemoval : crfun: no visible global function definition for
  'splinefun'
detrend: no visible binding for global variable 'sd'
duplex: no visible global function definition for 'prcomp'
e2m: no visible global function definition for 'cov'
kenStone: no visible global function definition for 'prcomp'
naes: no visible global function definition for 'prcomp'
naes: no visible global function definition for 'kmeans'
puchwein: no visible global function definition for 'prcomp'
readASD: no visible global function definition for 'read.table'
resample : resfun: no visible global function definition for 'approx'
resample : resfun: no visible global function definition for
  'splinefun'
shenkWest: no visible global function definition for 'prcomp'
spliceCorrection : extrapfun: no visible global function definition for
  'lm'
standardNormalVariate: no visible binding for global variable 'sd'
Undefined global functions or variables:
  approx chull cov kmeans legend lm matplot prcomp qf read.table sd
  splinefun var
Consider adding
  importFrom("grDevices", "chull")
  importFrom("graphics", "legend", "matplot")
  importFrom("stats", "approx", "cov", "kmeans", "lm", "prcomp", "qf",
             "sd", "splinefun", "var")
  importFrom("utils", "read.table")
to your NAMESPACE file.
addIonSatistics: no visible binding for global variable 'median'
adjustOne: no visible binding for global variable 'median'
attachModifications: no visible global function definition for
  'na.omit'
avrgLoadingCalculation: no visible binding for global variable 'median'
channelResponses : estimate: no visible binding for global variable
  'var'
responseStatisics : func: no visible global function definition for
  'aggregate'
testing: no visible global function definition for 'aov'
testingOneshot: no visible global function definition for 'anova'
testingTukey: no visible global function definition for 'TukeyHSD'
Undefined global functions or variables:
  TukeyHSD aggregate anova aov median na.omit var
Consider adding
  importFrom("stats", "TukeyHSD", "aggregate", "anova", "aov", "median",
             "na.omit", "var")
to your NAMESPACE file.
estimateLSEparam: no visible global function definition for 'lm'
estimateMLEparam: no visible global function definition for 'optim'
getCCnlL: no visible global function definition for 'dnorm'
iterateScampi: no visible global function definition for 'quantile'
plot.scampi: no visible global function definition for 'hist'
plot.scampiVal: no visible global function definition for 'par'
plot.scampiVal: no visible global function definition for 'hist'
plot.scampiVal: no visible global function definition for 'abline'
plot.scampiVal: no visible global function definition for 'qqnorm'
plot.scampiVal: no visible global function definition for 'qqline'
sampleInitialVector: no visible global function definition for 'runif'
Undefined global functions or variables:
  abline dnorm hist lm optim par qqline qqnorm quantile runif
Consider adding
  importFrom("graphics", "abline", "hist", "par")
  importFrom("stats", "dnorm", "lm", "optim", "qqline", "qqnorm",
             "quantile", "runif")
to your NAMESPACE file.
'library' or 'require' call to 'class' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'class'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
addcircle: no visible global function definition for 'lines'
addclassifierboundary: no visible global function definition for 'par'
addclassifierboundary: no visible global function definition for
  'contour'
plot.protoclass: no visible global function definition for 'plot'
plot.protoclass: no visible global function definition for 'box'
plot.protoclass: no visible global function definition for 'rgb2hsv'
plot.protoclass: no visible global function definition for 'col2rgb'
plot.protoclass: no visible global function definition for 'points'
plot.protoclass: no visible global function definition for 'hsv'
predict.protoclass: no visible global function definition for 'knn1'
Undefined global functions or variables:
  box col2rgb contour hsv knn1 lines par plot points rgb2hsv
Consider adding
  importFrom("grDevices", "col2rgb", "hsv", "rgb2hsv")
  importFrom("graphics", "box", "contour", "lines", "par", "plot",
             "points")
to your NAMESPACE file.
plotwithprototypes: no visible global function definition for 'plot'
plotwithprototypes: no visible global function definition for
  'strwidth'
plotwithprototypes: no visible global function definition for
  'strheight'
plotwithprototypes: no visible global function definition for 'rect'
plotwithprototypes: no visible global function definition for 'text'
protoclust: no visible global function definition for 'as.dist'
protocut: no visible global function definition for 'cutree'
Undefined global functions or variables:
  as.dist cutree plot rect strheight strwidth text
Consider adding
  importFrom("graphics", "plot", "rect", "strheight", "strwidth", "text")
  importFrom("stats", "as.dist", "cutree")
to your NAMESPACE file.
Extract_plant_grapevine_function: no visible global function definition
  for 'na.omit'
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Package in Depends field not imported from: 'rpart'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
mahalanobisComposite: no visible global function definition for
  'princomp'
prepareComposite: no visible global function definition for 'cov'
winsorizor : f: no visible global function definition for 'quantile'
Undefined global functions or variables:
  cov princomp quantile
Consider adding
  importFrom("stats", "cov", "princomp", "quantile")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/psidR.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/PsiHat.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
candidate.overlap: no visible global function definition for
  'write.table'
fisher: no visible global function definition for 'fisher.test'
fisher.iteration: no visible global function definition for
  'download.file'
fisher.iteration: no visible global function definition for
  'read.table'
pSI.list: no visible global function definition for 'write.table'
specificity.index: no visible global function definition for 'png'
specificity.index: no visible global function definition for 'par'
specificity.index: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.off download.file fisher.test par png read.table write.table
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "par")
  importFrom("stats", "fisher.test")
  importFrom("utils", "download.file", "read.table", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/PSM.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
'library' or 'require' call to 'numDeriv' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
test.problem : g: no visible global function definition for 'grad'
test.problem: no visible global function definition for 'new'
psoptim,test.problem-missing-missing-missing-missing: no visible global
  function definition for 'new'
show,test.result: no visible global function definition for 'show'
show,test.result: no visible global function definition for 'sd'
Undefined global functions or variables:
  grad new sd show
Consider adding
  importFrom("methods", "new", "show")
  importFrom("stats", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
pspearman: no visible global function definition for 'pt'
spearman.test: no visible global function definition for
  'complete.cases'
spearman.test: no visible global function definition for 'cor'
Undefined global functions or variables:
  complete.cases cor pt
Consider adding
  importFrom("stats", "complete.cases", "cor", "pt")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'EffectsRelBaseline' 'boot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
catEffectBootAdaptor: no visible binding for global variable 'sumSqCat'
compExclusionFraction: no visible global function definition for
  'rpois'
compExclusionFraction: no visible global function definition for
  't.test'
compExclusionFraction: no visible global function definition for 'glm'
compExclusionFraction: no visible global function definition for
  'anova'
compPowerCatSelectivity: no visible binding for global variable
  'fRatioStat'
compPowerGeneralRespDetection: no visible binding for global variable
  'sumSqCat'
compPowerRespDetection: no visible binding for global variable
  'sumSqCat'
compRejectionFraction: no visible global function definition for
  'rpois'
compRejectionFraction: no visible global function definition for
  't.test'
compRejectionFraction: no visible global function definition for 'glm'
compRejectionFraction: no visible global function definition for
  'anova'
simCatResp: no visible global function definition for 'rpois'
simNormCatResp: no visible global function definition for 'rnorm'
testCatEffectBoot: no visible global function definition for 'boot'
Undefined global functions or variables:
  anova boot fRatioStat glm rnorm rpois sumSqCat t.test
Consider adding
  importFrom("stats", "anova", "glm", "rnorm", "rpois", "t.test")
to your NAMESPACE file.
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'multilevel' 'nlme'
A package should be listed in only one of these fields.
'library' or 'require' calls to packages already attached by Depends:
  'multilevel' 'nlme'
  Please remove these calls from your code.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     1.6Mb
    doc   2.3Mb
Packages in Depends field not imported from:
  'R.utils' 'rmeta'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ChisqTest_expect: no visible global function definition for 'pchisq'
plot_chase_observed_expected: no visible global function definition for
  'meta.MH'
plot_chase_observed_expected: no visible global function definition for
  'txtProgressBar'
plot_chase_observed_expected: no visible global function definition for
  'setTxtProgressBar'
test.one.treated: no visible global function definition for
  'fisher.test'
test_one: no visible global function definition for 'rbinom'
test_one: no visible global function definition for 'fisher.test'
Undefined global functions or variables:
  fisher.test meta.MH pchisq rbinom setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "fisher.test", "pchisq", "rbinom")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
PurBayes: no visible global function definition for 'update'
PurBayes: no visible global function definition for 'sd'
plot.PurBayes: no visible global function definition for 'plot'
plot.PurBayes: no visible global function definition for 'quantile'
plot.PurBayes: no visible global function definition for 'lines'
summary.PurBayes : <anonymous>: no visible global function definition
  for 'quantile'
Undefined global functions or variables:
  lines plot quantile sd update
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "quantile", "sd", "update")
to your NAMESPACE file.
CandidateBio.getBio : <anonymous>: no visible global function
  definition for 'na.omit'
Committee.getCommittee : <anonymous>: no visible global function
  definition for 'na.omit'
getAllBios: no visible global function definition for 'txtProgressBar'
getAllBios: no visible global function definition for
  'setTxtProgressBar'
getAllLocalOfficials: no visible global function definition for
  'txtProgressBar'
getAllLocalOfficials: no visible global function definition for
  'setTxtProgressBar'
getAllVotes: no visible global function definition for 'txtProgressBar'
getAllVotes: no visible global function definition for
  'setTxtProgressBar'
Undefined global functions or variables:
  na.omit setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
trying URL 'http://github.com/dobriban/pweight/raw/master/vignettes/iGWAS.cad.example.RData'
Quitting from lines 34-38 (iGWAS-DataExample.Rmd) 
Error: processing vignette 'iGWAS-DataExample.Rmd' failed with diagnostics:
cannot open URL 'http://github.com/dobriban/pweight/raw/master/vignettes/iGWAS.cad.example.RData'
Execution halted
.grid.matrix: no visible global function definition for 'slot'
.matrix2grid: no visible global function definition for 'as'
.poly2grid: no visible global function definition for 'is'
.poly2grid: no visible global function definition for 'slot'
.poly2grid: no visible global function definition for 'as'
.pycno.core : smooth2D : s1d: no visible global function definition for
  'filter'
.pycno.core: no visible global function definition for 'flush.console'
.pycno2matrix: no visible global function definition for 'slot'
Undefined global functions or variables:
  as filter flush.console is slot
Consider adding
  importFrom("methods", "as", "is", "slot")
  importFrom("stats", "filter")
  importFrom("utils", "flush.console")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
pyramid: no visible global function definition for 'plot'
pyramid: no visible global function definition for 'segments'
pyramid: no visible global function definition for 'lines'
pyramid: no visible global function definition for 'text'
pyramid: no visible global function definition for 'rect'
pyramidf: no visible global function definition for 'segments'
pyramidf: no visible global function definition for 'lines'
pyramidf: no visible global function definition for 'text'
pyramidf: no visible global function definition for 'rect'
Undefined global functions or variables:
  lines plot rect segments text
Consider adding
  importFrom("graphics", "lines", "plot", "rect", "segments", "text")
to your NAMESPACE file.
csQCAbinTest: no visible global function definition for 'p.adjust'
fsQCApermTest: no visible global function definition for 'p.adjust'
mvQCAbinTest: no visible global function definition for 'p.adjust'
p.threshold.adjust: no visible global function definition for
  'p.adjust'
plot.fsQCApt: no visible global function definition for 'dev.cur'
plot.fsQCApt: no visible global function definition for 'dev.new'
plot.fsQCApt: no visible global function definition for 'par'
plot.fsQCApt: no visible global function definition for 'plot'
plot.fsQCApt: no visible global function definition for 'density'
plot.fsQCApt: no visible global function definition for 'axis'
plot.fsQCApt: no visible global function definition for 'polygon'
plot.fsQCApt: no visible global function definition for 'points'
plot.fsQCApt: no visible global function definition for 'hist'
summary.csQCAbt: no visible global function definition for
  'printCoefmat'
summary.fsQCApt: no visible global function definition for
  'printCoefmat'
summary.mvQCAbt: no visible global function definition for
  'printCoefmat'
Undefined global functions or variables:
  axis density dev.cur dev.new hist p.adjust par plot points polygon
  printCoefmat
Consider adding
  importFrom("grDevices", "dev.cur", "dev.new")
  importFrom("graphics", "axis", "hist", "par", "plot", "points",
             "polygon")
  importFrom("stats", "density", "p.adjust", "printCoefmat")
to your NAMESPACE file.
dmm_fn: no visible global function definition for 'dnorm'
dmm_noweights_fn: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
Package suggested but not available for checking: 'biom'
chooseMDoubleBootstrap: no visible global function definition for
  'model.matrix'
chooseMDoubleBootstrap: no visible global function definition for
  'as.formula'
chooseMDoubleBootstrap: no visible global function definition for
  'model.frame'
chooseMDoubleBootstrap: no visible global function definition for 'lm'
chooseMDoubleBootstrap: no visible global function definition for
  'coef'
chooseMDoubleBootstrap: no visible global function definition for
  'quantile'
chooseMDoubleBootstrap: no visible global function definition for
  'qnorm'
getModel: no visible global function definition for 'lm'
getModel: no visible global function definition for 'model.matrix'
getModel: no visible global function definition for 'as.formula'
getModel: no visible global function definition for 'model.frame'
getModel: no visible global function definition for 'model.response'
getModel: no visible global function definition for 'coef'
getModel: no visible global function definition for 'qnorm'
qLearn: no visible global function definition for 'model.matrix'
qLearn: no visible global function definition for 'as.formula'
qLearn: no visible global function definition for 'model.frame'
qLearn: no visible global function definition for 'coef'
qLearn: no visible global function definition for 'lm'
qLearn: no visible global function definition for 'quantile'
Undefined global functions or variables:
  as.formula coef lm model.frame model.matrix model.response qnorm
  quantile
Consider adding
  importFrom("stats", "as.formula", "coef", "lm", "model.frame",
             "model.matrix", "model.response", "qnorm", "quantile")
to your NAMESPACE file.
pcAxisCubeMake: no visible global function definition for 'aggregate'
pcAxisCubeToCSV: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  aggregate write.csv
Consider adding
  importFrom("stats", "aggregate")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/QoLR.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

Calc.Expr: no visible global function definition for 'read.csv'
Calc.Expr: no visible binding for global variable 'Type'
Calc.Expr: no visible binding for global variable 'Identifier'
Calc.Expr: no visible binding for global variable 'Fluor'
GroupPlot: no visible global function definition for 'read.csv'
GroupPlot: no visible binding for global variable 'Type'
GroupPlot: no visible global function definition for
  'aggregate.data.frame'
plot.CT: no visible global function definition for 'sd'
plot.CT: no visible global function definition for 'barplot'
plot.CT: no visible binding for global variable 'tr_gene_name'
plot.CT : errorbars: no visible global function definition for 'arrows'
plot.CT: no visible global function definition for 'box'
Undefined global functions or variables:
  Fluor Identifier Type aggregate.data.frame arrows barplot box
  read.csv sd tr_gene_name
Consider adding
  importFrom("graphics", "arrows", "barplot", "box")
  importFrom("stats", "aggregate.data.frame", "sd")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    data  11.8Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
ci.length: no visible global function definition for 'qexp'
detectable.bc: no visible global function definition for 'uniroot'
detectable.f2: no visible global function definition for 'uniroot'
detectable.ri: no visible global function definition for 'uniroot'
nu: no visible global function definition for 'pnorm'
nullinfo: no visible global function definition for 'qnorm'
nullinfo: no visible global function definition for 'dnorm'
optselection.bc: no visible global function definition for 'optimize'
optselection.f2: no visible global function definition for 'optimize'
optspacing.bc: no visible global function definition for 'optim'
optspacing.bc: no visible global function definition for 'optimize'
optspacing.f2: no visible global function definition for 'optim'
optspacing.f2: no visible global function definition for 'optimize'
powercalc.bc: no visible global function definition for 'pchisq'
powercalc.f2: no visible global function definition for 'pchisq'
samplesize.bc: no visible global function definition for 'uniroot'
samplesize.f2: no visible global function definition for 'uniroot'
samplesize.ri: no visible global function definition for 'uniroot'
tailprob: no visible global function definition for 'pchisq'
thresh: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  dnorm optim optimize pchisq pnorm qexp qnorm uniroot
Consider adding
  importFrom("stats", "dnorm", "optim", "optimize", "pchisq", "pnorm",
             "qexp", "qnorm", "uniroot")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'graph' 'igraph' 'pcalg' 'qtl' 'sem'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.6Mb
    doc       2.9Mb
Package required but not available: 'qtbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
'library' or 'require' call to 'Rmpfr' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
adjacencyMatrix: no visible global function definition for 'as'
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
quadp: no visible global function definition for 'var'
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
alphaf: no visible global function definition for 'pchisq'
alphaf: no visible global function definition for 'dbinom'
conout: no visible global function definition for 'sd'
ibgaout: no visible global function definition for 'qnorm'
ibgaout: no visible global function definition for 'pnorm'
plot.qualint: no visible global function definition for 'qnorm'
powerval: no visible global function definition for 'rnorm'
powerval: no visible global function definition for 'qnorm'
powerval: no visible global function definition for 'pnorm'
print.expplot: no visible global function definition for 'gray'
print.expplot: no visible binding for global variable 'coef'
print.outplot: no visible global function definition for 'gray'
print.outplot: no visible binding for global variable 'coef'
qualint: no visible global function definition for 'qnorm'
qualint: no visible global function definition for 'plot'
qualval: no visible global function definition for 'qnorm'
qualval: no visible global function definition for 'plot'
surout: no visible global function definition for 'tail'
surout: no visible global function definition for 'coef'
Undefined global functions or variables:
  coef dbinom gray pchisq plot pnorm qnorm rnorm sd tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "dbinom", "pchisq", "pnorm", "qnorm",
             "rnorm", "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   3.0Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   2.1Mb
File 'QUIC/libs/i386/QUIC.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'QUIC.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'QUIC.o'
File 'QUIC/libs/x64/QUIC.dll':
  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 use Fortran I/O
nor system RNGs.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
draw_legend: no visible global function definition for 'legend'
draw_legend: no visible global function definition for 'par'
draw_nodes: no visible global function definition for 'lines'
draw_nodes: no visible global function definition for 'points'
draw_nodes: no visible global function definition for 'text'
draw_vertical_lines: no visible global function definition for 'lines'
draw_vertical_lines: no visible global function definition for 'abline'
layout_large_plot: no visible global function definition for 'par'
layout_large_plot: no visible global function definition for 'mtext'
layout_large_plot: no visible global function definition for 'axis'
layout_large_plot: no visible global function definition for 'lines'
layout_small_plot: no visible global function definition for 'par'
rquipu: no visible global function definition for 'colors'
rquipu: no visible global function definition for 'jpeg'
rquipu: no visible global function definition for 'png'
rquipu: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  abline axis colors dev.off jpeg legend lines mtext par png points
  text
Consider adding
  importFrom("grDevices", "colors", "dev.off", "jpeg", "png")
  importFrom("graphics", "abline", "axis", "legend", "lines", "mtext",
             "par", "points", "text")
to your NAMESPACE file.
File 'qVarSel/libs/i386/qVarSel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'qVarSelH.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'qVarSelH.o'
File 'qVarSel/libs/x64/qVarSel.dll':
  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 use Fortran I/O
nor system RNGs.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
S3 methods shown with full name in documentation object 'summary_table':
  'cbind.qwraps2_summary_table'

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.
mutualCoherence : .setOneMutualP: no visible global function definition
  for 'combn'
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
conf2d.default: no visible global function definition for 'polygon'
conf2d_int: no visible global function definition for 'contourLines'
Undefined global functions or variables:
  contourLines polygon
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "polygon")
to your NAMESPACE file.
'library' or 'require' call to 'rgdal' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'matrixStats' 'rgdal' 'sp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
FancyPies: no visible global function definition for 'rainbow'
FancyPies: no visible global function definition for 'plot'
FancyPies: no visible global function definition for 'polygon'
Hist2GE: no visible global function definition for 'dist'
Pies2GE: no visible global function definition for 'rainbow'
Plots2GE: no visible global function definition for 'aggregate'
Plots2GE: no visible global function definition for 'x11'
Plots2GE: no visible global function definition for 'title'
Plots2GE: no visible global function definition for 'png'
Plots2GE: no visible global function definition for 'dev.off'
PolyLines2GE: no visible global function definition for 'rainbow'
Shapes2GE: no visible global function definition for 'rainbow'
Undefined global functions or variables:
  aggregate dev.off dist plot png polygon rainbow title x11
Consider adding
  importFrom("grDevices", "dev.off", "png", "rainbow", "x11")
  importFrom("graphics", "plot", "polygon", "title")
  importFrom("stats", "aggregate", "dist")
to your NAMESPACE file.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    Output   2.2Mb
    bin      9.3Mb
Packages suggested but not available for checking: 'rcom' 'RDCOMClient'
'library' or 'require' calls in package code:
  'RDCOMClient' 'rcom'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
PPT.AddBlankSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'write.table'
PPT.AddDataFrame: no visible global function definition for 'write.csv'
PPT.AddGraphicstoSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddGraphicstoSlide: no visible global function definition for
  'dev.cur'
PPT.AddGraphicstoSlide: no visible global function definition for
  'dev.list'
PPT.AddGraphicstoSlide: no visible global function definition for
  'savePlot'
PPT.AddTextSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleOnlySlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleSlide: no visible global function definition for
  'comIsValidHandle'
PPT.ApplyTemplate: no visible global function definition for
  'comIsValidHandle'
PPT.Close: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'comCreateObject'
PPT.Init: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'COMCreate'
PPT.Present: no visible global function definition for
  'comIsValidHandle'
PPT.SaveAs: no visible global function definition for
  'comIsValidHandle'
PPT.getAbsolutePath : PPT.filePath: no visible global function
  definition for 'readWindowsShortcut'
Undefined global functions or variables:
  COMCreate comCreateObject comIsValidHandle dev.cur dev.list
  readWindowsShortcut savePlot write.csv write.table
Consider adding
  importFrom("grDevices", "dev.cur", "dev.list", "savePlot")
  importFrom("utils", "write.csv", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  Note: possible error in 'unlist(strsplit(.$removeSpaces(.$ivField)), ': unused argument (fixed = TRUE) 
See 'd:/Rcompile/CRANpkg/local/3.5/R2STATS.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
r2stl: no visible global function definition for 'persp'
Undefined global functions or variables:
  persp
Consider adding
  importFrom("graphics", "persp")
to your NAMESPACE file.
'library' or 'require' call to 'rgl' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'lattice' 'leaps' 'rgl' 's20x'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: 'rpvm'
'library' or 'require' call to 'rpvm' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
race : killSlaves.exit: no visible global function definition for
  '.PVM.initsend'
race : killSlaves.exit: no visible global function definition for
  '.PVM.send'
race : killSlaves.exit: no visible global function definition for
  '.PVM.exit'
race: no visible global function definition for '.PVM.mytid'
race: no visible global function definition for '.PVM.spawn'
race: no visible global function definition for '.PVM.initsend'
race: no visible global function definition for '.PVM.pkstrvec'
race: no visible global function definition for '.PVM.send'
race: no visible global function definition for '.PVM.recv'
race: no visible global function definition for '.PVM.bufinfo'
race: no visible global function definition for '.PVM.upkstrvec'
race : job.start: no visible global function definition for
  '.PVM.initsend'
race : job.start: no visible global function definition for
  '.PVM.pkint'
race : job.start: no visible global function definition for '.PVM.send'
race : job.wait: no visible global function definition for '.PVM.recv'
race : job.wait: no visible global function definition for
  '.PVM.bufinfo'
race : job.wait: no visible global function definition for
  '.PVM.upkint'
race : job.wait: no visible global function definition for
  '.PVM.upkdblvec'
race : aux2.friedman: no visible global function definition for
  'pchisq'
race : aux2.friedman: no visible global function definition for 'qt'
race : aux.friedman: no visible global function definition for
  'wilcox.test'
race : aux.ttest: no visible global function definition for 't.test'
race : aux.ttest: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  .PVM.bufinfo .PVM.exit .PVM.initsend .PVM.mytid .PVM.pkint
  .PVM.pkstrvec .PVM.recv .PVM.send .PVM.spawn .PVM.upkdblvec
  .PVM.upkint .PVM.upkstrvec p.adjust pchisq qt t.test wilcox.test
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "qt", "t.test",
             "wilcox.test")
to your NAMESPACE file.
getsonde: no visible global function definition for 'read.table'
plotsonde: no visible global function definition for 'par'
plotwind: no visible global function definition for 'plot'
plotwind: no visible global function definition for 'mtext'
plotwind: no visible global function definition for 'abline'
skewt.axis: no visible global function definition for 'par'
skewt.axis: no visible global function definition for 'plot'
skewt.axis: no visible global function definition for 'axis'
skewt.axis: no visible global function definition for 'mtext'
skewt.axis: no visible global function definition for 'segments'
skewt.axis: no visible global function definition for 'text'
skewt.axis: no visible global function definition for 'lines'
skewt.lines: no visible global function definition for 'lines'
skewt.points: no visible global function definition for 'points'
station.symbol: no visible global function definition for 'sd'
station.symbol: no visible global function definition for 'par'
station.symbol: no visible global function definition for 'lines'
station.symbol: no visible global function definition for 'polygon'
station.symbol: no visible global function definition for 'text'
station.symbol: no visible global function definition for 'segments'
Undefined global functions or variables:
  abline axis lines mtext par plot points polygon read.table sd
  segments text
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "mtext", "par",
             "plot", "points", "polygon", "segments", "text")
  importFrom("stats", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
RnDif.het: no visible global function definition for 'runif'
RnDif.hom: no visible global function definition for 'runif'
RnDifAdv.hom: no visible global function definition for 'runif'
SoilAdv.hom: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
cpc_get_rawdata: no visible global function definition for
  'download.file'
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
plot.rsm: no visible global function definition for 'par'
plot.rsm: no visible global function definition for 'abline'
plot.rsm: no visible global function definition for 'barplot'
Undefined global functions or variables:
  abline barplot par
Consider adding
  importFrom("graphics", "abline", "barplot", "par")
to your NAMESPACE file.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    htmlwidgets   6.0Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/ramidst.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs   2.8Mb
.disableThreads: no visible global function definition for
  'stopCluster'
.enableThreads: no visible global function definition for 'detectCores'
.enableThreads: no visible global function definition for
  'makePSOCKcluster'
.enableThreads: no visible global function definition for
  'clusterExport'
.enableThreads: no visible global function definition for 'clusterCall'
.forwardSelection: no visible binding for global variable 'var'
.forwardSelection: no visible global function definition for 'glm'
.forwardSelection: no visible global function definition for 'formula'
.forwardSelection: no visible global function definition for 'binomial'
.forwardSelection: no visible global function definition for 'lm'
.forwardSelection: no visible global function definition for 'predict'
.predict.internal: no visible global function definition for 'predict'
randomGLM: no visible binding for global variable 'cor'
randomGLM: no visible binding for global variable 'sd'
randomGLM: no visible global function definition for 'var'
thinRandomGLM: no visible global function definition for 'glm'
thinRandomGLM: no visible global function definition for 'binomial'
thinRandomGLM: no visible global function definition for 'lm'
Undefined global functions or variables:
  binomial clusterCall clusterExport cor detectCores formula glm lm
  makePSOCKcluster predict sd stopCluster var
Consider adding
  importFrom("stats", "binomial", "cor", "formula", "glm", "lm",
             "predict", "sd", "var")
to your NAMESPACE file.
anovaF: no visible global function definition for 'anova'
anovaF: no visible global function definition for 'lm'
randInterval: no visible global function definition for 'quantile'
randInterval : <anonymous>: no visible global function definition for
  'quantile'
randPlot: no visible global function definition for 'par'
randPlot: no visible global function definition for 'hist'
randPlot: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline anova hist lm par quantile
Consider adding
  importFrom("graphics", "abline", "hist", "par")
  importFrom("stats", "anova", "lm", "quantile")
to your NAMESPACE file.
bartels.rank.test: no visible global function definition for 'na.omit'
bartels.rank.test: no visible global function definition for 'pbeta'
bartels.rank.test: no visible global function definition for 'pnorm'
cox.stuart.test: no visible global function definition for 'pbinom'
difference.sign.test: no visible global function definition for
  'na.omit'
difference.sign.test: no visible global function definition for 'pnorm'
rank.test: no visible global function definition for 'na.omit'
rank.test: no visible global function definition for 'pnorm'
rruns: no visible global function definition for 'runif'
runs.test: no visible global function definition for 'median'
runs.test: no visible global function definition for 'na.omit'
runs.test: no visible global function definition for 'points'
runs.test: no visible global function definition for 'abline'
runs.test: no visible global function definition for 'gray'
runs.test: no visible global function definition for 'pnorm'
turning.point.test: no visible global function definition for 'embed'
turning.point.test: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline embed gray median na.omit pbeta pbinom pnorm points runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "points")
  importFrom("stats", "embed", "median", "na.omit", "pbeta", "pbinom",
             "pnorm", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  congruRand.c:180:3: warning: ISO C does not support the 'I64' ms_scanf length modifier [-Wformat=]
  congruRand.c:187:2: warning: ISO C does not support the 'I64' ms_scanf length modifier [-Wformat=]
  congruRand.c:188:2: warning: ISO C does not support the 'I64' ms_scanf length modifier [-Wformat=]
  congruRand.c:189:2: warning: ISO C does not support the 'I64' ms_scanf length modifier [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/3.5/randtoolbox.Rcheck/00install.out' for details.
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.
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.
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'
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs   2.3Mb
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.
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.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   1.8Mb
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.
Running examples in 'RAtmosphere-Ex.R' failed
The error most likely occurred in:

> ### Encoding: UTF-8
> 
> ### Name: suncalc
> ### Title: Sunrise and Sunset calculations
> ### Aliases: suncalc
> ### Keywords: sun sunset sunrise
> 
> ### ** Examples
> 
> t<-Sys.time()+seq(-3600*12,3600*12,,by=600)
> t0=as.POSIXlt(Sys.time(),tz='UTC')
> plot(t,90-SZA(t,Lat=0,Lon=0),main='SZA',xlab='Time',ylab='El [Â°deg]')
> sun=suncalc(t0[['yday']],UTC=TRUE)
Error in FUN(X[[i]], ...) : subscript out of bounds
Calls: suncalc -> [[ -> [[.POSIXlt -> .POSIXlt -> lapply
Execution halted
.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.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
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.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
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.
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.
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.
'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.
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    cont  23.3Mb
.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.
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.
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.
'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.
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.
'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.
Package suggested but not available for checking: 'ROpenOffice'
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   2.7Mb
    po    2.1Mb
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.
Running 'testthat.R' [157s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(testthat)
  > library(rcongresso)
  > 
  > test_check("rcongresso")
  -- 1. Failure: Dimensoes do dataframe (@test_votacoes.R#54)  -------------------
  dim(votos_pec241) not equal to c(478, 10).
  1/2 mismatches
  [1] 500 - 478 == 22
  
  == testthat results  ===========================================================
  OK: 66 SKIPPED: 0 FAILED: 1
  1. Failure: Dimensoes do dataframe (@test_votacoes.R#54) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/Rcplex.Rcheck/00install.out' for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    include   5.5Mb
    libs      1.6Mb
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    include  25.3Mb
    libs      1.8Mb
File which contains pragma(s) suppressing diagnostics:
  'inst/include/RcppBlazeConfig.h'
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    include   7.8Mb
    libs      1.8Mb
Gauss: no visible global function definition for 'dnorm'
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
This is BibTeX, Version 0.99d (MiKTeX 2.9)
The top-level auxiliary file: RcppGSL-intro.aux
I couldn't open database file Rcpp.bib
---line 151 of file RcppGSL-intro.aux
 : \bibdata{Rcpp
 :              }
I'm skipping whatever remains of this command
The style file: jss.bst
I found no database files---while reading file RcppGSL-intro.aux
Warning--I didn't find a database entry for "GSL"
Warning--I didn't find a database entry for "JSS:Rcpp"
Warning--I didn't find a database entry for "Eddelbuettel:2013:Rcpp"
Warning--I didn't find a database entry for "CRAN:Rcpp"
Warning--I didn't find a database entry for "R:Main"
Warning--I didn't find a database entry for "CRAN:RcppArmadillo"
Warning--I didn't find a database entry for "Eddelbuettel+Sanderson:2013:RcppArmadillo"
Warning--I didn't find a database entry for "Sanderson:2010:Armadillo"
Warning--I didn't find a database entry for "CRAN:RcppEigen"
Warning--I didn't find a database entry for "JSS:RcppEigen"
Warning--I didn't find a database entry for "CRAN:inline"
Warning--I didn't find a database entry for "CRAN:Rcpp:Attributes"
(There were 2 error messages)
Error: processing vignette 'RcppGSL-intro.Rmd' failed with diagnostics:
Failed to build the bibliography via bibtex
Execution halted
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib       3.9Mb
    libs      2.9Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    include   6.4Mb
    libs      1.7Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib       8.9Mb
    libs      1.0Mb
installed size is 35.0Mb
  sub-directories of 1Mb or more:
    include   8.8Mb
    libs     26.1Mb
Files which contain pragma(s) suppressing diagnostics:
  'inst/include/ql/math/distributions/normaldistribution.hpp'
  'inst/include/ql/math/matrix.hpp'
  'inst/include/ql/math/optimization/levenbergmarquardt.hpp'
  'inst/include/ql/math/statistics/incrementalstatistics.hpp'
  'inst/include/ql/time/date.hpp' 'inst/include/ql/time/imm.hpp'
  'inst/include/ql/utilities/dataparsers.hpp'
  'inst/include/ql/utilities/null.hpp'
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    include   6.3Mb
    libs      2.0Mb
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.
installed size is 30.7Mb
  sub-directories of 1Mb or more:
    include   4.5Mb
    lib      22.1Mb
    libs      3.9Mb
Package suggested but not available for checking: 'Rcompression'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
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').
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.
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/RDieHarder.Rcheck/00install.out' for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
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.
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.
Error in re-building vignettes:
  ...
Quitting from lines 112-121 (rdwd.Rmd) 
Error: processing vignette 'rdwd.Rmd' failed with diagnostics:
invalid 'description' argument
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   2.6Mb
Files which contain pragma(s) suppressing diagnostics:
  'inst/include/re2/prog.h' 'inst/include/re2/re2.h'
  'inst/include/re2/regexp.h' 'src/dfa.cc' 'src/onepass.cc'
File 'readr/libs/i386/readr.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_WriteConnection'
File 'readr/libs/x64/readr.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_WriteConnection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  `encoding(rt, verbose = TRUE)` produced unexpected messages.
  Expected match: Probable encoding: UTF-8
  Actual values:
  * Probable encoding: ISO-8859-2
  * 
  
  
  == testthat results  ===========================================================
  OK: 127 SKIPPED: 11 FAILED: 3
  1. Failure: test encoding function on simple text files (@test-encoding.R#7) 
  2. Failure: test encoding function on simple text files (@test-encoding.R#12) 
  3. Failure: test encoding function on simple text files (@test-encoding.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
'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.
Package required but not available: 'Rmosek'

See section 'The DESCRIPTION file' 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.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
mergeNamespace_roclet: no visible global function definition for
  'new_roclet'
Undefined global functions or variables:
  new_roclet
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.
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.
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 significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/refund.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
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.
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.
Package which this enhances but not available for checking: 'Rcplex'
.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
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/relax.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
'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.
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.
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.
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.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    java   5.8Mb
CA: no visible global function definition for 'readClipboard'
LL: no visible global function definition for 'readClipboard'
US: no visible global function definition for 'readClipboard'
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'
latexlist: no visible global function definition for 'readClipboard'
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'
strWrap: no visible global function definition for 'readClipboard'
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 readClipboard tail unzip
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "download.file", "head", "menu", "readClipboard",
             "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.
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.
.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').
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<-
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.
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').
'library' or 'require' call to 'pso' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested 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.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
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.
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.
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
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.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
.testLTS: no visible binding for global variable 'stackloss'
Undefined global functions or variables:
  stackloss
Consider adding
  importFrom("datasets", "stackloss")
to your NAMESPACE file.
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.
installed size is 80.2Mb
  sub-directories of 1Mb or more:
    gdal       3.9Mb
    libs      68.7Mb
    pictures   1.3Mb
    proj       5.0Mb
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
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.7Mb
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.
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(testthat)
  > test_check("rglobi")
  Loading required package: rglobi
  -- 1. Failure: interactions subsetted by adding additional information all inter
  dim(unique(rbind(rattusaves, rattus))) not equal to dim(unique(rattus)).
  1/2 mismatches
  [1] 632 - 628 == 4
  
  == testthat results  ===========================================================
  OK: 32 SKIPPED: 2 FAILED: 1
  1. Failure: interactions subsetted by adding additional information all interaction types include observations (@test-globi.R#70) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    fonts   1.5Mb
    libs    2.0Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/RGoogleAnalytics.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
Packages suggested but not available for checking: 'pmg' 'SVGAnnotation'
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extra   9.3Mb
'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.
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    R      3.6Mb
    help  10.6Mb
    libs   5.1Mb
File 'RGtk2/libs/i386/RGtk2.dll':
  Found non-API calls to R: 'R_new_custom_connection',
    'Rf_EncodeInteger', 'Rf_EncodeLogical', 'Rf_EncodeReal',
    'Rf_formatInteger', 'Rf_formatLogical', 'Rf_formatReal'
File 'RGtk2/libs/x64/RGtk2.dll':
  Found non-API calls to R: 'R_new_custom_connection',
    '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.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc   9.8Mb
.quick_fetch: no visible global function definition for 'POST'
.quick_fetch: no visible global function definition for 'add_headers'
.quick_fetch: no visible global function definition for
  'stop_for_status'
.quick_fetch: no visible global function definition for 'content'
fetch_healthdata: no visible binding for global variable 'resources'
fetch_healthdata : <anonymous>: no visible binding for global variable
  'filters'
Undefined global functions or variables:
  POST add_headers content filters resources stop_for_status
Packages in Depends field not imported from:
  'RCurl' 'XML' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ECL: no visible global function definition for 'new'
ECLDataset: no visible global function definition for 'new'
ECLDedUp: no visible global function definition for 'new'
ECLDistribute: no visible global function definition for 'new'
ECLIterate: no visible global function definition for 'new'
ECLJoin: no visible global function definition for 'new'
ECLOutput: no visible global function definition for 'new'
ECLProject: no visible global function definition for 'new'
ECLRecord: no visible global function definition for 'new'
ECLRollUp: no visible global function definition for 'new'
ECLSort: no visible global function definition for 'new'
ECLTOPN: no visible global function definition for 'new'
ECLTable: no visible global function definition for 'new'
ECLTransform: no visible global function definition for 'new'
eclDirectCall: no visible global function definition for 'postForm'
parseResults: no visible global function definition for 'xmlRoot'
parseResults: no visible global function definition for 'xmlTreeParse'
parseResults: no visible global function definition for 'getNodeSet'
parseResults: no visible global function definition for 'xmlGetAttr'
parseResults: no visible global function definition for 'xmlValue'
parseResults: no visible global function definition for 'write.table'
Undefined global functions or variables:
  getNodeSet new postForm write.table xmlGetAttr xmlRoot xmlTreeParse
  xmlValue
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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.
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.
Error in re-building vignettes:
  ...
Quitting from lines 100-102 (rinatVignette.Rmd) 
Error: processing vignette 'rinatVignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
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.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    lib    3.5Mb
    libs   4.8Mb
File 'RInside/libs/i386/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/i386/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/i386/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/i386/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Running 'test-all.R' [17s]
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  -- 1. Error: Import Remote GitHub File (@test_remote.R#19)  --------------------
  No yaml delimiters found
  1: expect_true(inherits(import(lfile), "data.frame"), label = "Import local copy successfully") at testthat/test_remote.R:19
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: inherits(import(lfile), "data.frame")
  5: import(lfile)
  6: .import(file = file, ...)
  7: .import.rio_csvy(file = file, ...)
  8: csvy::read_csvy(file = file, ...)
  9: stop("No yaml delimiters found")
  
  == DONE ========================================================================
  Error: Test failures
  Execution halted
'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.
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.
Running 'test-BinomialRegression.R' [0s]
  Running 'test-BrierScore.R' [10s]
  Running 'test-CauseSpecificCoxRegression.R' [5s]
  Running 'test-FineGrayRegression.R' [5s]
  Running 'test-ate.R' [30s]
  Running 'test-boxplotScore.R' [3s]
  Running 'test-confidenceBand_vs_timereg.R' [8s]
  Running 'test-iidCox.R' [4s]
  Running 'test-phreg.R' [0s]
  Running 'test-predictCSC_vs_mstate.R' [7s]
  Running 'test-predictCox-CSC-Risk_internal.R' [8s]
  Running 'test-predictCox_vs_timereg.R' [6s]
  Running 'test-score.R' [12s]
Running the tests in 'tests/test-predictCSC_vs_mstate.R' failed.
Last 13 lines of output:
  [14] NaN - 0.0350 == NaN
  [15] NaN - 0.0367 == NaN
  [16] NaN - 0.0383 == NaN
  [17] NaN - 0.0399 == NaN
  ...
  * as.double(pred.RR1d$absRisk.se) not equal to pred.probtrans[, "se3"].
  72/80 mismatches (average diff: Inf)
  [9]  Inf - 0.0156 == Inf
  [10] Inf - 0.0156 == Inf
  [11] Inf - 0.0156 == Inf
  [12] Inf - 0.0156 == Inf
  [13] Inf - 0.0156 == Inf
  [14] Inf - 0.0156 == Inf
  [15] I
  Execution halted
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 : exitWiz: no visible global function definition for 'bringToTop'
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 bringToTop browseURL capture.output help help.search
  loadhistory na.omit packageDescription savehistory update.packages
Consider adding
  importFrom("grDevices", "bringToTop")
  importFrom("stats", "na.omit")
  importFrom("utils", "Sweave", "apropos", "browseURL", "capture.output",
             "help", "help.search", "loadhistory", "packageDescription",
             "savehistory", "update.packages")
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.
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.
Found the following significant warnings:
  jri.h:21:20: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri.c:308:27: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri_glue.c:24:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.5/rJava.Rcheck/00install.out' for details.
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 for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.5/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.5/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'rJava/libs/i386/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'
File 'rJava/libs/x64/rJava.dll':
  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 use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Undocumented S4 methods:
  generic 'dbExistsTable' and siglist 'JDBCConnection,ANY'
  generic 'dbListFields' and siglist 'JDBCConnection,ANY'
  generic 'dbRemoveTable' and siglist 'JDBCConnection,ANY'
  generic 'dbWriteTable' and siglist 'JDBCConnection,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
cubeHelix : <anonymous>: no visible global function definition for
  'rgb'
rdirichlet: no visible global function definition for 'rgamma'
Undefined global functions or variables:
  rgamma rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "rgamma")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/rJPSGCS.Rcheck/00install.out' for details.
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: invoking macro json_global_decl argument 3: empty macro arguments are undefined in ISO C90 and ISO C++98
  libjson/Source/JSONGlobals.h:44:49: warning: invoking macro json_global_decl argument 3: empty macro arguments are undefined in ISO C90 and ISO C++98
  libjson/Source/JSONSharedString.h:297:17: warning: 'json_shared_string::len' will be initialized after [-Wreorder]
  libjson/Source/JSONSharedString.h:295:40: warning:   'json_shared_string::json_shared_string_internal* json_shared_string::_str' [-Wreorder]
  libjson/Source/JSONSharedString.h:180:9: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONSharedString.h:182:9: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONStream.h:79:7: warning: 'JSONStream::state' will be initialized after [-Wreorder]
  libjson/Source/JSONStream.h:76:28: warning:   'void (* JSONStream::call)(void*, void*)' [-Wreorder]
  JSONStream.cpp:8:1: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONStream.h:77:27: warning: 'JSONStream::err_call' will be initialized after [-Wreorder]
  libjson/Source/JSONStream.h:75:17: warning:   'json_string JSONStream::buffer' [-Wreorder]
  JSONStream.cpp:12:1: warning:   when initialized here [-Wreorder]
  JSONValidator.cpp:394:105: warning: invoking macro JSON_ASSERT_SAFE argument 3: empty macro arguments are undefined in ISO C90 and ISO C++98
  JSONValidator.cpp:397:104: warning: invoking macro JSON_ASSERT_SAFE argument 3: empty macro arguments are undefined in ISO C90 and ISO C++98
  libjson/Source/internalJSONNode.h:257:18: warning: 'internalJSONNode::_name_encoded' will be initialized after [-Wreorder]
  libjson/Source/internalJSONNode.h:256:17: warning:   'json_string internalJSONNode::_name' [-Wreorder]
  internalJSONNode.cpp:78:1: warning:   when initialized here [-Wreorder]
See 'd:/Rcompile/CRANpkg/local/3.5/RJSONIO.Rcheck/00install.out' for details.
'library' or 'require' call to 'rJava' which was already attached by Depends.
  Please remove these calls from your code.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    datasets   8.6Mb
installed size is 45.1Mb
  sub-directories of 1Mb or more:
    exe  45.1Mb
Found the following significant warnings:
  Note: possible error in 'write(self$rules, file = paste0(fileName, ': unused argument (col.names = NA) 
See 'd:/Rcompile/CRANpkg/local/3.5/RKEEL.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
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.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
':::' 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.
Found the following Makefile(s) without a final LF:
  src/Makevars.in
Some 'make' programs ignore lines not ending in LF.
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.
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.
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.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    rmd   5.9Mb
.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/i386/RMC.dll':
  Found '_ZSt4cout', possibly from 'std::cout' (C++)
    Objects: 'RMC.o', 'predict.o'
  Found 'rand', possibly from 'rand' (C)
    Object: 'ap.o'
File 'RMC/libs/x64/RMC.dll':
  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 use Fortran I/O
nor system RNGs.

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.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   2.1Mb
CI: no visible global function definition for 'sd'
CI: no visible global function definition for 'qt'
L: no visible global function definition for 'sd'
L: no visible global function definition for 'residuals'
Qa: no visible global function definition for 'logLik'
Qb: no visible global function definition for 'residuals'
Qc: no visible global function definition for 'residuals'
Qc: no visible global function definition for 'logLik'
STDERR: no visible global function definition for 'sd'
group.UCL: no visible global function definition for 'aggregate'
lr.glover: no visible binding for global variable 'logLik'
lr.glover: no visible binding for global variable 'update'
lr.glover : nobs0: no visible binding for global variable 'nobs'
lr.glover : nobs0 : nobs2: no visible global function definition for
  'residuals'
lr.glover : tlab: no visible global function definition for 'terms'
lr.glover : name: no visible global function definition for 'formula'
lr.glover : modelUpdate: no visible global function definition for
  'as.formula'
lr.glover: no visible global function definition for 'model.frame'
lr.glover: no visible binding for global variable 'AIC'
lr.glover: no visible binding for global variable 'BIC'
summarySE : <anonymous>: no visible global function definition for 'sd'
summarySE: no visible global function definition for 'qt'
Undefined global functions or variables:
  AIC BIC aggregate as.formula formula logLik model.frame nobs qt
  residuals sd terms update
Consider adding
  importFrom("stats", "AIC", "BIC", "aggregate", "as.formula", "formula",
             "logLik", "model.frame", "nobs", "qt", "residuals", "sd",
             "terms", "update")
to your NAMESPACE file.
Combi: no visible global function definition for 'new'
barplotMixCluster: no visible global function definition for 'is'
barplotMixCluster: no visible global function definition for 'par'
barplotMixCluster: no visible global function definition for 'lines'
barplotMixCluster: no visible global function definition for 'text'
barplotMixCluster: no visible global function definition for 'title'
barplotMixCluster: no visible global function definition for 'mtext'
histMixCluster: no visible global function definition for 'is'
histMixCluster: no visible global function definition for 'par'
histMixCluster: no visible global function definition for 'dnorm'
histMixCluster: no visible global function definition for 'lines'
mixmodEntPlot: no visible global function definition for 'par'
mixmodEntPlot: no visible global function definition for 'lines'
mixmodEntPlot: no visible global function definition for 'axis'
mixmodEntPlot: no visible global function definition for 'title'
mixmodEntPlot: no visible binding for global variable 'par'
plot,MixmodCombi: no visible global function definition for 'par'
plot,MixmodCombi: no visible global function definition for 'plot.new'
plot,MixmodCombi: no visible global function definition for 'title'
Undefined global functions or variables:
  axis dnorm is lines mtext new par plot.new text title
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "par", "plot.new",
             "text", "title")
  importFrom("methods", "is", "new")
  importFrom("stats", "dnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.pLGP_qvec: no visible global function definition for 'ppois'
.qLGP_pvec: no visible global function definition for 'qpois'
.rLGP.failsafe: no visible global function definition for 'runif'
.subdmg: no visible global function definition for 'dbinom'
dnegbin: no visible global function definition for 'dnbinom'
pLGP: no visible global function definition for 'ppois'
qLGP: no visible global function definition for 'qpois'
rLGP: no visible global function definition for 'rpois'
rLGP: no visible global function definition for 'rnorm'
rLGP: no visible global function definition for 'runif'
rbinegbin: no visible global function definition for 'rnbinom'
rmanaclash: no visible global function definition for 'rbinom'
rmanaclash: no visible global function definition for 'runif'
Undefined global functions or variables:
  dbinom dnbinom ppois qpois rbinom rnbinom rnorm rpois runif
Consider adding
  importFrom("stats", "dbinom", "dnbinom", "ppois", "qpois", "rbinom",
             "rnbinom", "rnorm", "rpois", "runif")
to your NAMESPACE file.
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/Rmosek.Rcheck/00install.out' for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/Rmpi.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
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.
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.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/RM.weights.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
'library' or 'require' calls in package code:
  'DESeq' 'seqinr' 'topGO'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: 'rnaturalearthhires'
.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.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.5/progress/include/RProgress.h:172:27: warning: ISO C++ forbids variable length array 'bar' [-Wvla]
  d:/RCompile/CRANpkg/lib/3.5/progress/include/RProgress.h:220:26: warning: ISO C++ forbids variable length array 'spaces' [-Wvla]
See 'd:/Rcompile/CRANpkg/local/3.5/rncl.Rcheck/00install.out' for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Packages suggested but not available for checking: 'rrdf' 'Sxslt'
Running 'test-all.R' [81s]
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  8: xml2::read_xml(repeat_until_it_works(errors_to_catch, "esearch", query = list(db = "taxonomy", 
         term = term, api_key = key), ...))
  9: read_xml.character(repeat_until_it_works(errors_to_catch, "esearch", query = list(db = "taxonomy", 
         term = term, api_key = key), ...))
  10: path_to_connection(x)
  11: check_path(path)
  12: stop("'", path, "' does not exist", if (!is_absolute_path(path)) paste0(" in current working directory ('", 
         getwd(), "')"), ".", call. = FALSE)
  
  == testthat results  ===========================================================
  OK: 164 SKIPPED: 3 FAILED: 1
  1. Error: (unknown) (@test_taxonomy.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: ape
No ENTREZ API key provided
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Struthioniformes'

Quitting from lines 85-86 (metadata.Rmd) 
Error: processing vignette 'metadata.Rmd' failed with diagnostics:
'{"error":"API key invalid","api-key":"","type":"invalid","status":"unknown"}' does not exist in current working directory ('d:/RCompile/CRANpkg/local/3.5/RNeXML.Rcheck/vign_test/RNeXML/vignettes').
Execution halted
.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.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      5.5Mb
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.
'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.
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.
Package suggested but not available for checking: 'SSOAP'
'LinkingTo' for
  'mgcv' 'robustbase'
are unused as they have no 'include' directory
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.
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.
Packages in Depends field not imported from:
  'penalized' 'splines' 'survival' 'survivalROC'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
boot.ROC: no visible global function definition for 'qnorm'
boot.ROC: no visible global function definition for 'penalized'
boot.ROC: no visible global function definition for 'coefficients'
boot.ROC: no visible global function definition for 'sd'
boot.ROC: no visible global function definition for 'optL1'
boot.ROCt: no visible global function definition for 'qnorm'
boot.ROCt: no visible global function definition for 'penalized'
boot.ROCt: no visible global function definition for 'Surv'
boot.ROCt: no visible global function definition for 'coefficients'
boot.ROCt: no visible global function definition for 'sd'
boot.ROCt: no visible global function definition for 'survivalROC'
boot.ROCt: no visible global function definition for 'optL1'
Undefined global functions or variables:
  Surv coefficients optL1 penalized qnorm sd survivalROC
Consider adding
  importFrom("stats", "coefficients", "qnorm", "sd")
to your NAMESPACE file.
'library' or 'require' call to 'ROCR' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'ROCR'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
o.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of 'level' to 'levels'
p.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of 'level' to 'levels'
o.rocc: no visible global function definition for 'prediction'
o.rocc: no visible global function definition for 'performance'
o.rocc: no visible global function definition for 'binom.test'
tr.rocc: no visible global function definition for 'prediction'
tr.rocc: no visible global function definition for 'performance'
Undefined global functions or variables:
  binom.test performance prediction
Consider adding
  importFrom("stats", "binom.test")
to your NAMESPACE file.
NPROCwoGS: no visible global function definition for 'quantile'
NPROCwoGS : rdirichlet: no visible global function definition for
  'rgamma'
NPROCwoGS: no visible global function definition for 'rbinom'
NPROCwoGS: no visible global function definition for 'rbeta'
NPROCwoGS: no visible binding for global variable 'quantile'
Undefined global functions or variables:
  quantile rbeta rbinom rgamma
Consider adding
  importFrom("stats", "quantile", "rbeta", "rbinom", "rgamma")
to your NAMESPACE file.
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.
Package required but not available: 'Rcplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package which this enhances but not available for checking: 'ROI.plugin.cplex'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/ROracle.Rcheck/00install.out' for details.
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.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.3Mb
    libs   2.2Mb
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.
S3 methods shown with full name in documentation object 'cbind.fill':
  'cbind.fill'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
royston.test: no visible global function definition for 'shapiro.test'
royston.test: no visible global function definition for 'cor'
royston.test: no visible global function definition for 'qnorm'
royston.test: no visible global function definition for 'pnorm'
royston.test: no visible global function definition for 'cov'
royston.test: no visible global function definition for 'mahalanobis'
royston.test: no visible global function definition for 'qqplot'
royston.test: no visible global function definition for 'qchisq'
royston.test: no visible global function definition for 'ppoints'
royston.test: no visible global function definition for 'abline'
royston.test: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  abline cor cov mahalanobis pchisq pnorm ppoints qchisq qnorm qqplot
  shapiro.test
Consider adding
  importFrom("graphics", "abline")
  importFrom("stats", "cor", "cov", "mahalanobis", "pchisq", "pnorm",
             "ppoints", "qchisq", "qnorm", "qqplot", "shapiro.test")
to your NAMESPACE file.
'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.
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
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      2.8Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    extdata  12.5Mb
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.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.4Mb
rpygeo.geoprocessor: warning in system(py.call, invisible = TRUE,
  minimize = TRUE, wait = wait): partial argument match of 'minimize'
  to 'minimized'
Package which this enhances but not available for checking: 'rjpod'
rrBlupM6: no visible global function definition for 'optimize'
Undefined global functions or variables:
  optimize
Consider adding
  importFrom("stats", "optimize")
to your NAMESPACE file.
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.
'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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/RSAP.Rcheck/00install.out' for details.
Files named as vignettes but with no recognized vignette engine:
   'vignettes/Untitled.Rnw'
(Is a VignetteBuilder field missing?)
stripslash: no visible global function definition for 'tail'
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
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.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/RSEIS.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
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.
Found the following significant warnings:
   #warning Please include winsock2.h before windows.h
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.5/Rserve.Rcheck/00install.out' for details.
Rserve: no visible global function definition for 'shortPathName'
Undefined global functions or variables:
  shortPathName
Consider adding
  importFrom("utils", "shortPathName")
to your NAMESPACE file.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.5/Rserve/libs/i386/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'd:/Rcompile/CRANpkg/lib/3.5/Rserve/libs/x64/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/i386/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

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.
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.
Running examples in 'RSMET-Ex.R' failed
The error most likely occurred in:

> ### Name: meteofrance
> ### Title: Snow Weather Data in France
> ### Aliases: meteofrance
> 
> ### ** Examples
> 
>  
> 
> library(ggmap)
Loading required package: ggplot2
> data(meteofrance)
> 
> dates <- as.Date(meteofrance$timestamp)
> 
> data=meteofrance[dates==dates[1],]
> 
> 
> 
> map <- get_map(location ="France", zoom = 6)
Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=France&zoom=6&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=France&sensor=false
Warning: geocode failed with status OVER_QUERY_LIMIT, location = "France"
Error in data.frame(ll.lat = ll[1], ll.lon = ll[2], ur.lat = ur[1], ur.lon = ur[2]) : 
  arguments imply differing number of rows: 0, 1
Calls: get_map -> get_googlemap -> data.frame
Execution halted
negbin.pow : negbin.disp: no visible global function definition for
  'rpois'
negbin.pow : negbin.disp: no visible global function definition for
  'rnbinom'
negbin.pow : inner.fcn: no visible global function definition for
  'na.omit'
negbin.pow : inner.fcn: no visible global function definition for
  'quantile'
negbin.pow: no visible global function definition for 'txtProgressBar'
negbin.pow: no visible global function definition for
  'setTxtProgressBar'
poiss.pow : inner.fcn: no visible global function definition for
  'rpois'
poiss.pow : inner.fcn: no visible global function definition for
  'quantile'
poiss.pow: no visible global function definition for 'txtProgressBar'
poiss.pow: no visible global function definition for
  'setTxtProgressBar'
Undefined global functions or variables:
  na.omit quantile rnbinom rpois setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit", "quantile", "rnbinom", "rpois")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Undocumented S4 methods:
  generic 'dbExistsTable' and siglist 'SQLServerConnection,ANY'
  generic 'dbRemoveTable' and siglist 'SQLServerConnection,ANY'
  generic 'dbWriteTable' and siglist 'SQLServerConnection,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    2.4Mb
    libs  17.3Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
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.
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.
RStorm: no visible global function definition for 'alply'
Undefined global functions or variables:
  alply
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/rsunlight.Rcheck/00install.out' for details.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/RSurvey.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
Running examples in 'RSVGTipsDevice-Ex.R' failed
The error most likely occurred in:

> ### Name: RSVGTipsDevice
> ### Title: A SVG Graphics Driver with dynamic tips
> ### Aliases: RSVGTipsDevice
> ### Keywords: device package
> 
> ### ** Examples
> 
> library("RSVGTipsDevice")
> sessionInfo()
R Under development (unstable) (2017-12-30 r73992)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2008 x64 (build 6002) Service Pack 2

Matrix products: default

locale:
[1] LC_COLLATE=C                 LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=C                LC_NUMERIC=C                
[5] LC_TIME=C                   

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RSVGTipsDevice_1.0-7

loaded via a namespace (and not attached):
[1] compiler_3.5.0
> devSVGTips("svgplot1.svg", toolTipMode=1,
+     title="SVG example plot 1: Shapes and Points, Tooltips are Title + 1 Line")
> plot(c(0,10),c(0,10), type="n", xlab="x", ylab="y",
+     main="Example SVG plot with title + 1 line tips (mode=1)")
> setSVGShapeToolTip(title="A rectangle", desc="that is yellow")
> rect(1,1,4,6, col='yellow')
> setSVGShapeToolTip(title="1st circle with title only")
> points(5.5,7.5,cex=20,pch=19,col='red')
> setSVGShapeToolTip(title="A triangle", desc="big and green")
> polygon(c(3,6,8), c(3,6,3), col='green')
> # no tooltips on these points
> points(2:8, 8:2, cex=3, pch=19, col='black')
> # tooltips on each these points
> invisible(sapply(1:7, function(x)
+ {setSVGShapeToolTip(title=paste("point", x))
+  points(x+1, 8-x, cex=3, pch=1, col='black')}))
> setSVGShapeToolTip(title="Text", desc="can have a tool tip too!")
> text(x=4, y=9, lab="Poke me!", col="blue")
> dev.off()
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    Lib  11.5Mb
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
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.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
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.
.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.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs       1.7Mb
    projects   2.5Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   2.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
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.
Package suggested but not available for checking: 'gpuR'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    include   5.2Mb
S3 methods shown with full name in documentation object 'cbind.rv':
  'cbind.rv' 'rbind.rv'

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.
lc_TDT: no visible global function definition for 'pchisq'
rvTDT: no visible global function definition for 'dbeta'
Undefined global functions or variables:
  dbeta pchisq
Consider adding
  importFrom("stats", "dbeta", "pchisq")
to your NAMESPACE file.
LASSO: no visible global function definition for 'lm'
LASSO: no visible global function definition for 'anova'
LASSO: no visible global function definition for 'glm'
LASSO: no visible global function definition for 'pchisq'
LASSO : <anonymous>: no visible global function definition for
  'extractAIC'
PCR : <anonymous>: no visible global function definition for 'cor'
PLS : <anonymous>: no visible global function definition for 'cor'
RR : RRscore: no visible binding for global variable 'sd'
SPLS: no visible global function definition for 'lm'
SPLS: no visible global function definition for 'anova'
SPLS : <anonymous>: no visible global function definition for
  'extractAIC'
VTWOD : getScores: no visible global function definition for 'sd'
VTWOD : getScores: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  anova cor extractAIC glm lm pchisq pnorm sd
Consider adding
  importFrom("stats", "anova", "cor", "extractAIC", "glm", "lm",
             "pchisq", "pnorm", "sd")
to your NAMESPACE file.
check_ISO_code: no visible binding for global variable 'NoAm_country'
check_ISO_code: no visible binding for global variable 'SoAm_country'
check_ISO_code: no visible binding for global variable 'Oceana_country'
check_ISO_code: no visible binding for global variable 'Africa_country'
check_ISO_code: no visible binding for global variable 'Asia_country'
check_ISO_code: no visible binding for global variable 'Eur_country'
climate_map: no visible binding for global variable 'data'
date_correct: no visible global function definition for 'tail'
Undefined global functions or variables:
  Africa_country Asia_country Eur_country NoAm_country Oceana_country
  SoAm_country data tail
Consider adding
  importFrom("utils", "data", "tail")
to your NAMESPACE file.
RWBP.default: no visible global function definition for 'na.omit'
RWBP.default: no visible global function definition for 'kmeans'
RWBP.formula: no visible global function definition for 'model.extract'
plot.RWBP: no visible global function definition for 'plot'
predict.RWBP: no visible global function definition for 'head'
Undefined global functions or variables:
  head kmeans model.extract na.omit plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "kmeans", "model.extract", "na.omit")
  importFrom("utils", "head")
to your NAMESPACE file.
weblogo: no visible global function definition for 'browseURL'
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    java  10.6Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/RWildbook.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
File 'RWinEdt/R/zzz.R':
  .onAttach calls:
    writeLines(edtFile, con = send2RedtLoc)
    writeLines(edtFile, con = send2RedtLoc)

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
getcolors: no visible global function definition for 'rainbow'
lines.rief: no visible global function definition for 'lines.default'
lines.riif: no visible global function definition for 'lines.default'
lines.rirf: no visible global function definition for 'lines.default'
plot.ifile: no visible global function definition for 'plot'
plot.rief: no visible global function definition for 'plot.default'
plot.rief: no visible global function definition for 'lines'
plot.riif: no visible global function definition for 'plot.default'
plot.riif: no visible global function definition for 'lines'
plot.rirf: no visible global function definition for 'plot.default'
plot.rirf: no visible global function definition for 'lines'
plot.rtef: no visible global function definition for 'plot.default'
plot.rtif: no visible global function definition for 'plot.default'
plot.rtrf: no visible global function definition for 'plot.default'
read.ifile: no visible global function definition for 'read.table'
read.pfile: no visible global function definition for 'read.table'
write.wdat: no visible global function definition for 'write.table'
Undefined global functions or variables:
  lines lines.default plot plot.default rainbow read.table write.table
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "lines", "lines.default", "plot",
             "plot.default")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
.dwt: no visible global function definition for 'median'
.udwt: no visible global function definition for 'median'
plotSignalTransformation: no visible global function definition for
  'plot'
plotSignalTransformation: no visible global function definition for
  'box'
plotSignalTransformation: no visible global function definition for
  'axis'
plotSignalTransformation: no visible global function definition for
  'lines'
plotSignalTransformation: no visible global function definition for
  'legend'
Undefined global functions or variables:
  axis box legend lines median plot
Consider adding
  importFrom("graphics", "axis", "box", "legend", "lines", "plot")
  importFrom("stats", "median")
to your NAMESPACE file.
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: 'countrycode_data' is not an exported object from 'namespace:countrycode'
Execution halted
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.
Package suggested but not available for checking: 'SnakeCharmR'
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/Ryacas.Rcheck/00install.out' for details.
Found the following significant warnings:
  Note: possible error in 'saveSession(force = TRUE)': unused argument (force = TRUE) 
See 'd:/Rcompile/CRANpkg/local/3.5/Rz.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
'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.
.onAttach: no visible global function definition for 'winMenuAdd'
.onAttach: no visible global function definition for 'winMenuAddItem'
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 winMenuAdd winMenuAddItem
  write.table
Consider adding
  importFrom("grDevices", "colors", "nclass.FD", "nclass.Sturges",
             "nclass.scott", "rgb")
  importFrom("stats", "addmargins", "as.formula")
  importFrom("utils", "localeToCharset", "winMenuAdd", "winMenuAddItem",
             "write.table")
to your NAMESPACE file.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    sample_data   3.0Mb
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.
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.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/SAENET.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
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.
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.
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.
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.
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.
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.
'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.
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.
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.
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.
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.
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 which contains pragma(s) suppressing important diagnostics:
  'src/Eigen/src/Core/arch/SSE/Complex.h'
File which contains pragma(s) suppressing diagnostics:
  'src/Eigen/src/Core/util/DisableStupidWarnings.h'
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.
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.
Found the following significant warnings:
  d:/Compiler/gcc-4.9.3/local330/include/gmp-x64.h:140:23: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/Compiler/gcc-4.9.3/local330/include/gmp-x64.h:141:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.5/sbrl.Rcheck/00install.out' for details.
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.
ChooseBest: no visible global function definition for 'head'
GetScores: no visible global function definition for 'write.table'
ReportTable: no visible binding for global variable 'sd'
ReportTable: no visible global function definition for 'write.table'
Undefined global functions or variables:
  head sd write.table
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "head", "write.table")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'MASS' 'lars'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
lse: no visible global function definition for 'lm'
predict.scalreg: no visible global function definition for 'fitted'
slassoEst: no visible global function definition for 'qnorm'
slassoEst: no visible global function definition for 'lars'
slassoEst: no visible global function definition for 'predict.lars'
Undefined global functions or variables:
  fitted lars lm predict.lars qnorm
Consider adding
  importFrom("stats", "fitted", "lm", "qnorm")
to your NAMESPACE file.
plot.scair: no visible global function definition for 'par'
plot.scair: no visible global function definition for 'plot'
plot.scair: no visible global function definition for 'points'
plot.scar: no visible global function definition for 'par'
plot.scar: no visible global function definition for 'plot'
plot.scar: no visible global function definition for 'points'
predict.scair: no visible global function definition for 'approx'
predict.scar: no visible global function definition for 'approx'
scair: no visible global function definition for 'gaussian'
scair: no visible global function definition for 'runif'
scair: no visible global function definition for 'rnorm'
scar: no visible global function definition for 'gaussian'
scar: no visible global function definition for 'glm.fit'
scar: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx gaussian glm.fit par plot points rnorm runif
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "approx", "gaussian", "glm.fit", "rnorm", "runif")
to your NAMESPACE file.
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.
'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.
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
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.
'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.
Files which contain pragma(s) suppressing diagnostics:
  'src/scrm/macros.h' 'src/scrm/model.h'
lahiri.design: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   3.5Mb
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.
'library' or 'require' calls in package code:
  'raster' 'sp'
  Please use :: or requireNamespace() instead.
  See section 'Suggested 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
adx: no visible global function definition for 'abline'
adx: no visible global function definition for 'legend'
dx: no visible global function definition for 'abline'
dx: no visible global function definition for 'legend'
maxd: no visible global function definition for 'abline'
maxd: no visible global function definition for 'legend'
pc: no visible global function definition for 'rainbow'
pc: no visible global function definition for 'plot'
pc: no visible global function definition for 'abline'
pc: no visible global function definition for 'legend'
pc: no visible global function definition for 'points'
pcu: no visible global function definition for 'rainbow'
pcu: no visible global function definition for 'plot'
pcu: no visible global function definition for 'abline'
pcu: no visible global function definition for 'legend'
pcu: no visible global function definition for 'points'
rmsd: no visible global function definition for 'abline'
rmsd: no visible global function definition for 'legend'
rsd: no visible global function definition for 'abline'
rsd: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline legend plot points rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "legend", "plot", "points")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'NADA' 'lubridate' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package in Depends field not imported from: 'JM'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SEchart: no visible global function definition for 'plot'
SEchart: no visible global function definition for 'rect'
SEchart: no visible global function definition for 'par'
SEchart: no visible global function definition for 'grid'
SEchart: no visible global function definition for 'axis'
SEchart: no visible global function definition for 'text'
SEchart: no visible global function definition for 'lines'
SEchart: no visible global function definition for 'heat.colors'
SEchart: no visible global function definition for 'topo.colors'
SEchart: no visible global function definition for 'cm.colors'
SEchart: no visible global function definition for 'terrain.colors'
SEchart: no visible global function definition for 'gray.colors'
SEchart: no visible global function definition for 'rainbow'
SEchart: no visible global function definition for 'points'
SEchart: no visible global function definition for 'legend'
Undefined global functions or variables:
  axis cm.colors gray.colors grid heat.colors legend lines par plot
  points rainbow rect terrain.colors text topo.colors
Consider adding
  importFrom("grDevices", "cm.colors", "gray.colors", "heat.colors",
             "rainbow", "terrain.colors", "topo.colors")
  importFrom("graphics", "axis", "grid", "legend", "lines", "par",
             "plot", "points", "rect", "text")
to your NAMESPACE file.
fdc2s: no visible global function definition for 'lm'
fdc3s: no visible global function definition for 'lm'
fds2s: no visible global function definition for 'lm'
fds3s: no visible global function definition for 'lm'
Undefined global functions or variables:
  lm
Consider adding
  importFrom("stats", "lm")
to your NAMESPACE file.
.read.SeerStatTXT: no visible global function definition for
  'read.table'
.write.SeerStatTXT: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.5Mb
'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.
get.infectiousness: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  qchisq
Consider adding
  importFrom("stats", "qchisq")
to your NAMESPACE file.
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.
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.
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.
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' 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'
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.
.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.
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.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/sensors4plumes.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
S3 methods shown with full name in documentation object 'cbind.Simulations':
  'cbind.Simulations'

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.
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.
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.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    6.0Mb
    libs   2.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
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.
Running examples in 'SequenceAnalysis-Ex.R' failed
The error most likely occurred in:

> ### Name: SequenceAnalysis.Complement
> ### Title: SequenceAnalysis.Complement
> ### Aliases: SequenceAnalysis.Complement
> 
> ### ** Examples
> 
> SequenceAnalysis.Complement("actagtcacgatcag")
       Complement 
"TGATCAGTGCTAGTC" 
> SequenceAnalysis.Complement(UniprotKB="O15131")
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Complement 
     "N/A" 
> SequenceAnalysis.Complement(UniprotKB="O15131",CDS=TRUE)
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in Nucleotide_Sequence[[3]] : subscript out of bounds
Calls: SequenceAnalysis.Complement
Execution halted
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.
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.
'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.
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.
installed size is 87.5Mb
  sub-directories of 1Mb or more:
    doc     10.1Mb
    gdal     3.9Mb
    libs    64.6Mb
    proj     5.0Mb
    sqlite   1.5Mb
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.
.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.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   7.7Mb
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.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    www   9.4Mb
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.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    www   6.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    semantic   5.6Mb
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.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/shp2graph.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
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.
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.
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').
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.
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.
signmedian.test: no visible global function definition for 'median'
signmedian.test: no visible global function definition for 'binom.test'
signmedian.test: no visible global function definition for 'pbinom'
signmedian.test: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  binom.test median pbinom pnorm
Consider adding
  importFrom("stats", "binom.test", "median", "pbinom", "pnorm")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'gdata' 'splines'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.SII: no visible global function definition for 'plot'
plot.SII: no visible global function definition for 'lines'
plot.SII: no visible global function definition for 'abline'
plot.SII: no visible global function definition for 'legend'
sii : approx.l: no visible global function definition for 'approx'
sii.excel: no visible global function definition for 'predict'
sii.excel : approx.l: no visible global function definition for
  'approx'
Undefined global functions or variables:
  abline approx legend lines plot predict
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "plot")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
linearextrapolation: no visible global function definition for 'coef'
linearextrapolation: no visible global function definition for 'lm'
plotsimexaft: no visible global function definition for 'plot'
plotsimexaft: no visible global function definition for 'lm'
plotsimexaft: no visible global function definition for 'predict'
plotsimexaft: no visible global function definition for 'lines'
plotsimexaft: no visible global function definition for 'points'
plotsimexaft: no visible global function definition for 'legend'
print.simexaft: no visible global function definition for 'coef'
quadraticextrapolation: no visible global function definition for
  'coef'
quadraticextrapolation: no visible global function definition for 'lm'
simexaft: no visible global function definition for 'terms'
simexaft: no visible global function definition for 'rnorm'
simexaft: no visible binding for global variable 'var'
simexaft: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  coef legend lines lm plot pnorm points predict rnorm terms var
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("stats", "coef", "lm", "pnorm", "predict", "rnorm", "terms",
             "var")
to your NAMESPACE file.
getFormula: no visible global function definition for 'as.formula'
internalSimXyplot : f: no visible global function definition for
  'median'
runSimulation: no visible global function definition for 'runif'
setup: no visible global function definition for 'runif'
clusterSetup,ANY-data.frame-SampleControl: no visible binding for
  global variable 'cnam'
clusterSetup,ANY-data.frame-TwoStageControl: no visible binding for
  global variable 'cnam'
initialize,DCARContControl: no visible binding for global variable
  'rnorm'
initialize,DataControl: no visible binding for global variable 'rnorm'
Undefined global functions or variables:
  as.formula cnam median rnorm runif
Consider adding
  importFrom("stats", "as.formula", "median", "rnorm", "runif")
to your NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
cumallcausehr: no visible global function definition for 'integrate'
plotbe: no visible global function definition for 'plot'
plotbe: no visible global function definition for 'lines'
plotbe: no visible global function definition for 'legend'
plotcph: no visible global function definition for 'confint'
plotcph: no visible global function definition for 'plot'
plotcph: no visible global function definition for 'abline'
plotcph: no visible global function definition for 'axis'
plotcph: no visible global function definition for 'polygon'
plotcph: no visible global function definition for 'lines'
plotnae: no visible global function definition for 'plot'
simCR: no visible global function definition for 'rnorm'
simEBMT: no visible global function definition for 'model.matrix'
simexit: no visible global function definition for 'runif'
simexitinner: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  abline axis confint integrate legend lines model.matrix plot polygon
  rnorm runif uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "plot",
             "polygon")
  importFrom("stats", "confint", "integrate", "model.matrix", "rnorm",
             "runif", "uniroot")
to your NAMESPACE file.
'library' or 'require' call to 'boot' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'boot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
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.
simrel: no visible global function definition for 'runif'
simrel: no visible global function definition for 'rnorm'
simrelplot: no visible global function definition for 'par'
simrelplot: no visible global function definition for 'layout'
simrelplot: no visible global function definition for 'devAskNewPage'
simrelplot: no visible global function definition for 'dev.hold'
simrelplot: no visible global function definition for 'plot'
simrelplot: no visible global function definition for 'abline'
simrelplot: no visible global function definition for 'dev.flush'
simrelplot: no visible global function definition for 'points'
simrelplot: no visible global function definition for 'axis'
simrelplot: no visible global function definition for 'mtext'
simrelplot: no visible global function definition for 'box'
simrelplot: no visible global function definition for 'cov'
Undefined global functions or variables:
  abline axis box cov dev.flush dev.hold devAskNewPage layout mtext par
  plot points rnorm runif
Consider adding
  importFrom("grDevices", "dev.flush", "dev.hold", "devAskNewPage")
  importFrom("graphics", "abline", "axis", "box", "layout", "mtext",
             "par", "plot", "points")
  importFrom("stats", "cov", "rnorm", "runif")
to your NAMESPACE file.
Found the following hidden files and directories:
  vignettes/.Rhistory
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'abind' 'svUnit'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
simSummary: no visible global function definition for 'abind'
simSummary_unitTests: no visible global function definition for
  'clearLog'
simSummary_unitTests: no visible global function definition for
  'runTest'
simSummary_unitTests: no visible global function definition for
  'svSuite'
simSummary_unitTests: no visible global function definition for 'Log'
simSummary_unitTests: no visible global function definition for 'stats'
simSummary_unitTests: no visible global function definition for
  'metadata'
simSummary_unitTests: no visible global function definition for
  'errorLog'
Undefined global functions or variables:
  Log abind clearLog errorLog metadata runTest stats svSuite
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.
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.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   2.3Mb
Running examples in 'sisus-Ex.R' failed
The error most likely occurred in:

> ### Name: sisus.run
> ### Title: driver program for SISUS
> ### Aliases: sisus.run
> 
> ### ** Examples
> 
> # set working directory for many output files with setwd()
> # see http://statacumen.com/sisus for workbook
> filename = "http://statacumen.com/sw/sisus/examples/SISUS_v0_09_template.xls";
> sisus.run(filename)
trying URL 'http://statacumen.com/sw/sisus/examples/SISUS_v0_09_template.xls'
Warning in download.file(xls, tf, mode = "wb") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in download.file(xls, tf, mode = "wb") : 
  cannot open URL 'http://statacumen.com/sw/sisus/examples/SISUS_v0_09_template.xls'
Calls: sisus.run ... as.matrix -> <Anonymous> -> xls2sep -> download.file
Error in file.exists(tfn) : invalid 'file' argument
Calls: sisus.run ... get.data -> as.matrix -> <Anonymous> -> file.exists
Execution halted
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
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.
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tthread/tinythread.h:632:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tbb_stddef.h:470:37: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/atomic.h:29:30: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:42:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:43:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:75:21: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:102:10: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:80:37: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:127:30: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.5/skm.Rcheck/00install.out' for details.
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.
cvsmac: no visible global function definition for 'predict'
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
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 '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.
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.
'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.
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.
'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.
'library' or 'require' calls in package code:
  'MASS' 'survival'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
lines.SmithWilsonYieldCurve: no visible global function definition for
  'lines'
plot.SmithWilsonYieldCurve: no visible global function definition for
  'plot'
points.SmithWilsonYieldCurve: no visible global function definition for
  'points'
Undefined global functions or variables:
  lines plot points
Consider adding
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
Fourier2d: no visible global function definition for 'fft'
kernel2dsmooth: no visible global function definition for 'fft'
Undefined global functions or variables:
  fft
Consider adding
  importFrom("stats", "fft")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/sm.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
'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.
Running 'test_scripts.R' [16s]
Running the tests in 'tests/test_scripts.R' failed.
Last 13 lines of output:
  > print(gam(log(Density) ~ lo(log(mack.depth)) + lo(Temperature), 
  +     data = mackerel))
  Call:
  gam(formula = log(Density) ~ lo(log(mack.depth)) + lo(Temperature), 
      data = mackerel)
  
  Degrees of Freedom: 278 total; 270.9924 Residual
  Residual Deviance: 335.5316 
  
  > par(mfrow = c(2, 2))
  
  > plot.gam(model1, se = TRUE)
  Error in plot.gam(model1, se = TRUE) : could not find function "plot.gam"
  Calls: source -> withVisible -> eval -> eval
  Execution halted
Running 'test_scripts.R' [18s]
Running the tests in 'tests/test_scripts.R' failed.
Last 13 lines of output:
  > print(gam(log(Density) ~ lo(log(mack.depth)) + lo(Temperature), 
  +     data = mackerel))
  Call:
  gam(formula = log(Density) ~ lo(log(mack.depth)) + lo(Temperature), 
      data = mackerel)
  
  Degrees of Freedom: 278 total; 270.9924 Residual
  Residual Deviance: 335.5316 
  
  > par(mfrow = c(2, 2))
  
  > plot.gam(model1, se = TRUE)
  Error in plot.gam(model1, se = TRUE) : could not find function "plot.gam"
  Calls: source -> withVisible -> eval -> eval
  Execution halted
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.
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.
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.
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.
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.
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 significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/SocialMediaLab.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
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.
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'
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.
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.
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.
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.
'library' or 'require' calls in package code:
  'chemometrics' 'spatstat'
  Please use :: or requireNamespace() instead.
  See section 'Suggested 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.
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.
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.
'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.
Package suggested but not available for checking: 'r2cytoscape'
analyzeSP23Design: no visible global function definition for 'plot'
exploreSP23Design: no visible global function definition for
  'txtProgressBar'
exploreSP23Design: no visible global function definition for
  'setTxtProgressBar'
generateClinicalTrialData : <anonymous>: no visible global function
  definition for 'runif'
generateClinicalTrialData: no visible global function definition for
  'rbinom'
generateClinicalTrialData: no visible global function definition for
  'rexp'
mHP.b : crossingProbDiff: no visible global function definition for
  'pnorm'
mHP.b : crossingProbDiff: no visible global function definition for
  'Miwa'
mHP.b: no visible global function definition for 'qnorm'
mHP.b: no visible global function definition for 'uniroot'
mHP.c : crossingProbDiff: no visible global function definition for
  'Miwa'
mHP.c: no visible global function definition for 'uniroot'
mHP.c: no visible global function definition for 'qnorm'
performInterimLook: no visible global function definition for 'optim'
performInterimLook: no visible global function definition for
  'constrOptim'
performInterimLook: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  Miwa constrOptim optim plot pnorm qnorm rbinom rexp runif
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "constrOptim", "optim", "pnorm", "qnorm", "rbinom",
             "rexp", "runif", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
SPA: no visible global function definition for 'var'
Score.Test.Interact: no visible global function definition for 'pchisq'
Score.Test.Overall: no visible global function definition for 'var'
Score.Test.Overall: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  pchisq var
Consider adding
  importFrom("stats", "pchisq", "var")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/spaceExt.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
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.
'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.
GenPar: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
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.
Running 'test-all.R' [49s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("SpaDES.tools")
  Loading required package: SpaDES.tools
hausman: no visible global function definition for 'pchisq'
span.formula: no visible global function definition for 'model.frame'
span.formula: no visible global function definition for 'model.matrix'
span.formula: no visible global function definition for
  'model.response'
spbe: no visible global function definition for 'cor'
spbe: no visible global function definition for 'pt'
spfe: no visible global function definition for 'cor'
spfe: no visible global function definition for 'pt'
sprandom: no visible global function definition for 'cor'
sprandom: no visible global function definition for 'pt'
summary.span: no visible global function definition for 'printCoefmat'
Undefined global functions or variables:
  cor model.frame model.matrix model.response pchisq printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.frame", "model.matrix",
             "model.response", "pchisq", "printCoefmat", "pt")
to your NAMESPACE file.
plot.spa: no visible global function definition for 'plot'
plot.spa: no visible global function definition for 'lines'
plot.spa: no visible global function definition for 'points'
plot.spa: no visible global function definition for 'gray'
plot.spa: no visible global function definition for 'box'
predict.spa: no visible global function definition for 'fitted'
predict.spa: no visible global function definition for 'coef'
spa.gcv: no visible global function definition for 'density'
spa.gcv: no visible global function definition for 'quantile'
spa.sim: no visible global function definition for 'runif'
spa.sim: no visible global function definition for 'rnorm'
spa.sim: no visible global function definition for 'rbinom'
update.spa: no visible global function definition for 'quantile'
Undefined global functions or variables:
  box coef density fitted gray lines plot points quantile rbinom rnorm
  runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "box", "lines", "plot", "points")
  importFrom("stats", "coef", "density", "fitted", "quantile", "rbinom",
             "rnorm", "runif")
to your NAMESPACE file.
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.
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.
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.
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.
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.
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.
Missing link or links in documentation object 'FeatureAxis.Rd':
  'bounding.box'

Missing link or links in documentation object 'FeatureProps.Rd':
  'bounding.box'

Missing link or links in documentation object 'locperf.Rd':
  'bounding.box'

See section 'Cross-references' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tthread/tinythread.h:632:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tbb_stddef.h:470:37: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/atomic.h:29:30: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:42:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:43:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:75:21: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:102:10: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:80:37: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tbb/tick_count.h:127:30: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.5/SpatMCA.Rcheck/00install.out' for details.
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    R      4.9Mb
    doc    4.7Mb
    help   4.9Mb
    libs   1.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.5Mb
GenerateCliquesCovariance: no visible global function definition for
  'rnorm'
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Package suggested but not available for checking: 'spDataLarge'
bartlett: no visible global function definition for 'pchisq'
local.rbfdot: no visible binding for global variable 'sd'
local.rbfdot: no visible global function definition for 'dist'
local.rbfdot : <anonymous>: no visible global function definition for
  'median'
speccalt: no visible global function definition for 'kmeans'
Undefined global functions or variables:
  dist kmeans median pchisq sd
Consider adding
  importFrom("stats", "dist", "kmeans", "median", "pchisq", "sd")
to your NAMESPACE file.
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.
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.
'library' or 'require' call to 'leaps' which was already attached by Depends.
  Please remove these calls from your code.
modSearch: no visible global function definition for 'glm'
modSearch: no visible binding for global variable 'binomial'
modSearch: no visible global function definition for 'na.omit'
modSearch: no visible global function definition for 'as.formula'
speff: no visible binding for global variable 'na.pass'
speff: no visible global function definition for 'model.matrix'
speff: no visible global function definition for 'terms'
speff: no visible global function definition for 'model.response'
speff: no visible global function definition for 'as.formula'
speff: no visible global function definition for 'predict'
speff: no visible global function definition for 'na.omit'
speff: no visible global function definition for 'glm'
speff: no visible binding for global variable 'na.omit'
speffSurv: no visible global function definition for 'model.matrix'
speffSurv: no visible global function definition for 'terms'
speffSurv: no visible global function definition for 'model.response'
speffSurv: no visible global function definition for 'as.formula'
speffSurv: no visible global function definition for 'uniroot'
summary.speff: no visible global function definition for 'qnorm'
summary.speff: no visible global function definition for 'pnorm'
summary.speffSurv: no visible global function definition for 'qnorm'
summary.speffSurv: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  as.formula binomial glm model.matrix model.response na.omit na.pass
  pnorm predict qnorm terms uniroot
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "model.matrix",
             "model.response", "na.omit", "na.pass", "pnorm", "predict",
             "qnorm", "terms", "uniroot")
to your NAMESPACE file.
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nr' to 'nrow'
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nc' to 'ncol'
spe: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
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.
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.
'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.
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.
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.
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.
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.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   2.6Mb
plot.SPRT: no visible global function definition for 'par'
plot.SPRT: no visible global function definition for 'plot'
plot.SPRT: no visible global function definition for 'abline'
print.SPRT: no visible global function definition for 'head'
Undefined global functions or variables:
  abline head par plot
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("utils", "head")
to your NAMESPACE file.
fssa20: no visible global function definition for 'runif'
fssa2d: no visible global function definition for 'runif'
fssa30: no visible global function definition for 'runif'
fssa3d: no visible global function definition for 'runif'
ssa20: no visible global function definition for 'runif'
ssa2d: no visible global function definition for 'runif'
ssa30: no visible global function definition for 'runif'
ssa3d: no visible global function definition for 'runif'
ssi20: no visible global function definition for 'runif'
ssi2d: no visible global function definition for 'runif'
ssi30: no visible global function definition for 'runif'
ssi3d: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   1.9Mb
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.
.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.
sGda : <anonymous>: no visible global function definition for 'cov'
sortgene: no visible global function definition for 'model.matrix'
Undefined global functions or variables:
  cov model.matrix
Consider adding
  importFrom("stats", "cov", "model.matrix")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'RJDBC' 'RMySQL' 'RODBC' 'RPostgreSQL' 'RSQLite' 'tcltk'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
cacheQuery: no visible global function definition for 'read.csv'
cacheQuery: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  read.csv write.csv
Consider adding
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
SQN: no visible binding for global variable 'median'
SQN: no visible global function definition for 'quantile'
SQN.demo.data: no visible global function definition for 'rnorm'
mix.qn: no visible global function definition for 'ecdf'
mix.qn: no visible global function definition for 'quantile'
Undefined global functions or variables:
  ecdf median quantile rnorm
Consider adding
  importFrom("stats", "ecdf", "median", "quantile", "rnorm")
to your NAMESPACE file.
plot.srafit: no visible global function definition for 'layout'
plot.srafit: no visible global function definition for 'par'
sraData : vartruncGauss : ff: no visible global function definition for
  'dnorm'
sraData : vartruncGauss : ff: no visible global function definition for
  'pnorm'
sraData : vartruncGauss: no visible global function definition for
  'uniroot'
sraPlotMean: no visible global function definition for 'axis'
sraPlotMean: no visible global function definition for 'points'
sraPlotMean: no visible global function definition for 'lines'
sraPlotMeanResid: no visible global function definition for 'axis'
sraPlotMeanResid: no visible global function definition for 'abline'
sraPlotMeanResid: no visible global function definition for 'points'
sraPlotVar: no visible global function definition for 'axis'
sraPlotVar: no visible global function definition for 'points'
sraPlotVar: no visible global function definition for 'lines'
sraPlotVarResid: no visible global function definition for 'axis'
sraPlotVarResid: no visible global function definition for 'abline'
sraPlotVarResid: no visible global function definition for 'points'
sraPlotlegend: no visible global function definition for 'legend'
sraStartingvalues : sraStartingvalues.mu0: no visible global function
  definition for 'rnorm'
sraStartingvalues : sraStartingvalues.logvarA0: no visible global
  function definition for 'rnorm'
sraStartingvalues : sraStartingvalues.logvarE0: no visible global
  function definition for 'rnorm'
sraStartingvalues: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  abline axis dnorm layout legend lines par pnorm points rnorm uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "layout", "legend", "lines",
             "par", "points")
  importFrom("stats", "dnorm", "pnorm", "rnorm", "uniroot")
to your NAMESPACE file.
Found the following hidden files and directories:
  .Rapp.history
  inst/script/.Rapp.history
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
File 'sROC/R/onload.R':
  .onLoad calls:
    packageStartupMessage("sROC 0.1-2 loaded")

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

AUC : TrapezInt: no visible global function definition for 'approx'
AUC : SimpsonInt: no visible global function definition for 'approx'
CI.CDF: no visible global function definition for 'qnorm'
bw.CDF: no visible global function definition for 'sd'
bw.CDF: no visible global function definition for 'IQR'
bw.CDF.pi: no visible global function definition for 'sd'
bw.CDF.pi: no visible global function definition for 'bw.nrd0'
bw.CDF.pi: no visible global function definition for 'bw.nrd'
bw.CDF.pi: no visible global function definition for 'bw.ucv'
bw.CDF.pi: no visible global function definition for 'bw.bcv'
bw.CDF.pi: no visible global function definition for 'bw.SJ'
bw.CDF.pi: no visible global function definition for 'IQR'
plot.CDF: no visible global function definition for 'plot.default'
plot.CDF: no visible global function definition for 'lines'
plot.CDF: no visible global function definition for 'polygon'
plot.ROC: no visible global function definition for 'plot.default'
plot.ROC: no visible global function definition for 'abline'
Undefined global functions or variables:
  IQR abline approx bw.SJ bw.bcv bw.nrd bw.nrd0 bw.ucv lines
  plot.default polygon qnorm sd
Consider adding
  importFrom("graphics", "abline", "lines", "plot.default", "polygon")
  importFrom("stats", "IQR", "approx", "bw.SJ", "bw.bcv", "bw.nrd",
             "bw.nrd0", "bw.ucv", "qnorm", "sd")
to your NAMESPACE file.
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
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.
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.
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.
.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.
'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.
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.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    include   8.5Mb
Error in re-building vignettes:
  ...
Quitting from lines 47-52 (staple_example.Rmd) 
Error: processing vignette 'staple_example.Rmd' failed with diagnostics:
incorrect number of dimensions
Execution halted
'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.
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.
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.
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.
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.
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.
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.
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.
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.5/RcppParallel/include/tthread/tinythread.h:632:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.5/StMoSim.Rcheck/00install.out' for details.
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.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R          2.0Mb
    datasets   2.6Mb
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
Error in re-building vignettes:
  ...
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "VignetteforSTPGA.ltx" --max-iterations=20 -I "D:/RCompile/recent/R/share/texmf/tex/latex" -I "D:/RCompile/recent/R/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'VignetteforSTPGA.ltx' failed with diagnostics:
running 'texi2dvi' on 'VignetteforSTPGA.ltx' failed

LaTeX errors:
! LaTeX Error: File `dirtytalk.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

Execution halted
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.
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.
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.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/streamR.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
'library' or 'require' call to 'ROAuth' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    libs  33.4Mb
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.
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').
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.
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.
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.
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.
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.
Package which this enhances but not available for checking: 'gputools'
HCLtree: no visible global function definition for 'hclust'
HCLtree: no visible global function definition for 'as.dist'
plotProfilesAcrossAllSamples: no visible global function definition for
  'matplot'
plotProfilesAcrossAllSamples: no visible global function definition for
  'matlines'
plotProfilesAcrossAllSamples: no visible global function definition for
  'axis'
plotProfilesAcrossAllSamples: no visible global function definition for
  'box'
plotProfilesWithinBicluster: no visible global function definition for
  'matplot'
plotProfilesWithinBicluster: no visible global function definition for
  'title'
plotProfilesWithinBicluster: no visible global function definition for
  'axis'
plotProfilesWithinBicluster: no visible global function definition for
  'par'
plotProfilesWithinBicluster: no visible global function definition for
  'box'
plotProfilesWithinBicluster: no visible global function definition for
  'matlines'
plotProfilesWithinBicluster: no visible global function definition for
  'legend'
Undefined global functions or variables:
  as.dist axis box hclust legend matlines matplot par title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "matlines", "matplot",
             "par", "title")
  importFrom("stats", "as.dist", "hclust")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'boa' 'coda'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
superdiag: no visible global function definition for 'as.mcmc.list'
superdiag: no visible global function definition for 'as.mcmc'
superdiag: no visible global function definition for 'runif'
superdiag: no visible global function definition for 'geweke.diag'
superdiag: no visible global function definition for 'heidel.diag'
superdiag: no visible global function definition for 'raftery.diag'
superdiag: no visible global function definition for 'gelman.diag'
Undefined global functions or variables:
  as.mcmc as.mcmc.list gelman.diag geweke.diag heidel.diag raftery.diag
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
TrainSuperMDS: no visible global function definition for 'rnorm'
TrainSuperMDSOnce: no visible global function definition for 'cmdscale'
TrainSuperMDSOnce: no visible global function definition for 'quantile'
distmat: no visible global function definition for 'dist'
Undefined global functions or variables:
  cmdscale dist quantile rnorm
Consider adding
  importFrom("stats", "cmdscale", "dist", "quantile", "rnorm")
to your NAMESPACE file.
Files named as vignettes but with no recognized vignette engine:
   'vignettes/copulas-concordance.tex'
   'vignettes/surrosurv.tex'
(Is a VignetteBuilder field missing?)
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.
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.
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.
Files named as vignettes but with no recognized vignette engine:
   'vignettes/survClip.Rnw'
(Is a VignetteBuilder field missing?)
pearson: no visible global function definition for 'cor'
plot.survcorr: no visible global function definition for 'pnorm'
plot.survcorr: no visible global function definition for 'par'
plot.survcorr: no visible global function definition for 'plot'
plot.survcorr: no visible global function definition for 'points'
survcorr: no visible global function definition for 'model.frame'
survcorr: no visible global function definition for 'qnorm'
survcorr: no visible global function definition for 'runif'
survcorr: no visible global function definition for 'pnorm'
survcorr: no visible global function definition for 'var'
survcorr: no visible global function definition for 'qt'
Undefined global functions or variables:
  cor model.frame par plot pnorm points qnorm qt runif var
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "cor", "model.frame", "pnorm", "qnorm", "qt",
             "runif", "var")
to your NAMESPACE file.
'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.
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/math/special_functions/detail/bernoulli_details.hpp:72:36: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.5/BH/include/boost/math/special_functions/detail/bernoulli_details.hpp:96:9: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.5/survHE.Rcheck/00install.out' for details.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
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.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.6Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
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').
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Running examples in 'survtmle-Ex.R' failed
The error most likely occurred in:

> ### Name: plot.tp.survtmle
> ### Title: Plot Results of Cumulative Incidence Estimates
> ### Aliases: plot.tp.survtmle
> 
> ### ** Examples
> 
> library(survtmle)
> set.seed(341796)
> n <- 100
> t_0 <- 10
> W <- data.frame(W1 = runif(n), W2 = rbinom(n, 1, 0.5))
> A <- rbinom(n, 1, 0.5)
> T <- rgeom(n,plogis(-4 + W$W1 * W$W2 - A)) + 1
> C <- rgeom(n, plogis(-6 + W$W1)) + 1
> ftime <- pmin(T, C)
> ftype <- as.numeric(ftime == T)
> suppressWarnings(
+   fit <- survtmle(ftime = ftime, ftype = ftype,
+                   adjustVars = W, glm.ftime = "I(W1*W2) + trt + t",
+                   trt = A, glm.ctime = "W1 + t", method = "hazard",
+                   verbose = TRUE,  t0 = t_0, maxIter = 2)
+ )
> tpfit <- timepoints(fit, times = seq_len(t_0))
> plot(tpfit)
Error in names(x) <- value : 
  'names' attribute [3] must be the same length as the vector [2]
Calls: plot -> plot.tp.survtmle -> colnames<-
Execution halted
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.
dlgMessage.tcltkGUI: no visible global function definition for 'alarm'
dlgMessage.tcltkGUI: no visible global function definition for
  'bringToTop'
Undefined global functions or variables:
  alarm bringToTop
Consider adding
  importFrom("grDevices", "bringToTop")
  importFrom("utils", "alarm")
to your NAMESPACE file.
svd3dplot: no visible global function definition for 'wireframe'
svd3dplot: no visible global function definition for 'levelplot'
Undefined global functions or variables:
  levelplot wireframe
startHttpServer : <anonymous> : Rjsonp: no visible global function
  definition for 'localeToCharset'
Undefined global functions or variables:
  localeToCharset
Consider adding
  importFrom("utils", "localeToCharset")
to your NAMESPACE file.
.onAttach : svBrowser: no visible global function definition for
  'browseURL'
.onAttach: no visible global function definition for 'loadhistory'
Undefined global functions or variables:
  browseURL loadhistory
Consider adding
  importFrom("utils", "browseURL", "loadhistory")
to your NAMESPACE file.
File 'svmpath/libs/i386/svmpath.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'mi10unix.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'mi10unix.o'
File 'svmpath/libs/x64/svmpath.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'mi10unix.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'mi10unix.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
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.
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)
See 'd:/Rcompile/CRANpkg/local/3.5/SWATmodel.Rcheck/00install.out' for details.
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    libs  25.5Mb
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.
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').
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/sybilEFBA.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
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').
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Packages suggested but not available for checking:
  'sylly.de' 'sylly.en' 'sylly.es'
symbol: no visible global function definition for 'plot.new'
symbol: no visible global function definition for 'plot.window'
symbol: no visible global function definition for 'axis'
symbol: no visible global function definition for 'box'
symbol: no visible global function definition for 'title'
symbol: no visible global function definition for 'rainbow'
symbol: no visible global function definition for 'hsv'
symbol: no visible global function definition for 'rect'
symbol: no visible global function definition for 'polygon'
symbol: no visible global function definition for 'lines'
symbol: no visible global function definition for 'text'
Undefined global functions or variables:
  axis box hsv lines plot.new plot.window polygon rainbow rect text
  title
Consider adding
  importFrom("grDevices", "hsv", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "polygon", "rect", "text", "title")
to your NAMESPACE file.
integrate.polynomial : f: no visible global function definition for
  'dmvnorm'
Undefined global functions or variables:
  dmvnorm
Package in Depends field not imported from: 'fields'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cwt_fw: no visible global function definition for 'fft'
cwt_iw: no visible global function definition for 'fft'
est_riskshrink_thresh: no visible global function definition for
  'median'
Undefined global functions or variables:
  fft median
Consider adding
  importFrom("stats", "fft", "median")
to your NAMESPACE file.
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.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/SynergizeR.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
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.
'library' or 'require' calls to packages already attached by Depends:
  'tcltk' 'tkrplot'
  Please remove these calls from your code.
Namespaces with empty importFrom:
  'Rcpp' 'methods'
mainNetFunction: no visible global function definition for 'png'
mainNetFunction: no visible global function definition for 'plot'
mainNetFunction: no visible global function definition for 'lines'
mainNetFunction: no visible global function definition for 'legend'
mainNetFunction: no visible global function definition for 'dev.off'
plotPR: no visible global function definition for 'plot'
plotROC: no visible global function definition for 'plot'
plotROC: no visible global function definition for 'lines'
simulatedData: no visible global function definition for 'rpois'
simulatedData : <anonymous>: no visible global function definition for
  'rpois'
simulatedData : rlognormpois: no visible global function definition for
  'rnorm'
simulatedData : rlognormpois: no visible global function definition for
  'rpois'
Undefined global functions or variables:
  dev.off legend lines plot png rnorm rpois
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "rnorm", "rpois")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'LowRankQP' 'rgenoud'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
fn.V: no visible global function definition for 'LowRankQP'
gaps.plot: no visible global function definition for 'abline'
path.plot: no visible global function definition for 'lines'
path.plot: no visible global function definition for 'abline'
path.plot: no visible global function definition for 'legend'
synth: no visible binding for global variable 'sd'
synth: no visible binding for global variable 'var'
synth: no visible global function definition for 'LowRankQP'
Undefined global functions or variables:
  LowRankQP abline legend lines sd var
Consider adding
  importFrom("graphics", "abline", "legend", "lines")
  importFrom("stats", "sd", "var")
to your NAMESPACE file.
Package unavailable to check Rd xrefs: 'unix'
.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.
S3 methods shown with full name in documentation object 'rbind.tableList':
  'rbind.tableList'

S3 methods shown with full name in documentation object 'rbind.tableMatrix':
  'rbind.tableMatrix'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
'library' or 'require' call to '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.
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.
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.
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.
'library' or 'require' calls in package code:
  'gdata' 'ggplot2' 'grid' 'lattice' 'xtable'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
AnalyzeLVZ: no visible global function definition for 'approx'
ConvP2Vdepthinv: no visible global function definition for 'approx'
DistSummary: no visible global function definition for 'heat.colors'
Earthplot: no visible global function definition for 'heat.colors'
Earthplot: no visible global function definition for 'par'
Earthplot: no visible global function definition for 'plot'
Earthplot: no visible global function definition for 'approx'
Earthplot: no visible global function definition for 'image'
Earthplot: no visible binding for global variable 'lines'
FindRoots: no visible global function definition for 'uniroot'
InterpModel: no visible global function definition for 'approx'
LinInterp: no visible global function definition for 'approx'
PolarPlot: no visible binding for global variable 'plot'
Rayfan: no visible binding for global variable 'lines'
polaraxis: no visible global function definition for 'text'
Undefined global functions or variables:
  approx heat.colors image lines par plot text uniroot
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "image", "lines", "par", "plot", "text")
  importFrom("stats", "approx", "uniroot")
to your NAMESPACE file.
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.
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
         x)
  8: classification(id, callopts = callopts, return_id = return_id, ...)
  9: classification.uid(id, callopts = callopts, return_id = return_id, ...)
  10: lapply(id, fun, callopts = callopts)
  11: FUN(X[[i]], ...)
  12: res$raise_for_status()
  13: stop(sprintf("%s (HTTP %s)", x$message, x$status_code), call. = FALSE)
  
  == testthat results  ===========================================================
  OK: 451 SKIPPED: 0 FAILED: 2
  1. Error: Taxmap can be intialized from queried data (@test--taxmap_parsers.R#106) 
  2. Error: Taxmap can be intialized from raw strings (@test--taxmap_parsers.R#167) 
  
  Error: testthat unit tests failed
  Execution halted
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.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.9Mb
    libs   1.5Mb
S3 methods shown with full name in documentation object 'top.fun':
  'slice.fun'

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.
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.
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.
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.
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.
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.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
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.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/tensorBF.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
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
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.
installed size is 35.0Mb
  sub-directories of 1Mb or more:
    libs      13.2Mb
    tessdata  20.9Mb
File which contains pragma(s) suppressing diagnostics:
  'inst/include/testthat/vendor/catch.h'
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    3.6Mb
    libs   2.1Mb
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.
.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.
Found the following significant warnings:
  Matrix.h:27:18: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.5/TFMPvalue.Rcheck/00install.out' for details.
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.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    3.8Mb
Thinknum: no visible global function definition for 'URLencode'
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
coef_traceplot: no visible global function definition for 'rainbow'
coef_traceplot: no visible global function definition for 'plot'
coef_traceplot: no visible global function definition for 'abline'
coef_traceplot : <anonymous>: no visible global function definition for
  'lines'
coef_traceplot: no visible global function definition for 'text'
ee.GEE.aux : <anonymous>: no visible global function definition for
  'combn'
Undefined global functions or variables:
  abline combn lines plot rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "plot", "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
summary.tsls: no visible global function definition for 'printCoefmat'
threesls: no visible global function definition for 'cor'
threesls: no visible global function definition for 'pt'
tsls.formula: no visible global function definition for 'model.matrix'
tsls.formula: no visible global function definition for
  'model.response'
Undefined global functions or variables:
  cor model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.matrix", "model.response",
             "printCoefmat", "pt")
to your NAMESPACE file.
.LoadTickDataHK: no visible global function definition for 'read.csv'
.LoadTickDataSHSZ: no visible global function definition for 'read.csv'
DrawDown: no visible global function definition for 'na.omit'
PerformanceReport: no visible global function definition for
  'aggregate'
PerformanceReport: no visible global function definition for 'sd'
Undefined global functions or variables:
  aggregate na.omit read.csv sd
Consider adding
  importFrom("stats", "aggregate", "na.omit", "sd")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
newTiddler: no visible global function definition for 'new'
twImage: no visible global function definition for 'new'
twLink: no visible global function definition for 'new'
twList: no visible global function definition for 'new'
twTable: no visible global function definition for 'new'
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  12: shannon_entropy(.)
  13: reduce_data(.data, !(!enquo(X)), numvars = 1, na.rm = na.rm)
  14: tidyselect::vars_select(names(reduced_tab), !(!(!quos(...))))
  15: vars_select_eval(.vars, quos)
  16: map_lgl(quos, quo_is_helper)
  17: .f(.x[[i]], ...)
  18: extract_expr(quo)
  19: is_call(expr, paren_sym)
  
  == testthat results  ===========================================================
  OK: 37 SKIPPED: 0 FAILED: 1
  1. Error: right number of columns given (@test-errors.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [30s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  3: eval_bare(get_expr(quo), get_env(quo))
  4: nrow(unnest(test1))
  5: unnest(test1)
  6: unnest.default(test1)
  7: unnest_(data, unnest_cols = unnest_cols, .drop = .drop, .id = .id, .sep = .sep, .preserve = .preserve)
  
  == testthat results  ===========================================================
  OK: 140 SKIPPED: 2 FAILED: 4
  1. Failure: Test returns tibble with correct rows and columns. (@test_tq_get_key_ratios.R#14) 
  2. Failure: Test returns tibble with correct rows and columns. (@test_tq_get_key_ratios.R#16) 
  3. Failure: Test returns tibble with correct rows and columns. (@test_tq_get_key_ratios.R#18) 
  4. Error: Test unnest returns correct rows. (@test_tq_get_key_ratios.R#23) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
v readr   1.1.1     v forcats 0.3.0
-- Conflicts ------------------------------------- tidyverse_conflicts() --
x lubridate::as.difftime() masks base::as.difftime()
x lubridate::date()        masks base::date()
x dplyr::filter()          masks stats::filter()
x dplyr::first()           masks xts::first()
x lubridate::intersect()   masks base::intersect()
x dplyr::lag()             masks stats::lag()
x dplyr::last()            masks xts::last()
x lubridate::setdiff()     masks base::setdiff()
x lubridate::union()       masks base::union()
Getting data...

Warning in download.file(url, destfile = tmp, quiet = TRUE) :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Warning in value[[3L]](cond) :
  Error at nasdaq during call to tq_exchange.
additional arguments ignored in warning()
Warning in with_tz(Sys.time(), tzone) : Unrecognized time zone ''
Warning: x = 'AAPL', get = 'key.ratios': Error in value[[3L]](cond): object 'key_ratios' not found

Quitting from lines 182-185 (TQ01-core-functions-in-tidyquant.Rmd) 
Error: processing vignette 'TQ01-core-functions-in-tidyquant.Rmd' failed with diagnostics:
no applicable method for 'filter_' applied to an object of class "logical"
Execution halted
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    level type   token
    <int> <chr>  <chr>
  1     0 number 1    
  -- 1. Failure: sheet names are returned correctly (@test-xlsx_sheet_names.R#4)  
  xlsx_sheet_names("./examples.xlsx")[1:2] not equal to c("Sheet1", "1~`!@#$%^&()_-+={}|;\"'<,>.£¹÷¦°").
  1/2 mismatches
  x[2]: "1~`!@#$%^&()_-+={}|;\"'<,>.Â£Â¹Ã·Â¦Â°"
  y[2]: "1~`!@#$%^&()_-+={}|;\"'<,>.£¹÷¦°"
  
  == testthat results  ===========================================================
  OK: 327 SKIPPED: 0 FAILED: 1
  1. Failure: sheet names are returned correctly (@test-xlsx_sheet_names.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    level type   token
    <int> <chr>  <chr>
  1     0 number 1    
  -- 1. Failure: sheet names are returned correctly (@test-xlsx_sheet_names.R#4)  
  xlsx_sheet_names("./examples.xlsx")[1:2] not equal to c("Sheet1", "1~`!@#$%^&()_-+={}|;\"'<,>.£¹÷¦°").
  1/2 mismatches
  x[2]: "1~`!@#$%^&()_-+={}|;\"'<,>.Â£Â¹Ã·Â¦Â°"
  y[2]: "1~`!@#$%^&()_-+={}|;\"'<,>.£¹÷¦°"
  
  == testthat results  ===========================================================
  OK: 327 SKIPPED: 0 FAILED: 1
  1. Failure: sheet names are returned correctly (@test-xlsx_sheet_names.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
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.
'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
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.
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
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.
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.
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.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc         3.7Mb
    rmarkdown   1.3Mb
tipom.car: no visible global function definition for 'abline'
tipom.car: no visible global function definition for 'axis'
tipom.heat: no visible global function definition for 'image'
tipom.heat: no visible global function definition for 'gray'
tipom.lw: no visible global function definition for 'plot'
tipom.lw: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline axis gray image plot
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "image", "plot")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'MASS' 'boot' 'lattice' 'splines' 'tcltk'
  Please remove these calls from your code.
ls.tree: no visible global function definition for 'lm'
ls.tree: no visible global function definition for 'coef'
Undefined global functions or variables:
  coef lm
Consider adding
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
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.
.my.tkdev: no visible global function definition for 'win.metafile'
tkpersp : draw: no visible global function definition for 'par'
tkpersp : draw: no visible global function definition for 'persp'
Undefined global functions or variables:
  par persp win.metafile
Consider adding
  importFrom("grDevices", "win.metafile")
  importFrom("graphics", "par", "persp")
to your NAMESPACE file.
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.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.3Mb
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    examples  19.2Mb
    include    2.9Mb
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.
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' 'Rpoppler' 'tm.lexicon.GeneralInquirer'
Package unavailable to check Rd xrefs: 'Rpoppler'
Package suggested but not available for checking: 'corpus.JSS.papers'
Tosls.formula: no visible global function definition for 'model.matrix'
Tosls.formula: no visible global function definition for
  'model.response'
summary: no visible global function definition for 'coef'
summary: no visible global function definition for 'pt'
Undefined global functions or variables:
  coef model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.matrix", "model.response", "pt")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  'Cairo' 'RGtk2' 'colorspace' 'gWidgets' 'tourr'
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'TeachingDemos' 'ash'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'Cairo' 'RGtk2' 'colorspace' 'gWidgets' 'tourr'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: 'rmongodb'
ConfA: no visible global function definition for 'qf'
EstM2Sn: no visible global function definition for 'nlm'
EstM2Sn: no visible global function definition for 'qnorm'
TV.model: no visible global function definition for 'dev.new'
TV.model: no visible global function definition for 'points'
betaBino: no visible global function definition for 'pbinom'
doseD: no visible global function definition for 'lm'
doseD: no visible global function definition for 'dev.new'
doseD: no visible global function definition for 'par'
doseD: no visible global function definition for 'plot'
doseD: no visible global function definition for 'axTicks'
doseD: no visible global function definition for 'axis'
doseD: no visible global function definition for 'lines'
doseD: no visible global function definition for 'abline'
doseD: no visible global function definition for 'legend'
setD: no visible global function definition for 'dev.new'
setD: no visible global function definition for 'par'
setD: no visible global function definition for 'pbinom'
setD: no visible global function definition for 'abline'
setD: no visible global function definition for 'axis'
setD: no visible global function definition for 'rect'
setD: no visible global function definition for 'lines'
setD: no visible global function definition for 'text'
setD: no visible global function definition for 'axTicks'
setD: no visible global function definition for 'legend'
spoD : spoD_A: no visible global function definition for 'chisq.test'
Undefined global functions or variables:
  abline axTicks axis chisq.test dev.new legend lines lm nlm par pbinom
  plot points qf qnorm rect text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axTicks", "axis", "legend", "lines",
             "par", "plot", "points", "rect", "text")
  importFrom("stats", "chisq.test", "lm", "nlm", "pbinom", "qf", "qnorm")
to your NAMESPACE file.
align1d : obj: no visible global function definition for 'dist'
align2d : obj: no visible global function definition for 'dist'
align2d : pen: no visible global function definition for 'dist'
align2d: no visible global function definition for 'dist'
sumt: no visible global function definition for 'optim'
tpe1d: no visible global function definition for 'hclust'
tpe2d: no visible global function definition for 'hclust'
tpe2d: no visible global function definition for 'cmdscale'
Undefined global functions or variables:
  cmdscale dist hclust optim
Consider adding
  importFrom("stats", "cmdscale", "dist", "hclust", "optim")
to your NAMESPACE file.
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.
File 'tpr/libs/i386/tpr.dll':
  Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
    Object: 'utils.o'
File 'tpr/libs/x64/tpr.dll':
  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 use Fortran I/O
nor system RNGs.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
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.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/TrajDataMining.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
microsoftTranslate: no visible global function definition for
  'URLencode'
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
rtrapezoid: no visible global function definition for 'runif'
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
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.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.4Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
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.
'library' or 'require' call to 'fpc' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' 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.
'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.
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.
'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.
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.
tfDetails: no visible global function definition for 'start'
tfDetails: no visible global function definition for 'end'
Undefined global functions or variables:
  end start
Consider adding
  importFrom("stats", "end", "start")
to your NAMESPACE file.
Qhat: no visible global function definition for 'pnorm'
plrt: no visible global function definition for 'uniroot'
plrt: no visible global function definition for 'optimize'
simulatedata: no visible global function definition for 'rnorm'
tsc.test: no visible global function definition for 'shapiro.test'
tsc.test: no visible global function definition for 'p.adjust'
tsc.test: no visible global function definition for 'glm'
tsc.test : f: no visible global function definition for 'pnorm'
tsc.test: no visible global function definition for 'uniroot'
tsc.test: no visible global function definition for 'optimize'
variance: no visible global function definition for 'density'
variance: no visible global function definition for 'ecdf'
Undefined global functions or variables:
  density ecdf glm optimize p.adjust pnorm rnorm shapiro.test uniroot
Consider adding
  importFrom("stats", "density", "ecdf", "glm", "optimize", "p.adjust",
             "pnorm", "rnorm", "shapiro.test", "uniroot")
to your NAMESPACE file.
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.
vintageMap: no visible global function definition for 'read.table'
TSget,character-TSfameLocalConnection: no visible global function
  definition for 'as.ts'
TSget,character-TSfameLocalConnection: no visible global function
  definition for 'zoo'
TSget,character-TSfameLocalConnection: no visible global function
  definition for 'frequency'
TSget,character-TSfameServerConnection: no visible global function
  definition for 'as.ts'
TSget,character-TSfameServerConnection: no visible global function
  definition for 'zoo'
TSget,character-TSfameServerConnection: no visible global function
  definition for 'frequency'
Undefined global functions or variables:
  as.ts frequency read.table zoo
Consider adding
  importFrom("stats", "as.ts", "frequency")
  importFrom("utils", "read.table")
to your NAMESPACE file.
DstandardizedLoadings.TSFmodel: no visible global function definition
  for 'cov'
FAfitStats.TSFmodel: no visible global function definition for 'cov'
FAfitStats.default: no visible global function definition for 'cor'
FAfitStats.default: no visible global function definition for
  'factanal'
FAfitStats.default: no visible global function definition for 'pchisq'
FAmodelFitStats: no visible global function definition for 'pchisq'
checkResiduals.TSFmodel: no visible global function definition for
  'cov'
distribution.factorsEstEval: no visible global function definition for
  'par'
distribution.factorsEstEval: no visible binding for global variable
  'par'
distribution.factorsEstEval: no visible global function definition for
  'density'
distribution.factorsEstEval: no visible global function definition for
  'matplot'
distribution.factorsEstEval: no visible global function definition for
  'title'
summary.TSFmodel: no visible global function definition for 'start'
summary.TSFmodel: no visible global function definition for 'end'
Undefined global functions or variables:
  cor cov density end factanal matplot par pchisq start title
Consider adding
  importFrom("graphics", "matplot", "par", "title")
  importFrom("stats", "cor", "cov", "density", "end", "factanal",
             "pchisq", "start")
to your NAMESPACE file.
Func.SAX: no visible global function definition for 'sd'
Func.SAX: no visible global function definition for 'qnorm'
Func.matrix: no visible global function definition for 'qnorm'
Func.motif: no visible global function definition for 'sd'
Func.motif: no visible global function definition for 'na.omit'
Func.motif: no visible global function definition for 'combn'
Func.motif.multivariate: no visible global function definition for
  'txtProgressBar'
Func.motif.multivariate: no visible global function definition for
  'setTxtProgressBar'
Undefined global functions or variables:
  combn na.omit qnorm sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit", "qnorm", "sd")
  importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
dLag : dlag.f: no visible global function definition for
  'complete.cases'
distmat: no visible global function definition for 'dist'
fitCity: no visible global function definition for 'glm.control'
fitCity: no visible global function definition for 'terms'
ldmvnorm: no visible global function definition for 'mahalanobis'
lspline: no visible global function definition for 'quantile'
plot.tsdecomp: no visible global function definition for 'par'
plot.tsdecomp: no visible global function definition for 'plot'
setupFormula: no visible global function definition for 'as.formula'
spatialgibbs: no visible global function definition for 'rnorm'
spatialgibbs: no visible global function definition for 'rgamma'
spatialgibbs: no visible global function definition for 'runif'
tsdecomp: no visible global function definition for 'fft'
Undefined global functions or variables:
  as.formula complete.cases dist fft glm.control mahalanobis par plot
  quantile rgamma rnorm runif terms
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.formula", "complete.cases", "dist", "fft",
             "glm.control", "mahalanobis", "quantile", "rgamma", "rnorm",
             "runif", "terms")
to your NAMESPACE file.
covTranspose11: warning in glasso(sc, 2 * rhoc/n, wi.init = gc$wi,
  w.init = gc$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
covTranspose11: warning in glasso(sr, 2 * rhor/p, wi.init = gr$wi,
  w.init = gr$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
.help.ESS: no visible global function definition for 'index.search'
TransSphere : ttin: no visible global function definition for 't.test'
TransSphere: no visible global function definition for 'sd'
TransSphere: no visible global function definition for 'quantile'
TransSphere: no visible global function definition for 'pt'
Undefined global functions or variables:
  index.search pt quantile sd t.test
Consider adding
  importFrom("stats", "pt", "quantile", "sd", "t.test")
to your NAMESPACE file.
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > 
  > library("TSP")
  > test_check("TSP")
  -- 1. Failure: (unknown) (@test-solve_TSP.R#56)  -------------------------------
  all(sapply(tours1, attr, "tour_length") == 0) isn't true.
  
  == testthat results  ===========================================================
  OK: 21 SKIPPED: 0 FAILED: 1
  1. Failure: (unknown) (@test-solve_TSP.R#56) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Running examples in 'TTR-Ex.R' failed
The error most likely occurred in:

> ### Name: TTR
> ### Title: Functions to create Technical Trading Rules (TTR)
> ### Aliases: TTR TTR-package
> ### Keywords: package
> 
> ### ** Examples
> 
> 
> data(ttrc)
> 
> # Bollinger Bands
> bbands <- BBands( ttrc[,c("High","Low","Close")] )
> 
> # Directional Movement Index
> adx <- ADX(ttrc[,c("High","Low","Close")])
> 
> # Moving Averages
> ema <- EMA(ttrc[,"Close"], n=20)
> sma <- SMA(ttrc[,"Close"], n=20)
> 
> # MACD
> macd <- MACD( ttrc[,"Close"] )
> 
> # RSI
> rsi <- RSI(ttrc[,"Close"])
> 
> # Stochastics
> stochOsc <- stoch(ttrc[,c("High","Low","Close")])
> 
> ### Note: you must have a working internet connection
> ### for the examples below to work!
> 
> # Fetch U.S. symbols from the internet
> nyseSymbols <- stockSymbols("NYSE")
Fetching NYSE symbols...
Warning in file(file, "rt") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in file(file, "rt") : cannot open the connection
Calls: stockSymbols -> read.csv -> read.table -> file
Execution halted
ttScreening: no visible global function definition for 'gaussian'
ttScreening: no visible global function definition for 'glm.control'
ttScreening: no visible global function definition for 'model.response'
ttScreening: no visible global function definition for 'is.empty.model'
ttScreening: no visible global function definition for 'model.matrix'
ttScreening: no visible global function definition for 'na.omit'
ttScreening: no visible global function definition for 'terms'
ttScreening: no visible global function definition for 'capture.output'
ttScreening: no visible global function definition for 'glm'
ttScreening: no visible binding for global variable 'gaussian'
ttScreening: no visible global function definition for 'pt'
ttScreening: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  capture.output gaussian glm glm.control is.empty.model model.matrix
  model.response na.omit p.adjust pt terms
Consider adding
  importFrom("stats", "gaussian", "glm", "glm.control", "is.empty.model",
             "model.matrix", "model.response", "na.omit", "p.adjust",
             "pt", "terms")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
.saveDevice: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.off
Consider adding
  importFrom("grDevices", "dev.off")
to your NAMESPACE file.
ttwa: no visible global function definition for 'aggregate'
ttwa: no visible global function definition for 'txtProgressBar'
ttwa: no visible global function definition for 'setTxtProgressBar'
Undefined global functions or variables:
  aggregate setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "aggregate")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
http.connection: no visible global function definition for 'setNames'
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
'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 significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/turboEM.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
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.
TwoCop: no visible global function definition for 'quantile'
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
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.
txtacf: no visible binding for global variable 'na.fail'
txtacf: no visible global function definition for 'acf'
txtboxplot : <anonymous>: no visible global function definition for
  'boxplot.stats'
txtboxplot: no visible global function definition for 'boxplot.stats'
txtdensity: no visible global function definition for 'density'
Undefined global functions or variables:
  acf boxplot.stats density na.fail
Consider adding
  importFrom("grDevices", "boxplot.stats")
  importFrom("stats", "acf", "density", "na.fail")
to your NAMESPACE file.
Crm: no visible global function definition for 'integrate'
Crm : <anonymous>: no visible global function definition for
  'integrate'
Crm: no visible global function definition for 'optimize'
ail1: no visible global function definition for 'uniroot'
ail2 : fu : <anonymous>: no visible global function definition for
  'integrate'
ail2: no visible global function definition for 'uniroot'
aip : fu : <anonymous>: no visible global function definition for
  'integrate'
aip: no visible global function definition for 'uniroot'
ait1: no visible global function definition for 'uniroot'
ait2 : fu : <anonymous>: no visible global function definition for
  'integrate'
ait2: no visible global function definition for 'uniroot'
sim3p3: no visible global function definition for 'rbinom'
simCrm: no visible global function definition for 'rbinom'
simCrm: no visible global function definition for 'palette'
simCrm: no visible global function definition for 'gray'
simCrm: no visible global function definition for 'plot'
simCrm: no visible global function definition for 'abline'
simCrm: no visible global function definition for 'lines'
ssim3p3: no visible global function definition for 'txtProgressBar'
ssim3p3: no visible global function definition for 'setTxtProgressBar'
ssimCrm: no visible global function definition for 'txtProgressBar'
ssimCrm: no visible global function definition for 'setTxtProgressBar'
Undefined global functions or variables:
  abline gray integrate lines optimize palette plot rbinom
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("grDevices", "gray", "palette")
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "integrate", "optimize", "rbinom", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
rmd2pdf: no visible global function definition for 'tail'
rnw2pdf: no visible global function definition for 'tail'
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    doc         5.3Mb
    dummydata   1.4Mb
    libs        4.1Mb
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.
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.
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.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    1.6Mb
    libs   1.7Mb
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.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
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.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
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.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    extdata   6.2Mb
File 'uuid/libs/i386/uuid.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'gen_uuid.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'gen_uuid.o'
File 'uuid/libs/x64/uuid.dll':
  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 use Fortran I/O
nor system RNGs.

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.
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
Packages suggested but not available for checking: 'vaers' 'vaersND'
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.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/VarReg.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
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.
Error in re-building vignettes:
  ...
Loading required package: MASS
Loading required package: strucchange
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: sandwich
Loading required package: urca
Loading required package: lmtest

Error: processing vignette 'vars.Rnw' failed with diagnostics:
 chunk 1 (label = source) 
Error in solve.default(infgamma) : 
  system is computationally singular: reciprocal condition number = 2.00294e-16
Execution halted
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.
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.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/vcfR.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
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.
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.
calculateParameters,AffineTransformation: no visible global function
  definition for 'lm'
calculateParameters,AffineTransformation: no visible global function
  definition for 'coef'
calculateParameters,SimilarityTransformation: no visible global
  function definition for 'lm'
calculateParameters,SimilarityTransformation: no visible global
  function definition for 'coef'
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for 'points'
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for 'legend'
Undefined global functions or variables:
  coef legend lm points
Consider adding
  importFrom("graphics", "legend", "points")
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
DrawDensity3D: no visible global function definition for 'colorRamp'
DrawDensity3D: no visible global function definition for 'rgb'
ReadFromFile3D: no visible global function definition for 'read.table'
Undefined global functions or variables:
  colorRamp read.table rgb
Consider adding
  importFrom("grDevices", "colorRamp", "rgb")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Running examples in 'vegalite-Ex.R' failed
The error most likely occurred in:

> ### Name: from_spec
> ### Title: Take a JSON Vega-Lite Spec and render as an htmlwidget
> ### Aliases: from_spec
> 
> ### ** Examples
> 
> from_spec("http://rud.is/dl/embedded.json")
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in file(con, "r") : cannot open the connection
Calls: from_spec -> readLines -> file
Execution halted
'library' or 'require' call to 'stats' which was already attached by Depends.
  Please remove these calls from your code.
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.
Running 'run.R' [28s]
Running the tests in 'tests/run.R' failed.
Last 13 lines of output:
  | User input required to proceed, but we are in non-interactive mode.
  
  | unitizer unchanged.
  
  |   * Fail: vetr:::attr_compare(structure(list(integer(), character())), 
  |     data.frame(a = 1:10, b = letters[1:10]), attr.mode = 2)
  | in 'unitizer/internal.R'
  
  | Newly evaluated tests do not match unitizer (Pass: 1063, Fail: 1); see above 
  | for more info, or run in interactive mode.
  
  Error in unitize_core(test.files = test.files, store.ids = store.ids,  : 
    Cannot proceed in non-interactive mode.
  Calls: unitize_dir -> unitize_core
  Execution halted
Running 'run.R' [35s]
Running the tests in 'tests/run.R' failed.
Last 13 lines of output:
  | User input required to proceed, but we are in non-interactive mode.
  
  | unitizer unchanged.
  
  |   * Fail: vetr:::attr_compare(structure(list(integer(), character())), 
  |     data.frame(a = 1:10, b = letters[1:10]), attr.mode = 2)
  | in 'unitizer/internal.R'
  
  | Newly evaluated tests do not match unitizer (Pass: 1063, Fail: 1); see above 
  | for more info, or run in interactive mode.
  
  Error in unitize_core(test.files = test.files, store.ids = store.ids,  : 
    Cannot proceed in non-interactive mode.
  Calls: unitize_dir -> unitize_core
  Execution halted
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      3.4Mb
    doc    1.2Mb
    help   2.7Mb
    libs   1.3Mb
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.
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.
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.
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.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc           4.7Mb
    htmlwidgets   3.6Mb
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.
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.
'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.
'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.
Error in re-building vignettes:
  ...
These can be examined and/or removed using the column 'NSamples'.
These occur at time bin(s): 1150
Subsequent Empirical Logit calculations may be influenced by the number of samples (depending on the number of observations requested).
Sampling rate(s) present in the data are: 20 Hz.

There are 50 samples per bin.
One data point every 50 millisecond(s)
Preparing ELogit output...
Number of Observations equal to Number of Samples. 
 Calculation will be based on Number of Samples.
Grand average of Proportion Looks calculated using Event means.
Grand average of Proportion Looks calculated using Event means.
Grand average of Proportion Looks calculated using Event means.
Grand average of Proportion Looks calculated using Event means.
Grand average of Proportion Looks calculated using Event means.
Grand average of Proportion Looks calculated using Event means.
Grand average of Proportion Looks calculated using Event means.
Grand average of Proportion Looks calculated using Event means.
Grand average of Proportion Looks calculated using Event means.
Grand average of Proportion Looks calculated using Subject means.
Grand average of Difference calculated using Event means.
Quitting from lines 204-218 (SR_Plotting.Rmd) 
Error: processing vignette 'SR_Plotting.Rmd' failed with diagnostics:
`UQ()` can only be used within a quasiquoted argument
Execution halted
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.
File 'waffect/libs/i386/waffect.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'waffect.o'
File 'waffect/libs/x64/waffect.dll':
  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 use Fortran I/O
nor system RNGs.

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.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   7.3Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    doc  12.1Mb
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.
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.
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
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  OK: 26 SKIPPED: 0 FAILED: 18
  1. Error: canCallChrome (@test-chrome.R#3) 
  2. Error: pickUpErrorFromReturnCode (@test-chrome.R#43) 
  3. Error: pickUpErrorFromPortInUse (@test-chrome.R#62) 
  4. Error: canCallGecko (@test-gecko.R#4) 
  5. Error: pickUpErrorFromReturnCode (@test-gecko.R#44) 
  6. Error: pickUpErrorFromPortInUse (@test-gecko.R#63) 
  7. Error: canCallIEDriver (@test-iedriver.R#4) 
  8. Error: pickUpErrorFromReturnCode (@test-iedriver.R#46) 
  9. Error: pickUpErrorFromPortInUse (@test-iedriver.R#68) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    client   8.9Mb
    doc      1.0Mb
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.
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.
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.
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').
'library' or 'require' call to 'markdown' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested 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.
'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.
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.
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.
.__A__.1 : <anonymous>: no visible binding for global variable '.hwnd'
Undefined global functions or variables:
  .hwnd
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
dbayes: no visible global function definition for 'mahalanobis'
dbayes: no visible global function definition for 'var'
wmd: no visible global function definition for 'cor'
wmd: no visible global function definition for 'var'
Undefined global functions or variables:
  cor mahalanobis var
Consider adding
  importFrom("stats", "cor", "mahalanobis", "var")
to your NAMESPACE file.
fit,Leader: no visible global function definition for 'lm'
plotfit,Leader: no visible global function definition for 'par'
plotfit,Leader: no visible global function definition for 'plot'
Undefined global functions or variables:
  lm par plot
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
'library' or 'require' call to 'tm' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   6.5Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.6Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.3Mb
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.
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.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    java  19.0Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    java   9.8Mb
.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.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
File 'xml2/libs/i386/xml2.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_WriteConnection'
File 'xml2/libs/x64/xml2.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_WriteConnection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  y[1]: "# ç\u008f¾è¡ã\u0081®å­¦æ ¡ææ³ã\u0081§ã\u0081¯ã\u0081è±èªã\u0081«ã\
  y[1]: u0081ããã\u0081ã\u0081ªãç®çèªã\u008dãè£èªã\u008d"
  
  -- 2. Failure: UTF-8 is OK (@test.R#78)  ---------------------------------------
  length(op) not equal to 1.
  1/1 mismatches
  [1] 0 - 1 == -1
  
  == testthat results  ===========================================================
  OK: 14 SKIPPED: 0 FAILED: 2
  1. Failure: UTF-8 is OK (@test.R#66) 
  2. Failure: UTF-8 is OK (@test.R#78) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    exampleData   1.3Mb
    examples      4.5Mb
    libs          4.2Mb
newXMLDoc: no visible binding for global variable 'doc'
source: no visible binding for global variable 'use_file'
xmlFlatListTree : f: no visible binding for global variable 'nodeNames'
xmlFlatListTree : f: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'parentCount'
xmlFlatListTree : addNode: no visible binding for global variable
  'parentCount'
xmlFlatListTree : <anonymous>: no visible binding for global variable
  'e'
xmlFlatTree : <anonymous>: no visible binding for global variable 'e'
Undefined global functions or variables:
  doc e idx nodeNames nodeSet parentCount use_file
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.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
big.read.table: no visible global function definition for 'read.table'
big.read.table: no visible global function definition for 'object.size'
sparkline: no visible global function definition for 'is.ts'
sparkline: no visible global function definition for 'time'
sparkline: no visible global function definition for 'boxplot'
Undefined global functions or variables:
  boxplot is.ts object.size read.table time
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "is.ts", "time")
  importFrom("utils", "object.size", "read.table")
to your NAMESPACE file.
bootstrapswapcurve: no visible global function definition for 'ts'
fitted: no visible global function definition for 'ts'
forwardrates: no visible global function definition for 'ts'
residuals: no visible global function definition for 'ts'
tZC_NS: no visible global function definition for 'cmpfun'
tZC_NS_extra: no visible global function definition for 'cmpfun'
tZC_SV: no visible global function definition for 'cmpfun'
tZC_SV_extra: no visible global function definition for 'cmpfun'
ycextra: no visible global function definition for 'new'
ycinter: no visible global function definition for 'new'
ycplot: no visible global function definition for 'par'
ycplot: no visible global function definition for 'points'
ycplot: no visible global function definition for 'abline'
ycplot: no visible global function definition for 'hist'
ycplot: no visible global function definition for 'lines'
ycplot: no visible global function definition for 'density'
ycplot: no visible global function definition for 'qqnorm'
ycplot: no visible global function definition for 'qqline'
ycsummary: no visible global function definition for 'shapiro.test'
ycsummary: no visible global function definition for 'pf'
Undefined global functions or variables:
  abline cmpfun density hist lines new par pf points qqline qqnorm
  shapiro.test ts
Consider adding
  importFrom("graphics", "abline", "hist", "lines", "par", "points")
  importFrom("methods", "new")
  importFrom("stats", "density", "pf", "qqline", "qqnorm",
             "shapiro.test", "ts")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.NS.estimator: no visible global function definition for 'lm'
.NS.estimator: no visible global function definition for 'coef'
.NS.estimator: no visible global function definition for 'na.omit'
.NS.estimator: no visible global function definition for 'resid'
.NSS.estimator: no visible global function definition for 'lm'
.NSS.estimator: no visible global function definition for 'coef'
.NSS.estimator: no visible global function definition for 'na.omit'
.NSS.estimator: no visible global function definition for 'resid'
NSrates: no visible global function definition for 'time'
Nelson.Siegel: no visible global function definition for 'optimize'
Srates: no visible global function definition for 'time'
Svensson: no visible global function definition for 'median'
Svensson: no visible global function definition for 'optimize'
Undefined global functions or variables:
  coef lm median na.omit optimize resid time
Consider adding
  importFrom("stats", "coef", "lm", "median", "na.omit", "optimize",
             "resid", "time")
to your NAMESPACE file.
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.
Package suggested but not available for checking: 'zdat'
S3 methods shown with full name in documentation object 'merge':
  'cbind.zoocat'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
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.
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 examples in ‘ApacheLogProcessor-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: read.multiple.apache.access.log
> ### Title: Reads multiple files of apache web server.
> ### Aliases: read.multiple.apache.access.log
> 
> ### ** Examples
> 
> path <- system.file("examples", package="ApacheLogProcessor")
> path <- paste(path, "/", sep="")
> 
> #read multiple gziped logs with the prefix m_access_log_combined_
> dfLog <- read.multiple.apache.access.log(path, "m_access_log_combined_")
[1] "Starting the log processing. This may take a long time..."
[1] "Processing file  m_access_log_combined_1.log.gz"
[1] "Unziping  m_access_log_combined_1.log.gz"
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/ApacheLogProcessor/examples/m_access_log_combined_1.log': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: read.multiple.apache.access.log -> write -> cat -> file
Execution halted
Running examples in ‘ASIP-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: arvi
> ### Title: Atmospherically Resistant Vegetation Index
> ### Aliases: arvi
> 
> ### ** Examples
> 
> library (raster)
Loading required package: sp
> library (rgdal)
rgdal: version: 1.2-18, (SVN revision 718)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.2.3, released 2017/11/20
 Path to GDAL shared files: /usr/share/gdal/2.2
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 5.0.0, March 1st, 2018, [PJ_VERSION: 500]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.2-7 
> # Finding the path of the sample satellite image directory.
> # User may define paths directly like "/home/ur_folder" or "C:/ur_folder"
> path <- system.file ("TM_sample", package = "ASIP")
> shapefil <- paste0 (path, "/test.shp")
> arvi (directory = path, crop = "y", ext2crop = shapefil)
OGR data source with driver: ESRI Shapefile 
Source: "/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/ASIP/TM_sample/test.shp", layer: "test"
with 1 features
It has 1 fields
Integer64 fields read as strings:  id 
Error in .local(.Object, ...) : Dataset copy failed
Calls: arvi ... <Anonymous> -> new -> initialize -> initialize -> .local -> .Call
Execution halted
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-patched-gcc/Work/PKGS/audio.Rcheck/00install.out’ for details.
Running examples in ‘bibliospec-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Bibliospec-class
> ### Title: R access to Bibliospec File
> ### Aliases: Bibliospec Bibliospec-class bibliospec blib
> 
> ### ** Examples
> 
> 
> library(bibliospec)
> 
> # use the sqlite file provided in the package
> dbfile <- file.path(path.package("bibliospec"),
+  "extdata/peptideStd.sqlite")
> 
> # call constructor
> BS <- Bibliospec(dbfile=dbfile)
database connected
> 
> # test; should return TRUE
> BS$getNrPSM() == 137
     count(*)
[1,]     TRUE
> 
> S <- BS$getPsmSet()
SELECT RefSpectra.id as RefSpectraId, numPeaks,  peptideSeq,
precursorCharge, precursorMZ, retentionTime,
peptideModSeq, score, SpectrumSourceFiles.fileName
FROM SpectrumSourceFiles, RefSpectra
WHERE SpectrumSourceFiles.id = RefSpectra.fileID;
getspectra
preparing Peaks as a list, will take a while if you blib file is large.
 extracted MZ
 extracted Intensity
assigning 28 modifications ...
> 
> ## Not run: 
> ##D  library(specL)
> ##D  print(S)
> ##D  lapply(S[1:10], plot)
> ## End(Not run)
> 
> peaks <- BS$getPeaks()
getspectra
preparing Peaks, will take a while if you blib file is large.
 extracted MZ
 extracted Intensity
to data frame
Error in rsqlite_send_query(conn@ptr, statement) : 
  attempt to write a readonly database
Calls: <Anonymous> ... initialize -> initialize -> rsqlite_send_query -> .Call
Execution halted
finalize
[1] "disconnected"
Running examples in ‘biclique-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bi.format
> ### Title: Add number of vertices and edges to the input file
> ### Aliases: bi.format
> 
> ### ** Examples
> 
> bi.format(system.file("extdata", "example2.el", package = "biclique"))
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/biclique/extdata/example2.el': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: bi.format -> cat -> file
Execution halted
Running examples in ‘BigQuic-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BigQuic
> ### Title: Big Quadratic Inverse Covariance Estimation
> ### Aliases: BigQuic
> ### Keywords: BigQUIC package covariance regularization graphical model
> ###   lasso Newton coordinate descent
> 
> ### ** Examples
> 
> lambda <- 0.91
> exampleResult <- BigQuic(inputFileName = paste(path.package("BigQuic"), 
+                          "/extdata/testInput", sep = ""), lambda = lambda, 
+                          numthreads = 1, memory_size = 512, seed = 1, 
+                          use_ram = TRUE)

 *** caught segfault ***
address 0xc0, cause 'memory not mapped'

Traceback:
 1: .Call("BigQuic_BigQuicHelper", PACKAGE = "BigQuic", argvPasser)
 2: BigQuicHelper(argvPasser = c("-l", lambda[i], "-n", numthreads,     "-t", maxit, "-e", epsilon, "-k", k, "-m", memory_size, "-q",     verbose, "-r", isnormalized, inputFileName, outputFileName))
 3: BigQuic(inputFileName = paste(path.package("BigQuic"), "/extdata/testInput",     sep = ""), lambda = lambda, numthreads = 1, memory_size = 512,     seed = 1, use_ram = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Running examples in ‘broom-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gam_tidiers
> ### Title: Tidying methods for a generalized additive model (gam)
> ### Aliases: gam_tidiers tidy.gam glance.gam
> 
> ### ** Examples
> 
> 
> if (require("gam", quietly = TRUE)) {
+     data(kyphosis)
+     g <- gam(Kyphosis ~ s(Age,4) + Number, family = binomial, data = kyphosis)
+     tidy(g)
+     augment(g)
+     glance(g)
+ }
Loaded gam 1.15

Error in 1:ncol(co) : argument of length 0
Calls: tidy -> tidy.lm -> tidy.summary.lm -> fix_data_frame
Execution halted
Error in re-building vignettes:
  ...
! LaTeX Error: Unknown graphics extension: .tiff.

Error: processing vignette ‘ciee.Rmd’ failed with diagnostics:
Failed to compile ciee.tex. See ciee.log for more info.
Execution halted
Error in re-building vignettes:
  ...
Loading required package: mvtnorm
Loading required package: RMTstat
Loading required package: grid
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: fit.models
Loading required package: foreach
Loading required package: PerformanceAnalytics

Attaching package: 'PerformanceAnalytics'

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

    legend

Loading required package: rugarch
Loading required package: parallel

Attaching package: 'rugarch'

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

    sigma


Attaching package: 'rmgarch'

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

    first, last

Quitting from lines 217-225 (CovarianceEstimation.Rmd) 
Error: processing vignette ‘CovarianceEstimation.Rmd’ failed with diagnostics:
all(sapply(args, function(x) is.zoo(x) || !is.plain(x) || (is.plain(x) &&  .... is not TRUE
Execution halted
Running examples in ‘CREAM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CREAM
> ### Title: CREAM is the main function for CORE identification
> ### Aliases: CREAM
> 
> ### ** Examples
> 
> CREAM(system.file("extdata", "A549_Chr21.bed", package = "CREAM"),
+ system.file("extdata", "A549_Chr21_COREs.bed", package = "CREAM"),
+ MinLength = 1000, peakNumMin = 2)
[1] "Please make sure there is no overlap between the input genomic regions. Overlap between the input regions may cause error."
[1] "Identifying window size for each Order"
[1] "Identifying COREs"
[1] "Filtering clusters of low order"
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/CREAM/extdata/A549_Chr21_COREs.bed': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: CREAM -> write.table -> file
Execution halted
Running ‘testthat.R’ [6s/55s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(curl)
  > 
  > test_check("curl")
  This is libcurl version 7.58.0 with GnuTLS/3.5.18 
  Using test server: http://hb.opencpu.org 
  ── 1. Error: IDN domain names (@test-idn.R#8)  ─────────────────────────────────
  SSL: certificate subject name (www.malmo.se) does not match target host name 'www.xn--malm-8qa.se'
  1: expect_is(curl::curl_fetch_memory(enc2utf8(malmo))$status_code, "integer") at testthat/test-idn.R:8
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: curl::curl_fetch_memory(enc2utf8(malmo))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 171 SKIPPED: 0 FAILED: 1
  1. Error: IDN domain names (@test-idn.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Cyclops.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: Rcpp

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Joining, by = "gene"
Joining, by = "cell"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "cell"
Joining, by = c("cell", "capture")
Have 35 cells after filtering
Joining, by = "cell"
Have 20 genes after filtering
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "cell"
Joining, by = c("cell", "capture")
Compiling model
the number of chains is less than 1; sampling not done
Saving compiled model to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/DeLorean/extdata/exact-sizes.rds
Quitting from lines 145-146 (DeLorean.Rmd) 
Error: processing vignette ‘DeLorean.Rmd’ failed with diagnostics:
cannot open the connection
Execution halted
Running examples in ‘dggridR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dgearthgrid
> ### Title: Return the coordinates constituting the boundary of cells for
> ###   the entire Earth
> ### Aliases: dgearthgrid
> 
> ### ** Examples
> 
> library(dggridR)
> dggs <- dgconstruct(res=20)
> res  <- dg_closest_res_to_spacing(dggs,spacing=1000,round='down',metric=FALSE)
Resolution: 3, Area (mi^2): 1173851.79791229, Spacing (mi): 843.496246531418, CLS (mi): 964.285490648183
> dggs <- dgsetres(dggs,res)
> gridfilename <- dgearthgrid(dggs,savegrid=TRUE) #Save directly to a file
Error: is.character(dsn) is not TRUE
Execution halted
Error in re-building vignettes:
  ...
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: raster
Loading required package: sp
Loading required package: ggplot2
Loaded dtwSat v0.2.3. See ?dtwSat for help, citation("dtwSat") for use in publication.

Loading required package: lattice
Loading required package: survival
Loading required package: Formula

Attaching package: 'Hmisc'

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

    mask, zoom

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

    format.pval, units

Read 137 items
Read 1 item

Attaching package: 'caret'

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

    cluster

This is BibTeX, Version 0.99d (TeX Live 2017/Debian)
The top-level auxiliary file: applying_twdtw.aux
The style file: jss.bst
Illegal, another \bibstyle command---line 155 of file applying_twdtw.aux
 : \bibstyle
 :          {jss}
I'm skipping whatever remains of this command
Database file #1: references.bib.bib
Warning--entry type for "Dutrieux:2014" isn't style-file defined
--line 584 of file references.bib.bib
(There was 1 error message)
Error: processing vignette ‘applying_twdtw.Rmd’ failed with diagnostics:
Failed to build the bibliography via bibtex
Execution halted
Running examples in ‘EasyStrata-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EasyStrata
> ### Title: Function to run EasyStrata (v8.6).
> ### Aliases: EasyStrata
> 
> ### ** Examples
> 
> extDataDir=system.file("extdata", package="EasyStrata")
> ## Example Pipeline:
> ecfPipe=paste(extDataDir,"example_pipeline.ecf",sep="/")
> EasyStrata(ecfPipe)
Warning message:
In file(fileLog, open = "a") :
  cannot open file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/EasyStrata/extdata/example_pipeline.ecf.out': Read-only file system
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ECctmc)
  > 
  > test_check("ECctmc")
  ── 1. Failure: Modified rejection sampling and uniformization target the same di
  t.test(MR_res[k, ], Unif_res[k, ])$p.value < 0.1 isn't false.
  
  ── 2. Failure: Modified rejection sampling and uniformization target the same di
  t.test(MR_res[k, ], Unif_res[k, ])$p.value < 0.1 isn't false.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 5 SKIPPED: 0 FAILED: 2
  1. Failure: Modified rejection sampling and uniformization target the same distribution (@test_simfcns.R#36) 
  2. Failure: Modified rejection sampling and uniformization target the same distribution (@test_simfcns.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: iteration 7 invokes undefined behavior [-Waggressive-loop-optimizations]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/expoRkit.Rcheck/00install.out’ for details.
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-patched-gcc/Work/PKGS/FastRWeb.Rcheck/00install.out’ for details.
Running examples in ‘forega-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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),  : 
  Evaluation error: only replacement of elements is allowed.
Calls: forecasting_ga -> .Call
Execution halted
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(gdns)
  > 
  > test_check("gdns")
  ── 1. Failure: we can do something (@test-gdns.R#4)  ───────────────────────────
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 11 - 10 == 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1 SKIPPED: 0 FAILED: 1
  1. Failure: we can do something (@test-gdns.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘GENEAread-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AccData
> ### Title: Methods for processing and summarising AccData.
> ### Aliases: AccData [.AccData $.AccData print.AccData plot.AccData
> ###   summary.AccData
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
> binfile  = system.file("binfile/TESTfile.bin", package = "GENEAread")[1]
> 
> #Read in the entire file, calibrated
> procfile<-read.bin(binfile)
Loading required package: mmap
Error in mmap(binfile, char()) : 
  unable to open file: possible permission issue.
Calls: read.bin -> header.info -> mmap -> .Call
Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'gglogo'

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

    fortify

Killed
Running ‘test-all.R’ [3s/4s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("hrbrthemes")
  Loading required package: hrbrthemes
  ── 1. Error: we can do something (@test-hrbrthemes.R#60)  ──────────────────────
  cannot open the connection
  1: import_roboto_condensed() at testthat/test-hrbrthemes.R:60
  2: suppressWarnings(suppressMessages(extrafont::font_import(rc_font_dir, prompt = FALSE)))
  3: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  4: suppressMessages(extrafont::font_import(rc_font_dir, prompt = FALSE))
  5: withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessage"))
  6: extrafont::font_import(rc_font_dir, prompt = FALSE)
  7: ttf_import(paths, recursive, pattern)
  8: ttf_extract(ttfiles)
  9: gzcopy_exclude(paste(tmpfiles[i], ".afm", sep = ""), paste(outfiles[i], ".afm.gz", 
         sep = ""), delete = TRUE, exclusions = c("^Characters"))
  10: gzfile(dest, "w")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 3 SKIPPED: 0 FAILED: 1
  1. Error: we can do something (@test-hrbrthemes.R#60) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘KODAMA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: knn.double.cv
> ### Title: Cross-Validation with k-Nearest Neighbors algorithm.
> ### Aliases: knn.double.cv
> 
> ### ** Examples
> 
>  data(iris)
>  data=iris[,-5]
>  labels=iris[,5]
>  pp=knn.double.cv(data,labels)
.....
 *** caught segfault ***
address (nil), cause 'unknown'

Traceback:
 1: .Call("KODAMA_double_knn_cv", PACKAGE = "KODAMA", x, yy, constrain,     type, verbose, compmax, optim, scaling)
 2: double_knn_cv(Xdata, as.numeric(Ydata), constrain, 1, 2, compmax,     optim, scal)
 3: knn.double.cv(data, labels)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Running examples in ‘lifelogr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_sleep_start_end
> ### Title: A function to plot sleep each night by start time and end time.
> ### Aliases: plot_sleep_start_end
> 
> ### ** Examples
> 
> data(EX)
> plot_sleep_start_end(person = EX)
Error in (function (dt, year, month, yday, mday, wday, hour, minute, second,  : 
  Invalid timezone of input vector: ""
Calls: plot_sleep_start_end ... reclass_date.POSIXlt -> as.POSIXlt -> do.call -> <Anonymous> -> .Call
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 141-142 (summary.Rmd) 
Error: processing vignette ‘summary.Rmd’ failed with diagnostics:
Invalid timezone of input vector: ""
Execution halted
Running examples in ‘lubridate-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ymd
> ### Title: Parse dates with *y*ear, *m*onth, and *d*ay components
> ### Aliases: ymd ydm mdy myd dmy dym yq
> ### Keywords: chron
> 
> ### ** Examples
> 
> x <- c("09-01-01", "09-01-02", "09-01-03")
> ymd(x)
[1] "2009-01-01" "2009-01-02" "2009-01-03"
> x <- c("2009-01-01", "2009-01-02", "2009-01-03")
> ymd(x)
[1] "2009-01-01" "2009-01-02" "2009-01-03"
> ymd(090101, 90102)
[1] "2009-01-01" "2009-01-02"
> now() > ymd(20090101)
Warning in with_tz(Sys.time(), tzone) : Unrecognized time zone ''
Error in C_force_tz(time, tz = tzone, roll) : 
  CCTZ: Unrecognized output timezone: ""
Calls: >.POSIXt -> date_to_posix -> force_tz -> C_force_tz -> .Call
Execution halted
Running examples in ‘MAGNAMWAR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: FormatMCLFastas
> ### Title: Format all raw GenBank fastas to single OrthoMCL compatible
> ###   fasta file
> ### Aliases: FormatMCLFastas
> 
> ### ** Examples
> 
> 
> dir <- system.file('extdata', 'fasta_dir', package='MAGNAMWAR')
> dir <- paste(dir,'/',sep='')
> formatted_file <- FormatMCLFastas(dir)
Warning in file.remove(outfile) :
  cannot remove file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/MAGNAMWAR/extdata/fasta_dir/MCLformatted_all.fasta', reason 'Read-only file system'
Writing out to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/MAGNAMWAR/extdata/fasta_dir/MCLformatted_all.fasta 
Warning in file(description = file.out, open = open) :
  cannot open file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/MAGNAMWAR/extdata/fasta_dir/MCLformatted_all.fasta': Read-only file system
Error in file(description = file.out, open = open) : 
  cannot open the connection
Calls: FormatMCLFastas -> <Anonymous> -> file
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/maGUI.Rcheck/00install.out’ for details.
Running examples in ‘MetaSubtract-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: meta.subtract
> ### Title: Subtracts GWAS results from one or more cohorts from the
> ###   meta-GWAS results
> ### Aliases: meta.subtract
> ### Keywords: Correct meta-GWAS results Leave-one-out
> 
> ### ** Examples
> 
> metafile="meta_results.txt"
> cohortfiles=c("cohort1_results.txt","cohort2_results.txt")
> # Subtract summary statistics of the two cohorts from the meta summary statistics in metafile.
> # Genomic control correction of the imported meta summary statistics will be undone using 
> # lambda.meta. Genomic control will be applied to the corrected meta summary statistics 
> # (gc_meta=TRUE by default) based on a lambda derived from the new meta summary statistics 
> # (calculate_lambda.meta=TRUE by default). The cohorts summary statistics will always be first 
> # corrected for genomic control before subtracting them from the meta summary statistics. By 
> # default, the lambda will be calculated from the data (calculate_lambdas.cohort=TRUE by default).
> m1<-meta.subtract(metafile=metafile, cohortfiles=cohortfiles, lambda.meta=1.046, 
+       dir=system.file("extdata", package="MetaSubtract"))
[1] "Mon Mar 19 05:21:38 2018"
Reading meta_results.txt 
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file 'MetaSubtract.log': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: meta.subtract -> write.table -> file
Execution halted
Error in re-building vignettes:
  ...
Use the user-defined lambda vector.
Using the criterion BIC to choose optimized penalty.
The chosen penalty throuth BIC is 3.6867.
The penalty term is selected automatically with 50 candidates.
Using the criterion BIC to choose optimized penalty.
The chosen penalty throuth BIC is 4.9895.
The penalty term is selected automatically with 50 candidates.
Using the criterion deviance to choose optimized penalty.
The chosen penalty throuth deviance is 2.4657.
trying URL ‘http://www.cs.columbia.edu/~andrews/mil/data/MIL-Data-2002-Musk-Corel-Trec9.tgz’
Content type 'application/x-gzip' length 6249673 bytes (6.0 MB)
==================================================
downloaded 6.0 MB

Warning in fread("MilData/Musk/musk1norm.svm", header = FALSE) :
  Starting data input on line 2 and discarding line 1 because it has too few or too many items to be column names or data: # Generated by musk_2_svm(/pro/webagents/stu/mil//experiments/musk//data/clean1.data, /pro/webagents/stu/mil//experiments/musk//generate_data/clean1.svm)
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Warning: 'switch' is deprecated.
Use 'strip.position' instead.
See help("Deprecated")
The penalty term is selected automatically with 100 candidates.
Using the criterion deviance to choose optimized penalty.
The chosen penalty throuth deviance is 3.5287.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Killed
Note: significantly better compression could be obtained
        by using R CMD build --resave-data
           old_size new_size compress
  cgps.rda    1.5Mb    1.4Mb       xz
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/MRMR.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
! Package pdftex.def Error: File `http://research.scilifelab.se/andrej_alexeyen
ko/downloads/test_data/aa.png' not found: using draft setting.

Error: processing vignette ‘NEArender_vignette.Rmd’ failed with diagnostics:
Failed to compile NEArender_vignette.tex. See NEArender_vignette.log for more info.
Execution halted
Running ‘testthat.R’ [21s/36s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > test_check("openxlsx")
  Loading required package: openxlsx
  ── 1. Error: loadWorkbook from different sources (@test-read_sources.R#49)  ────
  subscript out of bounds
  1: expect_true(all.equal.Workbook(wb_url, wb_file), "Loading from URL vs local not equal") at testthat/test-read_sources.R:49
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: all.equal.Workbook(wb_url, wb_file)
  5: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  9: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  10: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  11: attr.all.equal(target, current, ...)
  12: mode(current)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 505 SKIPPED: 2 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Killed
Running ‘testthat.R’ [7s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pxweb)
  pxweb: R tools for PX-WEB API.
  Copyright (C) 2014 Mans Magnusson, Leo Lahti, Love Hansson
  https://github.com/ropengov/pxweb
  
  New PXWEB API(s):
   - prognos.konj.se
   - data.ssb.no
   - pxweb.asub.ax
   - makstat.stat.gov.mk
   - data.csb.gov.lv
  
  Use update_pxweb_apis() to update the api catalogue.
  > test_check("pxweb")
  ── 1. Failure: pxweb_api_class (@test-pxweb_api_class.R#20)  ───────────────────
  NOT(success)
  
  ── 2. Failure: pxweb_api_class (@test-pxweb_api_class.R#22)  ───────────────────
  "foo.bar" %in% unlist(lapply(api_catalogue(), function(X) X$api)) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 98 SKIPPED: 16 FAILED: 2
  1. Failure: pxweb_api_class (@test-pxweb_api_class.R#20) 
  2. Failure: pxweb_api_class (@test-pxweb_api_class.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘R2GUESS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as.ESS.object
> ### Title: Compiles the main input and output files from a previous run of
> ###   'R2GUESS' and creates an ESS object.
> ### Aliases: as.ESS.object
> 
> ### ** Examples
> 
> dataX <- "data-X-C-CODE.txt"
> dataY <- "data-Y-ALL-C-CODE.txt"
> 
> path.input <- system.file("Input", package="R2GUESS")
> path.output <- system.file("Output", package="R2GUESS")
> path.par <- system.file("extdata", package="R2GUESS")
> file.par <- "Par_file_example_Hopx.xml"
> root.file.output <- "Example-GUESS-Y-Hopx"
> label.Y <- c("ADR","Fat","Heart","Kidney")
> my.env <- new.env()
> data(MAP.file,envir=my.env)
> MAP.file <- my.env$MAP.file
> modelY_Hopx <-as.ESS.object(dataY=dataY,dataX=dataX,path.input=path.input,
+     path.output=path.output,root.file.output=root.file.output,label.X=NULL,
+     label.Y=label.Y,path.par=path.par,file.par=file.par,MAP.file=MAP.file)
Warning in gzfile(file, "wb") :
  cannot open compressed file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/R2GUESS/Output/Example-GUESS-Y-Hopx_output_best_visited_models.RData', probable reason 'Read-only file system'
Error in gzfile(file, "wb") : cannot open the connection
Calls: as.ESS.object -> get.best.models -> save -> gzfile
Execution halted
Running ‘testthat.R’ [4s/98s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rcongresso)
  > 
  > test_check("rcongresso")
  ── 1. Failure: Dimensoes do dataframe (@test_votacoes.R#54)  ───────────────────
  dim(votos_pec241) not equal to c(478, 10).
  1/2 mismatches
  [1] 500 - 478 == 22
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 66 SKIPPED: 0 FAILED: 1
  1. Failure: Dimensoes do dataframe (@test_votacoes.R#54) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
This is BibTeX, Version 0.99d (TeX Live 2017/Debian)
The top-level auxiliary file: RcppGSL-intro.aux
I couldn't open database file Rcpp.bib
---line 148 of file RcppGSL-intro.aux
 : \bibdata{Rcpp
 :              }
I'm skipping whatever remains of this command
The style file: jss.bst
I found no database files---while reading file RcppGSL-intro.aux
Warning--I didn't find a database entry for "GSL"
Warning--I didn't find a database entry for "JSS:Rcpp"
Warning--I didn't find a database entry for "Eddelbuettel:2013:Rcpp"
Warning--I didn't find a database entry for "CRAN:Rcpp"
Warning--I didn't find a database entry for "R:Main"
Warning--I didn't find a database entry for "CRAN:RcppArmadillo"
Warning--I didn't find a database entry for "Eddelbuettel+Sanderson:2013:RcppArmadillo"
Warning--I didn't find a database entry for "Sanderson:2010:Armadillo"
Warning--I didn't find a database entry for "CRAN:RcppEigen"
Warning--I didn't find a database entry for "JSS:RcppEigen"
Warning--I didn't find a database entry for "CRAN:inline"
Warning--I didn't find a database entry for "CRAN:Rcpp:Attributes"
(There were 2 error messages)
Error: processing vignette ‘RcppGSL-intro.Rmd’ failed with diagnostics:
Failed to build the bibliography via bibtex
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RcppShark.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [50s/70s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rdomains)
  > 
  > test_check("rdomains")
  DMOZ Data saved to the following destination: . 
  ── 1. Error: shallalist cat (@test-shalla-cat.R#5)  ────────────────────────────
  Timeout was reached: Resolving timed out after 10000 milliseconds
  1: get_shalla_data() at testthat/test-shalla-cat.R:5
  2: curl_download("http://www.shallalist.de/Downloads/shallalist.tar.gz", tmp)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2 SKIPPED: 1 FAILED: 1
  1. Error: shallalist cat (@test-shalla-cat.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [5s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("rglobi")
  Loading required package: rglobi
  ── 1. Failure: interactions subsetted by adding additional information all inter
  dim(unique(rbind(rattusaves, rattus))) not equal to dim(unique(rattus)).
  1/2 mismatches
  [1] 632 - 628 == 4
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 32 SKIPPED: 2 FAILED: 1
  1. Failure: interactions subsetted by adding additional information all interaction types include observations (@test-globi.R#70) 
  
  Error: testthat unit tests failed
  Execution halted
Rjava.init.warning: stack size reduced from unlimited to 7944007 bytes after JVM initialization.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’
File ‘rJava/libs/rJava.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  libjson/Source/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-patched-gcc/Work/PKGS/RJSONIO.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: ape
No ENTREZ API key provided
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Struthioniformes'

Quitting from lines 85-86 (metadata.Rmd) 
Error: processing vignette ‘metadata.Rmd’ failed with diagnostics:
'{"error":"API key invalid","api-key":"","type":"invalid","status":"unknown"}' does not exist in current working directory ('/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RNeXML.Rcheck/vign_test/RNeXML/vignettes').
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for ‘Rpolyhedra’:
 .onLoad failed in loadNamespace() for ‘Rpolyhedra’, details:
  call: gzfile(file, mode)
  error: cannot open the connection
In addition: Warning message:
In gzfile(file, mode) :
  cannot open compressed file ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rpolyhedra/extdata/polyhedra.RDS’, probable reason ‘Read-only file system’
Execution halted
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pushSmetIntoIni
> ### Title: Pushes SMET object file into a 'meteoioini-class' object
> ### Aliases: pushSmetIntoIni
> 
> ### ** Examples
> 
> 
> ini <- as.meteoioini("test")
> 
> AA <- as.smet("test")
> BB <- as.smet("test")
> 
> 
> newini <- pushSmetIntoIni(AA,BB,ini=ini)
Warning in file(con, "w") :
  cannot open file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RSMET/temp/test_station.smet': Read-only file system
Error in file(con, "w") : cannot open the connection
Calls: pushSmetIntoIni -> lapply -> FUN -> print.smet -> <Anonymous> -> file
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rsunlight.Rcheck/00install.out’ for details.
Running examples in ‘satscanMapper-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: satscanMapper
> ### Title: Function to map Results data produced by a SaTScan (TM) cluster
> ###   analysis
> ### Aliases: satscanMapper
> 
> ### ** Examples
> 
> ######
> #
> #  These examples focus on mapping the SaTScan (TM) data after the analysis
> #  has been completed.
> #  See the section on the CreateGeo4SS function for an example of how 
> #  to build a coordinates file (.geo) that matches the satscanMapper 
> #  boundary data.
> #
> ######
> 
> ######
> #
> #  Example # 1 - Mapping existing SaTScan (TM) results - "USStateLung" result files
> #     Make sure SaTScan (TM) results files are still located in the directories
> #     documented in the session saved (.prm) file.
> #
> #     This example maps data for the US States containing circular clusters.
> #
> #   Get location of .prm file and location to write mapping output files
> #
> 
> SSMInstDir <- system.file(package="satscanMapper", "extdata")
> 
> TT =c("Contiguous US States All Lung Cancer Mortality, 2004")
> 
> satscanMapper(resDir=SSMInstDir,                # path to .prm file location for output files. 
+                      prmFile  = "stateLung.prm", 
+                      title    = TT          )
Error in pdf(file = OutputFNpdf, width = vW, height = vH) : 
  cannot open file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/satscanMapper/extdata/stateLung-R01.pdf'
Calls: satscanMapper -> pdf
Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

Loading required package: quickPlot
Loading required package: reproducible

Attaching package: 'reproducible'

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

    %>%

Warning in gzfile(file, mode) :
  cannot open compressed file ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/.snapshot.RDS’, probable reason ‘Read-only file system’
Quitting from lines 326-354 (ii-modules.Rmd) 
Error: processing vignette ‘ii-modules.Rmd’ failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

Loading required package: sp
loading reproducible     0.1.4
loading quickPlot        0.1.3
loading SpaDES.core      0.1.1
loading SpaDES.tools     0.1.1
loading SpaDES.addins    0.1.1

Default paths for SpaDES directories set to:
  cachePath:  /tmp/RtmpP9pC0d/SpaDES/cache
  inputPath:  /tmp/RtmpP9pC0d/SpaDES/inputs
  modulePath: /tmp/RtmpP9pC0d/SpaDES/modules
  outputPath: /tmp/RtmpP9pC0d/SpaDES/outputs
These can be changed using 'setPaths()'. See '?setPaths'.
Quitting from lines 48-61 (iii-cache.Rmd) 
Error: processing vignette ‘iii-cache.Rmd’ failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 30-35 (spThin_vignette.Rmd) 
Error: processing vignette ‘spThin_vignette.Rmd’ failed with diagnostics:
unable to install packages
Execution halted
Running examples in ‘stacomiR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: split_per_day
> ### Title: Create a dataframe suitable for charts per 24h and day
> ### Aliases: split_per_day
> 
> ### ** Examples
> 
> datatemp<-structure(list(per_dis_identifiant = c(1L, 1L, 1L), 
+ per_date_debut = structure(c(1420056600, 
+ 1420071000, 1420081200), class = c("POSIXct", "POSIXt"), tzone = ""), 
+ per_date_fin = structure(c(1420071000, 1420081200, 1421000000
+ ), class = c("POSIXct", "POSIXt"), tzone = ""), per_commentaires = c("fonct calcul", 
+ "fonct calcul", "fonct calcul"), per_etat_fonctionnement = c(1L, 
+ 0L, 0L), per_tar_code = 1:3, libelle = c("Fonc normal", "Arr ponctuel", 
+ "Arr maint")), .Names = c("per_dis_identifiant", "per_date_debut", 
+ "per_date_fin", "per_commentaires", "per_etat_fonctionnement", 
+ "per_tar_code", "libelle"), row.names = c(NA, 3L), class = "data.frame")
> newdf<-split_per_day(data=datatemp,horodatedebut="per_date_debut",
+ horodatefin="per_date_fin")
Error in (function (dt, year, month, yday, mday, wday, hour, minute, second,  : 
  Invalid timezone of input vector: ""
Calls: split_per_day ... reclass_date.POSIXlt -> as.POSIXlt -> do.call -> <Anonymous> -> .Call
Execution halted
Running examples in ‘Stickbreaker-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sim.data.from.priors.for.mod.selection
> ### Title: Simulate data from priors for doing model selection
> ### Aliases: sim.data.from.priors.for.mod.selection
> 
> ### ** Examples
> 
>  n.muts <- 4
>  n.muts <- length(Khan.data[1,])-1
>  geno.matrix <- Khan.data[,seq(1, n.muts)]
>  fit.matrix <- as.matrix(Khan.data[,(n.muts+1)])
>  outdir <- system.file("extdata",package="Stickbreaker")
>  file.name <- paste("Training_simulated_priors_fit_data_", n.muts, "muts.txt", sep="")
>  outpath <- paste(outdir, file.name, sep="/")
>  sim.data.from.priors.for.mod.selection(n.muts,
+    c(0.05, 0.5),
+    c(0, 0.25),
+    c(4),
+    1,
+    c(0.1, 10),
+    1.1,
+    1,
+    c(2,1),
+    outpath,
+    50,
+    coe.sim.model="identical",
+    coe.dist.par=NA,
+    print.interval=NA)
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Stickbreaker/extdata/Training_simulated_priors_fit_data_5muts.txt': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: sim.data.from.priors.for.mod.selection -> write.table -> file
Execution halted
Error in re-building vignettes:
  ...
Installing package into '/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages'
(as 'lib' is unspecified)
Quitting from lines 23-30 (summer-vignette.Rmd) 
Error: processing vignette ‘summer-vignette.Rmd’ failed with diagnostics:
unable to install packages
Execution halted
Error in re-building vignettes:
  ...
Loading required package: data.table
No methods found in package ‘RSQLite’ for request: ‘dbGetQuery’ when loading ‘tcpl’
tcpl (v1.2.2) loaded with the following settings:
  TCPL_DB:    /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/tcpl/sql/tcpldb.sqlite
  TCPL_USER:  NA
  TCPL_HOST:  NA
  TCPL_DRVR:  SQLite
Default settings stored in TCPL.conf. See ?tcplConf for more information.

Error: processing vignette ‘tcpl_Overview.Rnw’ failed with diagnostics:
 chunk 4 
Error in rsqlite_send_query(conn@ptr, statement) : 
  attempt to write a readonly database
Execution halted
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidyinftheo)
  > 
  > test_check("tidyinftheo")
  ── 1. Error: right number of columns given (@test-errors.R#10)  ────────────────
  argument "expr" is missing, with no default
  1: expect_length(tab %>% select(vs) %>% shannon_entropy(), 1) at testthat/test-errors.R:10
  2: quasi_label(enquo(object))
  3: eval_bare(get_expr(quo), get_env(quo))
  4: tab %>% select(vs) %>% shannon_entropy()
  5: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  6: eval(quote(`_fseq`(`_lhs`)), env, env)
  7: eval(quote(`_fseq`(`_lhs`)), env, env)
  8: `_fseq`(`_lhs`)
  9: freduce(value, `_function_list`)
  10: withVisible(function_list[[k]](value))
  11: function_list[[k]](value)
  12: shannon_entropy(.)
  13: reduce_data(.data, !(!enquo(X)), numvars = 1, na.rm = na.rm)
  14: tidyselect::vars_select(names(reduced_tab), !(!(!quos(...))))
  15: vars_select_eval(.vars, quos)
  16: map_lgl(quos, quo_is_helper)
  17: .f(.x[[i]], ...)
  18: extract_expr(quo)
  19: is_call(expr, paren_sym)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 37 SKIPPED: 0 FAILED: 1
  1. Error: right number of columns given (@test-errors.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘TSEtools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mcPrt
> ### Title: Matrix Conversion in Portfolio
> ### Aliases: mcPrt
> 
> ### ** Examples
> 
> fpath<-system.file("extdata", "sample.csv", package="TSEtools")
> asset0<-getTSE(fpath)$assets
proceeding...
SSPF1 compeleted! 
Last observations:
            Open  High   Low Close Volume  <NA>
2018-03-14 10034 10034 10034 10034   2540 10034

proceeding...
KMND1 compeleted! 
Last observations:
           Open High  Low Close Volume <NA>
2018-03-18 9901 9998 9900  9905  21000 9900

proceeding...
FPAF1 compeleted! 
Last observations:
            Open  High   Low Close  Volume  <NA>
2018-03-18 10045 10045 10011 10025 6530249 10044


 SSPF1 KMND1 FPAF1 are assigned!
> rtn<-mcPrt(asset0, sub="2016::", pstvRtn=TRUE, L=5)$return
Values in % base lag= 5 :
      meanReturn volatility sharpRatio
FPAF1          0       1.98       0.18

> 
> 
> 
> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
> base::cat("mcPrt", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> ### * <FOOTER>
> ###
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  1.334 0.024 6.465 0 0 
> grDevices::dev.off()
Error in grDevices::dev.off() : 
  cannot shut down device 1 (the null device)
Execution halted
Running examples in ‘WaterML-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AddMethods
> ### Title: AddMethods
> ### Aliases: AddMethods
> ### Keywords: waterml
> 
> ### ** Examples
> 
> user <- "admin"
> pass <- "password"
> server <- "http://worldwater.byu.edu/app/index.php/default/services/cuahsi_1_1.asmx"
> #make random site codes
> random_description <- sprintf("R Test Method %04d",sample(1:10000, 1))
> random_link <- "http://example.com"
> my_methods <- data.frame(
+   MethodDescription = random_description,
+   MethodLink = random_link
+ )
> 
> added_methods <- AddMethods(server, username=user, password=pass,
+                                 methods=my_methods)
[1] "{\n \"user\": \"admin\",\n\"password\": \"password\",\n\"MethodDescription\": \"R Test Method 2656\",\n\"MethodLink\": \"http://example.com\",\n\"VariableID\":      0 \n}"
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Connection timed out after 10000 milliseconds
Calls: AddMethods ... request_fetch -> request_fetch.write_memory -> <Anonymous> -> .Call
Execution halted
Running examples in ‘WHO-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_data
> ### Title: Retrieve Data from the World Health Organization
> ### Aliases: get_data
> 
> ### ** Examples
> 
> df <- get_data("WHOSIS_000001")
Error: parse error: premature EOF
                                       {   "dimension": [             
                     (right here) ------^
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(WHO)
  > 
  > test_check("WHO")
  ── 1. Error: get_data returns a data frame with positive length (@tests.R#4)  ──
  Please install xml2 package
  1: get_data(dataset) at testthat/tests.R:4
  2: get_result(url)
  3: httr::content(response, "parsed")
  4: parse_auto(raw, type, encoding, ...)
  5: parser(x = content, type = type, encoding = encoding, ...)
  6: need_package("xml2")
  7: stop("Please install ", pkg, " package", call. = FALSE)
  
  ── 2. Error: get_codes returns a data frame with positive length (@tests.R#11)  
  Please install xml2 package
  1: get_codes() at testthat/tests.R:11
  2: get_result(url)
  3: httr::content(response, "parsed")
  4: parse_auto(raw, type, encoding, ...)
  5: parser(x = content, type = type, encoding = encoding, ...)
  6: need_package("xml2")
  7: stop("Please install ", pkg, " package", call. = FALSE)
  
  ── 3. Error: get_codes(TRUE) returns a data frame with positive length and more
  
  Please install xml2 package
  1: get_codes(TRUE) at testthat/tests.R:18
  2: get_result(url)
  3: httr::content(response, "parsed")
  4: parse_auto(raw, type, encoding, ...)
  5: parser(x = content, type = type, encoding = encoding, ...)
  6: need_package("xml2")
  7: stop("Please install ", pkg, " package", call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 3
  1. Error: get_data returns a data frame with positive length (@tests.R#4) 
  2. Error: get_codes returns a data frame with positive length (@tests.R#11) 
  3. Error: get_codes(TRUE) returns a data frame with positive length and more
            than three columns (@tests.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

No encoding supplied: defaulting to UTF-8.
Warning: Unknown or uninitialised column: 'display'.
No encoding supplied: defaulting to UTF-8.
Quitting from lines 64-80 (who_vignette.Rmd) 
Error: processing vignette ‘who_vignette.Rmd’ failed with diagnostics:
Column `region` is unknown
Execution halted
Running examples in ‘yCrypticRNAs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bam_to_reads
> ### Title: Convert BAM files into BED files containing the reads overlaping
> ###   the specified annotations.
> ### Aliases: bam_to_reads
> 
> ### ** Examples
> 
> bamfile <- system.file("extdata", "wt_rep1.bam", package = "yCrypticRNAs")
> data(annotations)
> bam_to_reads(bamfile, annotations)
Error in FUN(X[[i]], ...) : failed to build index
  file: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/yCrypticRNAs/extdata/wt_rep1.bam
Calls: bam_to_reads -> .index_bam
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 48-60 (yCrypticRNAs.Rmd) 
Error: processing vignette ‘yCrypticRNAs.Rmd’ failed with diagnostics:
failed to build index
  file: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/yCrypticRNAs/extdata/wt_rep1.bam
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data       2.8Mb
    pictures   2.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 66-67 (ahn.Rmd) 
Error: processing vignette 'ahn.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 15-19 (ALA4R.Rmd) 
Error: processing vignette 'ALA4R.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
Package required but not available: ‘RWeka’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [228s/304s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > #Copyright © 2016 RTE Réseau de transport d’électricité
  > 
  > require(testthat)
  Loading required package: testthat
  > require(antaresRead)
  Loading required package: antaresRead
  > require(plyr)
  Loading required package: plyr
  > 
  > 
  > #Maybe include this in some test-file.R 
  > #is.solaris<-function(){
  > #  grepl('SunOS',Sys.info()['sysname'])
  > #}
  > 
  > #if(!is.solaris()){
  > 
  > test_check("antaresRead")
  
   *** caught segfault ***
  address 500000e, cause 'memory not mapped'
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 39-73 (antaresH5.Rmd) 
Error: processing vignette 'antaresH5.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘MBESS’
Running examples in ‘apaTables-Ex.R’ failed
The error most likely occurred in:

> ### Name: apa.aov.table
> ### Title: Creates a fixed-effects ANOVA table in APA style
> ### Aliases: apa.aov.table
> 
> ### ** Examples
> 
> #Example 1: 1-way from Field et al. (2012) Discovery Statistics Using R
> options(contrasts = c("contr.sum", "contr.poly"))
> lm_output <- lm(libido ~ dose, data = viagra)
> apa.aov.table(lm_output, filename = "ex1_anova_table.doc")
Error in loadNamespace(name) : there is no package called ‘MBESS’
Calls: apa.aov.table ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Package suggested but not available for checking: ‘kebabs’
Error in re-building vignettes:
  ...

Attaching package: 'apcluster'

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

    heatmap

Quitting from lines 293-307 (apcluster.Rnw) 
Error: processing vignette 'apcluster.Rnw' failed with diagnostics:
object 'apres1b' not found
Execution halted
Running examples in ‘AR1seg-Ex.R’ failed
The error most likely occurred in:

> ### Name: AR1seg-package
> ### Title: Segmentation of an AR(1) Gaussian process
> ### Aliases: AR1seg-package AR1seg
> 
> ### ** Examples
> 
> library(AR1seg)
> data(y)
> res=AR1seg_func(y,Kmax=15,rho=TRUE)
Error in cumsum(datasize)[breaks[k, 1:k]] : 
  only 0's may be mixed with negative subscripts
Calls: AR1seg_func -> Segmentor -> Segmentor.default
Execution halted
Package suggested but not available for checking: ‘qCBA’
Error in re-building vignettes:
  ...
Warning in summary.cross(cross) :
  Some markers at the same position on chr 1B1,1D,2B,2D1,3A,3B,3D,4A,5A,5B,5D,6D,7A,7B,7D; use jittermap().
Warning in summary.cross(cross) :
  Some chromosomes > 1000 cM in length; there may be a problem with the genetic map.
  (Perhaps it is in basepairs?)
Warning in summary.cross(cross) :
  Some markers at the same position on chr L.1,L.2,L.3,L.4,L.5,L.6,L.7,L.8,L.9; use jittermap().
Warning in heatMap(mapBC6, chr = c("L.3", "L.5", "L.8", "L.9"), lmax = 70) :
  Running est.rf.
Warning in summary.cross(cross) :
  Some markers at the same position on chr L.1,L.2,L.3,L.4,L.5,L.6,L.7; use jittermap().
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 173-190 (auk.Rmd) 
Error: processing vignette 'auk.Rmd' failed with diagnostics:
'countrycode_data' is not an exported object from 'namespace:countrycode'
Execution halted
Package required but not available: ‘MBESS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 73.8Mb
  sub-directories of 1Mb or more:
    java  73.8Mb
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 use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   9.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
Package suggested but not available for checking: ‘mzR’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 45-47 (use-ballr.Rmd) 
Error: processing vignette 'use-ballr.Rmd' failed with diagnostics:
Timeout was reached: Resolving timed out after 10010 milliseconds
Execution halted
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    2.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: survival
Quitting from lines 127-155 (hwbart.Rmd) 
Error: processing vignette 'hwbart.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 46-49 (v01-introduction.Rmd) 
Error: processing vignette 'v01-introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/BayesFM.Rcheck/00install.out’ for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.3Mb
    libs   1.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R     1.7Mb
    doc   3.7Mb
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 use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
File ‘BayHap/libs/BayHap.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘mcmc.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘mcmc.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [16s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bcgam)
  Loading required package: nimble
  nimble version 0.6-9 is loaded.
  For more information on NIMBLE and a User Manual,
  please visit http://R-nimble.org.
  
  Attaching package: 'nimble'
  
  The following object is masked from 'package:stats':
  
      simulate
  
  > 
  > test_check("bcgam")
  thin = 1: tau, betalpha, sigma, eta
  ── 1. Error: (unknown) (@testthat.R#3)  ────────────────────────────────────────
  Failed to create the shared library
  1: bcgam(income ~ sm.incr(prestige, space = "E") + sm.conv(education) + type, data = duncan) at testthat/testthat.R:3
  2: bcgam.fit(y, xmat0, shapes0, zmat, nums0, ks0, sps0, nloop, burnin, family, xmatnms0, 
         znms)
  3: compileNimble(gaus)
  4: project$compileModel(units[[i]], control = control, showCompilerOutput = showCompilerOutput)
  5: cppProj$compileFile(compileList, showCompilerOutput)
  6: compileDynamicRegistrations(showCompilerOutput = showCompilerOutput)
  7: compileStaticCode(dllName, cppName, showCompilerOutput)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@testthat.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in predictExtrapUp(alpha, lambda, beta, predictPositionsRescaled[depthIndRange],  :
  Unable to find suitable chronologies for top of core - truncated to date of extraction
Warning in predictExtrapUp(alpha, lambda, beta, predictPositionsRescaled[depthIndRange],  :
  Unable to find suitable chronologies for top of core - truncated to date of extraction
Warning in predictExtrapUp(alpha, lambda, beta, predictPositionsRescaled[depthIndRange],  :
  Unable to find suitable chronologies for top of core - truncated to date of extraction
Warning in predictExtrapUp(alpha, lambda, beta, predictPositionsRescaled[depthIndRange],  :
  Unable to find suitable chronologies for top of core - truncated to date of extraction
Warning in predictExtrapUp(alpha, lambda, beta, predictPositionsRescaled[depthIndRange],  :
  Unable to find suitable chronologies for top of core - truncated to date of extraction
Warning in predictExtrapUp(alpha, lambda, beta, predictPositionsRescaled[depthIndRange],  :
  Unable to find suitable chronologies for top of core - truncated to date of extraction
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.7Mb
Package suggested but not available for checking: ‘BRugs’
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Running examples in ‘berryFunctions-Ex.R’ failed
The error most likely occurred in:

> ### Name: normalizePathCP
> ### Title: normalizePath Cross Platform
> ### Aliases: normalizePathCP
> ### Keywords: file
> 
> ### ** Examples
> 
> 
> normalizePath  ("doesnotexist.file", mustWork=FALSE) # on linux not full path
[1] "doesnotexist.file"
> normalizePathCP("doesnotexist.file") # full path on all platforms
[1] "doesnotexist.file"
> 
> checknp <- function(a,b=a,d=getwd()) 
+   {
+   aa <- normalizePathCP(a)
+   bb <- if(d=="") b else paste0(d,"/",b)
+   if(aa != bb) stop("'", a, "' -> '", aa, "', should be '",bb, "'.")
+   aa
+   }
> 
> checknp("notexist.file")
Error in checknp("notexist.file") : 
  'notexist.file' -> 'notexist.file', should be '/home/ripley/R/packages/tests32/berryFunctions.Rcheck/notexist.file'.
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 183-186 (BETS_basic_usage.Rmd) 
Error: processing vignette 'BETS_basic_usage.Rmd' failed with diagnostics:
invalid time series parameters specified
Execution halted
installed size is 136.9Mb
  sub-directories of 1Mb or more:
    include  136.9Mb
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 use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Removed 199 rows containing non-finite values (stat_contour).
Warning in is.na(verts[, 2]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in is.na(verts[, 3]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in is.na(verts[, 1]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in is.na(verts[, 3]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in is.na(verts[, 1]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in is.na(verts[, 2]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in normalizePath(f2) :
  path[1]="./webshotf164fe7476b.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotf164fe7476b.png': No such file or directory
Quitting from lines 240-243 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc           2.3Mb
    htmlwidgets   1.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 37-44 (billboarder-intro.Rmd) 
Error: processing vignette 'billboarder-intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required but not available: ‘mzR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 64-67 (BioCircos.Rmd) 
Error: processing vignette 'BioCircos.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Parsed with column specification:
cols(
  .default = col_character()
)
See spec(...) for full column specifications.
Parsed with column specification:
cols(
  .default = col_double(),
  FREQ = col_character(),
  Frequency = col_character(),
  REF_AREA = col_character(),
  `Reference area` = col_character(),
  `Time Period` = col_character()
)
See spec(...) for full column specifications.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Quitting from lines 61-79 (BIS.Rmd) 
Error: processing vignette 'BIS.Rmd' failed with diagnostics:
Faceting variables must have at least one value
Execution halted
Invalid maximum heap size: -Xmx4G
The specified size exceeds the maximum representable size.
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’
Running examples in ‘blockcluster-Ex.R’ failed
The error most likely occurred in:

> ### Name: blockcluster
> ### Title: Co-Clustering Package
> ### Aliases: blockcluster
> 
> ### ** Examples
> 
> 
> ## Simple example with simulated binary data
> ## load data
> data(binarydata)
> ## usage of coclusterBinary function in its most simplest form
> out<-coclusterBinary(binarydata,nbcocluster=c(2,3))
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

blockcluster version 4.2.6 loaded

----------------
Copyright (C)  <MODAL team @INRIA,Lille & U.M.R. C.N.R.S. 6599 Heudiasyc, UTC>
Please post questions and bugs at: <https://gforge.inria.fr/forum/forum.php?forum_id=11190&group_id=3679>
Error in re-building vignettes:
  ...

Error: processing vignette 'BoolNet_package_vignette.Snw' failed with diagnostics:
 chunk 13 
Error in (function (interaction, index, gene)  : 
  No values for the "don't care" entries were specified for gene "Fkh2"!
Execution halted
File ‘brainwaver/libs/brainwaver.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘connexity_small_world.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: lattice
Loading required package: ggplot2
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R     2.4Mb
    doc   2.6Mb
Packages suggested but not available for checking: ‘xergm’ ‘btergm’
Package unavailable to check Rd xrefs: ‘btergm’
Package required but not available: ‘RSiena’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘FastRWeb’
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.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
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 use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data     1.8Mb
    models   2.5Mb
Running examples in ‘cdcfluview-Ex.R’ failed
The error most likely occurred in:

> ### Name: age_group_distribution
> ### Title: Age Group Distribution of Influenza Positive Tests Reported by
> ###   Public Health Laboratories
> ### Aliases: age_group_distribution
> 
> ### ** Examples
> 
> age_group_distribution(years=2015)
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
Calls: age_group_distribution ... request_fetch -> request_fetch.write_memory -> <Anonymous> -> .Call
Execution halted
Running examples in ‘CDECRetrieve-Ex.R’ failed
The error most likely occurred in:

> ### Name: cdec_available
> ### Title: Function returns a dataframe of the available data
> ### Aliases: cdec_available
> 
> ### ** Examples
> 
> # get a list of dataframes available for CCR
> cdec_datasets("ccr")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Connection timed out after 10000 milliseconds
Calls: cdec_datasets ... request_fetch -> request_fetch.write_memory -> <Anonymous> -> .Call
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   6.2Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extdata   9.8Mb
Found the following significant warnings:
  "cec_r.c", line 192: warning: improper pointer/integer combination: op "="
  "cec_r.c", line 267: warning: improper pointer/integer combination: op ":"
See ‘/home/ripley/R/packages/tests32/CEC.Rcheck/00install.out’ for details.
Running examples in ‘ChocoLattes-Ex.R’ failed
The error most likely occurred in:

> ### Name: make_productions_page
> ### Title: Generate HTML page with productions list and summary chart
> ### Aliases: make_productions_page
> 
> ### ** Examples
> 
> 
> # Load example data and convert it to a lattes list
> CV.dir <- system.file("extdata", package="ChocoLattes")
> 
> # Define the aliases of authors "Felipe Campelo" and "Lucas S. Batista":
> # (all aliases will be converted to the first name provided for each author)
> my.aliases <- list(c("Felipe Campelo",
+                      "Felipe Campelo Franca Pinto",
+                      "Felipe Campelo F. Pinto",
+                      "F.C.F. Pinto"),
+                    c("Lucas S. Batista",
+                      "Lucas Batista",
+                      "Lucas de Souza Batista",
+                      "Lucas Souza Batista"))
> 
> lattes.list <- lattes_to_list(CV.dir         = CV.dir,
+                               author.aliases = my.aliases)
> 
> 
> # Build productions page:
> make_productions_page(lattes.list,
+                       chart.type     = "ggplot2",
+                       h1.title       = "ORCS Lab",
+                       h2.title       = "UFMG, Brazil",
+                       language       = "EN")
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.6Mb
Running examples in ‘ChoR-Ex.R’ failed
The error most likely occurred in:

> ### Name: ChoR
> ### Title: Getting started with the ChoR package
> ### Aliases: ChoR ChoR-package
> ### Keywords: linear-log-analysis model package
> 
> ### ** Examples
> 
> # Warning: RJava requires to **copy** your data from R into a JVM.
> # If you need extra memory, use this option (here, for 4Gb) **before** loading choR.
> # Note: not needed in our case, kept for the example
> options( java.parameters = "-Xmx4g" )
> library(ChoR)
> 
> ## Test JAVA version
> jv <- rJava::.jcall("java/lang/System", "S", "getProperty", "java.runtime.version")
> jvn <- as.numeric(paste0(strsplit(jv, "[.]")[[1L]][1:2], collapse = "."))
> if(jvn < 1.8){ stop("Java 8 is needed for this package but not available") }
Error: Java 8 is needed for this package but not available
Execution halted
Package suggested but not available for checking: ‘userfriendlyscience’
Package suggested but not available for checking: ‘rggobi’
Installation failed.
See ‘/home/ripley/R/packages/tests32/ClinicalTrialSummary.Rcheck/00install.out’ for details.
*** caught segfault ***
address 0, cause 'memory not mapped'

Traceback:
 1: dyn.load(file, DLLpath = DLLpath, ...)
 2: library.dynam(lib, package, package.lib)
 3: loadNamespace(name)
 4: doTryCatch(return(expr), name, parentenv, handler)
 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6: tryCatchList(expr, classes, parentenv, handlers)
 7: tryCatch(loadNamespace(name), error = function(e) stop(e))
 8: getNamespace(package)
 9: withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessage"))
10: suppressMessages(getNamespace(package))
11: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
12: suppressWarnings(suppressMessages(getNamespace(package)))
13: tools:::.check_code_usage_in_package(package = "clpAPI")
An irrecoverable exception occurred. R is aborting now ...
Running examples in ‘clpAPI-Ex.R’ failed
The error occurred in:


R version 3.4.4 Patched (2018-03-15 r74414) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-pc-solaris2.10 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> pkgname <- "clpAPI"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> library('clpAPI')

 *** caught segfault ***
address 6c, cause 'memory not mapped'

Traceback:
 1: dyn.load(file, DLLpath = DLLpath, ...)
 2: library.dynam(lib, package, package.lib)
 3: loadNamespace(package, lib.loc)
 4: doTryCatch(return(expr), name, parentenv, handler)
 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6: tryCatchList(expr, classes, parentenv, handlers)
 7: tryCatch({    attr(package, "LibPath") <- which.lib.loc    ns <- loadNamespace(package, lib.loc)    env <- attachNamespace(ns, pos = pos, deps)}, error = function(e) {    P <- if (!is.null(cc <- conditionCall(e)))         paste(" in", deparse(cc)[1L])    else ""    msg <- gettextf("package or namespace load failed for %s%s:\n %s",         sQuote(package), P, conditionMessage(e))    if (logical.return)         message(paste("Error:", msg), domain = NA)    else stop(msg, call. = FALSE, domain = NA)})
 8: library("clpAPI")
An irrecoverable exception occurred. R is aborting now ...
Package which this enhances but not available for checking: ‘RWeka’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

error: arma::memory::acquire(): out of memory
Quitting from lines 404-417 (the_clusterR_package.Rmd) 
Error: processing vignette 'the_clusterR_package.Rmd' failed with diagnostics:
std::bad_alloc
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
    pdf   2.8Mb
Running examples in ‘cmpprocess-Ex.R’ failed
The error most likely occurred in:

> ### Name: cmpproc
> ### Title: COM Poisson Process Parameter Estimation.
> ### Aliases: cmpproc
> 
> ### ** Examples
> 
> ## Standard usage
> data(floodcount)
> cmpproc(floodcount$Counts)
Error in solve.default(H) : 
  system is computationally singular: reciprocal condition number = 0
Calls: cmpproc -> single.cmp -> diag -> solve -> solve.default
Execution halted
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data     3.8Mb
    exdata   5.5Mb
Found the following significant warnings:
  "collapsed_lpcm.c", line 74: warning: improper pointer/integer combination: op ">"
See ‘/home/ripley/R/packages/tests32/collpcm.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data      6.5Mb
    extdata   2.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 49-50 (chamber.Rmd) 
Error: processing vignette 'chamber.Rmd' failed with diagnostics:
Timeout was reached: Resolving timed out after 10000 milliseconds
Execution halted
Package suggested but not available for checking: ‘MonetDBLite’
Running examples in ‘cooccurNet-Ex.R’ failed
The error most likely occurred in:

> ### Name: coocnet
> ### Title: coocnet
> ### Aliases: coocnet
> 
> ### ** Examples
> 
> cooccurNetwork  = coocnet(dataFile=getexample(dataType="protein"), dataType="protein")
reading file......
completed. (10,329)
preprocess file......Error in if (pred >= memsize * alpha || ncol > 150 || (nrow > 30000 &  : 
  missing value where TRUE/FALSE needed
Calls: coocnet ... cooccur.dataprepreprocess.preprocess -> inmemoryflag
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 176-178 (Extending-cooccurNet.Rmd) 
Error: processing vignette 'Extending-cooccurNet.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
Execution halted
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    R     2.3Mb
    doc   7.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: mvtnorm
Loading required package: RMTstat
Loading required package: grid
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: fit.models
Loading required package: foreach
Loading required package: PerformanceAnalytics

Attaching package: 'PerformanceAnalytics'

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

    legend

Loading required package: rugarch
Loading required package: parallel

Attaching package: 'rugarch'

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

    sigma


Attaching package: 'rmgarch'

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

    first, last

Quitting from lines 217-225 (CovarianceEstimation.Rmd) 
Error: processing vignette 'CovarianceEstimation.Rmd' failed with diagnostics:
all(sapply(args, function(x) is.zoo(x) || !is.plain(x) || (is.plain(x) &&  .... is not TRUE
Execution halted
Found the following significant warnings:
  "bdsmatrix_stub.h", line 44: warning: improper pointer/integer combination: op "="
  "bdsmatrix_stub.h", line 53: warning: improper pointer/integer combination: op "="
See ‘/home/ripley/R/packages/tests32/coxme.Rcheck/00install.out’ for details.
Package required but not available: ‘rJPSGCS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/ripley/R/packages/tests32/csp.Rcheck/00install.out’ for details.
Package required but not available: ‘OpenMx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/ripley/R/packages/tests32/CuCubes.Rcheck/00install.out’ for details.
installed size is 32.2Mb
  sub-directories of 1Mb or more:
    extdata  32.2Mb
Running ‘testthat.R’ [6s/191s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(curl)
  > 
  > test_check("curl")
  This is libcurl version 7.56.1 with OpenSSL/1.0.2m 
  Using test server: http://hb.opencpu.org 
  ── 1. Error: IDN domain names (@test-idn.R#8)  ─────────────────────────────────
  SSL: no alternative certificate subject name matches target host name 'www.xn--malm-8qa.se'
  1: expect_is(curl::curl_fetch_memory(enc2utf8(malmo))$status_code, "integer") at testthat/test-idn.R:8
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: curl::curl_fetch_memory(enc2utf8(malmo))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 164 SKIPPED: 3 FAILED: 1
  1. Error: IDN domain names (@test-idn.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘CVXR-Ex.R’ failed
The error most likely occurred in:

> ### Name: diag,Expression-method
> ### Title: Matrix Diagonal
> ### Aliases: diag,Expression-method diag
> 
> ### ** Examples
> 
> C <- Variable(3,3)
> obj <- Maximize(C[1,3])
> constraints <- list(diag(C) == 1, C[1,2] == 0.6, C[2,3] == -0.3, C == Semidef(3))
> prob <- Problem(obj, constraints)
> result <- solve(prob)

 *** caught segfault ***
address 0, cause 'memory not mapped'

Traceback:
 1: .Call("scsr", data, cone, control, PACKAGE = "scs")
 2: (function (A, b, obj, cone, control = list(max_iters = 2500L,     normalize = TRUE, verbose = FALSE, cg_rate = 2, scale = 5,     rho_x = 0.001, alpha = 1.5, eps = 1e-06)) {    if (class(A) == "simple_triplet_matrix") {        A <- sparseMatrix(i = A$i, j = A$j, x = A$v, dims = c(A$nrow,             A$ncol))    }    else {        A <- as(A, "dgCMatrix")    }    data <- list(m = dim(A)[1], n = dim(A)[2], Ax = A@x, Ai = A@i,         Ap = A@p, b = b, c = obj)    ret <- .Call("scsr", data, cone, control, PACKAGE = "scs")    return(ret)})(A = <S4 object of class "dgCMatrix">, b = c(1, 1, 1, 0.6, -0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), obj = c(0, 0, 0, 0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 0, 0), cone = list(f = 14,     l = 0, ep = 0, s = 3), control = list(verbose = FALSE))
 3: do.call(scs::scs, c(scs_args, list(control = solver_opts)))
 4: Solver.solve(solver, objective, constraints, object@.cached_data,     warm_start, verbose, ...)
 5: Solver.solve(solver, objective, constraints, object@.cached_data,     warm_start, verbose, ...)
 6: CVXR::psolve(a, b, ...)
 7: CVXR::psolve(a, b, ...)
 8: solve.Problem(prob)
 9: solve(prob)
An irrecoverable exception occurred. R is aborting now ...
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 177-179 (cycling_data_analysis.Rmd) 
Error: processing vignette 'cycling_data_analysis.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/Cyclops.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 27-38 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    img   4.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    Pied_Flycatchers_1   2.5Mb
    Pied_Flycatchers_2   1.3Mb
    doc                  1.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot2884661c2768.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot2884661c2768.png': No such file or directory
Quitting from lines 57-68 (dataexplorer-intro.Rmd) 
Error: processing vignette 'dataexplorer-intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
sh: whoami:  not found
sh: git:  not found
Error in fallback_or_stop(fallback, "Cannot determine full name") : 
  Cannot determine full name
Data report generation is finished. Please wait while your output file is being rendered.
Quitting from lines 729-768 (extending_dataMaid.Rmd) 
Error: processing vignette 'extending_dataMaid.Rmd' failed with diagnostics:
pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   5.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot3390d435e.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot3390d435e.png': No such file or directory
Quitting from lines 512-515 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running examples in ‘dbarts-Ex.R’ failed
The error most likely occurred in:

> ### Name: bart
> ### Title: Bayesian Additive Regression Trees
> ### Aliases: bart bart2 plot.bart predict.bart
> ### Keywords: nonparametric tree regression nonlinear
> 
> ### ** Examples
> 
> ## simulate data (example from Friedman MARS paper)
> ## y = f(x) + epsilon , epsilon ~ N(0, sigma)
> ## x consists of 10 variables, only first 5 matter
> 
> f <- function(x) {
+     10 * sin(pi * x[,1] * x[,2]) + 20 * (x[,3] - 0.5)^2 +
+       10 * x[,4] + 5 * x[,5]
+ }
> 
> set.seed(99)
> sigma <- 1.0
> n     <- 100
> 
> x  <- matrix(runif(n * 10), n, 10)
> Ey <- f(x)
> y  <- rnorm(n, Ey, sigma)
> 
> ## run BART
> set.seed(99)
> bartFit <- bart(x, y)
Error in .Object$initialize(...) : adaptive radix tree not aligned
Calls: bart ... new -> initialize -> initialize -> <Anonymous> -> .Call
Execution halted
Package suggested but not available for checking: ‘RMariaDB’
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    sample_data   3.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Joining, by = "key"
Joining, by = "key"
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 102-122 (sjukhus.Rmd) 
Error: processing vignette 'sjukhus.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Rcpp

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Joining, by = "gene"
Joining, by = "cell"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "cell"
Joining, by = c("cell", "capture")
Have 35 cells after filtering
Joining, by = "cell"
Have 20 genes after filtering
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "cell"
Joining, by = c("cell", "capture")
Compiling model
Quitting from lines 145-146 (DeLorean.Rmd) 
Error: processing vignette 'DeLorean.Rmd' failed with diagnostics:
Compilation ERROR, function(s)/method(s) not created! "/home/ripley/R/Lib32/StanHeaders/include/stan/math/memory/stack_alloc.hpp", line 39: Error: The function "malloc" must have a prototype.
"/home/ripley/R/Lib32/StanHeaders/include/stan/math/memory/stack_alloc.hpp", line 148: Error: The function "free" must have a prototype.
"/home/ripley/R/Lib32/StanHeaders/include/stan/math/memory/stack_alloc.hpp", line 235: Error: The function "free" must have a prototype.
"/home/ripley/R/Lib32/BH/include/boost/config/compiler/sunpro_cc.hpp", line 117: Warning (Anachronism): Attempt to redefine BOOST_NO_CXX11_RVALUE_REFERENCES without using #undef.
"/home/ripley/R/Lib32/RcppEigen/include/Eigen/src/SparseCore/SparseCwiseUnaryOp.h", line 49: Error: Cannot define member of undefined specialization "unary_evaluator<CwiseUnaryOp<UnaryOp, ArgType>, Eigen::internal::IteratorBased>".
"/home/ripley/R/Lib32/RcppEigen/include/Eigen/src/Spars
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

---------------------
Welcome to dendextend version 1.7.0
Type citation('dendextend') for how to cite the package.

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

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

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


Attaching package: 'dendextend'

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

    cutree

Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'gplots'

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

    bluered, greenred

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

    lowess

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 931-933 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages suggested but not available for checking:
  ‘gurobi’ ‘Rcplex’ ‘Rsymphony’
Running ‘testthat.R’ [305s/329s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(detrendr)
  > 
  > test_check("detrendr")
  ── 1. Failure: best_tau works (@test-best_params.R#10)  ────────────────────────
  round(best_tau(img, seed = 7)) not equal to 6618.
  1/1 mismatches
  [1] NA - 6618 == NA
  
  ── 2. Failure: best_l works (@test-best_params.R#22)  ──────────────────────────
  round(best_tau(img, seed = 7)) not equal to 28372.
  1/1 mismatches
  [1] NA - 28372 == NA
  
  ── 3. Failure: best_l works (@test-best_params.R#27)  ──────────────────────────
  `best_l(img)` did not throw an error.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 75 SKIPPED: 0 FAILED: 3
  1. Failure: best_tau works (@test-best_params.R#10) 
  2. Failure: best_l works (@test-best_params.R#22) 
  3. Failure: best_l works (@test-best_params.R#27) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘dggridR-Ex.R’ failed
The error most likely occurred in:

> ### Name: dgearthgrid
> ### Title: Return the coordinates constituting the boundary of cells for
> ###   the entire Earth
> ### Aliases: dgearthgrid
> 
> ### ** Examples
> 
> library(dggridR)
> dggs <- dgconstruct(res=20)
> res  <- dg_closest_res_to_spacing(dggs,spacing=1000,round='down',metric=FALSE)
Resolution: 3, Area (mi^2): 1173851.79791229, Spacing (mi): 843.496246531418, CLS (mi): 964.285490648183
> dggs <- dgsetres(dggs,res)
> gridfilename <- dgearthgrid(dggs,savegrid=TRUE) #Save directly to a file
Error: is.character(dsn) is not TRUE
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: rgl
Loading required namespace: rmarkdown
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 230-234 (DGVM3D.Rmd) 
Error: processing vignette 'DGVM3D.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘rsvg’
Running ‘testthat.R’ [223s/295s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(diceR)
  > 
  > test_check("diceR")
  Selecting k and imputing non-clustered cases
  Computing consensus functions
  Evaluating output with consensus function results
  Diverse Cluster Ensemble Completed
  Selecting k and imputing non-clustered cases
  Computing consensus functions
  Evaluating output with consensus function results
  Diverse Cluster Ensemble Completed
  Selecting k and imputing non-clustered cases
  Computing consensus functions
  Evaluating output with consensus function results
  Diverse Cluster Ensemble Completed
  Selecting k and imputing non-clustered cases
  Computing consensus functions
  Diverse Cluster Ensemble Completed
  Selecting k and imputing non-clustered cases
  Computing consensus functions
  Diverse Cluster Ensemble Completed
  Selecting k and imputing non-clustered cases
  Computing consensus functions
  Diverse Cluster Ensemble Completed
  Selecting k and imputing non-clustered cases
  Computing consensus functions
  Diverse Cluster Ensemble Completed
  Error: C stack usage  236743488 is too close to the limit
  
  error: Mat::col(): index out of bounds
  
  error: Mat::col(): index out of bounds
  terminate called recursively
  terminate called after throwing an instance of 'std::logic_error
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    include  18.3Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/DMMF.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: cOde

Attaching package: 'dMod'

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

    profile

"jakstat.c", line 6: zero or negative subscript
"jakstat.c", line 7: zero or negative subscript
cc: acomp failed for jakstat.c
make: Fatal error: Command failed for target `jakstat.o'
Current working directory /home/ripley/R/packages/tests32/dMod.Rcheck/vign_test/dMod/vignettes
Warning: running command '/home/ripley/R/cc/bin/R CMD SHLIB jakstat.c' had status 1 and error message 'Illegal seek'
"jakstat_s.c", line 6: zero or negative subscript
"jakstat_s.c", line 7: zero or negative subscript
cc: acomp failed for jakstat_s.c
make: Fatal error: Command failed for target `jakstat_s.o'
Current working directory /home/ripley/R/packages/tests32/dMod.Rcheck/vign_test/dMod/vignettes
Warning: running command '/home/ripley/R/cc/bin/R CMD SHLIB jakstat_s.c' had status 1 and error message 'Illegal seek'
Quitting from lines 73-83 (dMod.Rmd) 
Error: processing vignette 'dMod.Rmd' failed with diagnostics:
'initfunc' not loaded  jakstat_s_initmod
Execution halted
File ‘DPpackage/libs/DPpackage.so’:
  Found ‘__f90_close’, possibly from ‘close’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDBDPdensity.o’, ‘LDDPdensity.o’,
      ‘LDDPsurvival.o’, ‘LDPDdoublyintsba.o’, ‘LDTFPdensity.o’,
      ‘LDTFPglmmpois.o’, ‘LDTFPsurvival.o’, ‘PSgamgam.o’,
      ‘PSgamgauss.o’, ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’,
      ‘ToolsLDTFP.o’
  Found ‘__f90_esuw’, possibly from ‘write’ (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’
  Found ‘__f90_open’, possibly from ‘open’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDBDPdensity.o’, ‘LDDPdensity.o’,
      ‘LDDPsurvival.o’, ‘LDPDdoublyintsba.o’, ‘LDTFPdensity.o’,
      ‘LDTFPglmmpois.o’, ‘LDTFPsurvival.o’, ‘PSgamgam.o’,
      ‘PSgamgauss.o’, ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’,
      ‘ToolsLDTFP.o’
  Found ‘__f90_rewind’, possibly from ‘rewind’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDDPdensity.o’, ‘LDDPsurvival.o’,
      ‘LDPDdoublyintsba.o’, ‘PSgamgam.o’, ‘PSgamgauss.o’,
      ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’, ‘ToolsLDTFP.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    shinyapps   5.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    lucc_MT   3.4Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    doc    1.6Mb
    libs   1.5Mb
Package required but not available: ‘OpenMx’

Package suggested but not available for checking: ‘rpf’

See section ‘The DESCRIPTION file’ 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 use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    hac    4.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
    doc    1.3Mb
Error in re-building vignettes:
  ...
Loading required package: foreign
This is vegdata 0.9.1

No Turbowin installation path found. 

############################################################
Turboveg root directory is set to "/tmp/Rtmps4aOjU"
If you want to change this use: options(tv_home="<path_to_your_Turbowin_root>")
############################################################
Quitting from lines 51-61 (eHOF.Rnw) 
Error: processing vignette 'eHOF.Rnw' failed with diagnostics:
unsupported conversion from 'CP437' to ''
Execution halted
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 use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [23s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if (packageVersion("testthat") >= "0.9.1") {
  +   library(testthat)
  +   test_check("emil")
  + }
  Loading required package: emil
  
  Attaching package: 'emil'
  
  The following object is masked from 'package:base':
  
      mode
  
  ── 1. Error: glmnet (@test-methods.r#23)  ──────────────────────────────────────
  dim(X) must have a positive length
  1: fit_glmnet(iris[-5], iris$Species) at testthat/test-methods.r:23
  2: glmnet::cv.glmnet(x, y, family = family, nfolds = nfolds, foldid = foldid, alpha = alpha, 
         lambda = lambda, ...)
  3: apply(nz, 1, median)
  4: stop("dim(X) must have a positive length")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 182 SKIPPED: 1 FAILED: 1
  1. Error: glmnet (@test-methods.r#23) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘emIRT-Ex.R’ failed
The error most likely occurred in:

> ### Name: dynIRT
> ### Title: Dynamic IRT estimation via Variational Inference
> ### Aliases: dynIRT
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> 
> ### Replication of Martin-Quinn Judicial Ideology Scores
> ### Based on July 23, 2014 (2014 Release 01) release of the Supreme Court Database
> ### Start values and priors based on replication code provided by Kevin Quinn
> 
> data(mq_data)
> 
> ## Estimate dynamic variational model using dynIRT()
> lout <- dynIRT(.data = mq_data$data.mq,
+                     .starts = mq_data$cur.mq,
+                     .priors = mq_data$priors.mq,
+                     .control = {list(
+                     threads = 1,
+                     verbose = TRUE,
+                     thresh = 1e-6,
+ 		    maxit=500
+                     )})

==================== 
dynIRT: Dynamic IRT via Variational Inference


error: inv_sympd(): matrix is singular or not positive definite
terminate called after throwing an instance of 'std::runtime_error'
  what():  inv_sympd(): matrix is singular or not positive definite
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    xsd   5.9Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.6Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    help   3.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot66993eb2666.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot66993eb2666.png': No such file or directory
Quitting from lines 150-151 (epicontacts.Rmd) 
Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages unavailable to check Rd xrefs: ‘MBESS’, ‘OpenMx’
Packages required but not available: ‘SNPRelate’ ‘gdsfmt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   6.2Mb
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    exiftool  13.7Mb
Running ‘testthat.R’ [46s/56s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(exifr)
  Using ExifTool version 10.61
  > 
  > test_check("exifr")
  ── 1. Failure: quiet argument supresses messages (@test_read_exif.R#24)  ───────
  `read_exif(test_files)` produced warnings.
  
  ── 2. Failure: recursive option works (@test_read_exif.R#32)  ──────────────────
  `read_exif(images_folder, recursive = TRUE)` produced warnings.
  
  ── 3. Failure: recursive option works (@test_read_exif.R#34)  ──────────────────
  `read_exif(system.file("", package = "exifr"), recursive = TRUE)` produced warnings.
  
    % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                   Dload  Upload   Total   Spent    Left  Speed
  
    0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
    0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
    0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0
    0     0    0     0    0     0      0      0 --:--:--  0:00:03 --:--:--     0
    0     0    0     0    0     0      0      0 --:--:--  0:00:03 --:--:--     0
  100 2838k  100 2838k    0     0   709k      0  0:00:04  0:00:04 --:--:--  619k
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 42 SKIPPED: 0 FAILED: 3
  1. Failure: quiet argument supresses messages (@test_read_exif.R#24) 
  2. Failure: recursive option works (@test_read_exif.R#32) 
  3. Failure: recursive option works (@test_read_exif.R#34) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘expm-Ex.R’ failed
The error most likely occurred in:

> ### Name: logm
> ### Title: Matrix Logarithm
> ### Aliases: logm
> ### Keywords: algebra math
> 
> ### ** Examples
> 
> m <- diag(2)
> logm(m)
     [,1] [,2]
[1,]    0    0
[2,]    0    0
> expm(logm(m))
     [,1] [,2]
[1,]    1    0
[2,]    0    1
> 
> ## Here, logm() is barely defined, and Higham08 has needed an amendment
> ## in order for not to loop forever:
> D0 <- diag(x=c(1, 0.))
> (L. <- logm(D0))
Warning in logm.Higham08(x) :
  Inverse scaling did not work (t = 1).
The matrix logarithm may not exist for this matrix.Setting m = 3 arbitrarily.
     [,1]     [,2]
[1,]    0        0
[2,]    0 -9576994
> stopifnot( all.equal(D0, expm(L.)) )
> 
> ## A matrix for which clearly no logm(.) exists:
> (m <- cbind(1:2, 1))
     [,1] [,2]
[1,]    1    1
[2,]    2    1
> (l.m <- logm(m)) ## all NA
Warning in sqrt(S[ij, ij]) : NaNs produced
Error in solve.default(X[ii, ii] + X[ij, ij], S[ii, ij] - sumU) : 
  system is computationally singular: reciprocal condition number = 0
Calls: logm ... logm.Higham08 -> rootS -> solve -> solve -> solve.default
Execution halted
Package suggested but not available for checking: ‘RWeka’
Package unavailable to check Rd xrefs: ‘RWeka’
Running ‘run-all.R’
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("farff")
  Loading required package: farff
  ── 1. Error: quick test with small arffs (@test_quick.R#6)  ────────────────────
  there is no package called 'RWeka'
  1: compareRWeka(INST_ARFF_DIR, "iris.arff", data.reader = dreader) at testthat/test_quick.R:6
  2: RWeka::read.arff at /home/ripley/R/packages/tests32/farff.Rcheck/tests/testthat/helper.R:17
  3: getExportedValue(pkg, name)
  4: asNamespace(ns)
  5: getNamespace(ns)
  6: tryCatch(loadNamespace(name), error = function(e) stop(e))
  7: tryCatchList(expr, classes, parentenv, handlers)
  8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 8 SKIPPED: 0 FAILED: 1
  1. Error: quick test with small arffs (@test_quick.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
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.
Package suggested but not available for checking: ‘Rserve’
Installation failed.
See ‘/home/ripley/R/packages/tests32/FastRWeb.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [12s/121s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(FedData)
  Loading required package: sp
  > 
  > test_check("FedData")
  ── 1. Error: The SSURGO inventory dataset is available at the correct URL (@test
  Timeout was reached: Operation timed out after 10660 milliseconds with 0 out of 0 bytes received
  1: expect_false(suppressWarnings(httr::http_error(url))) at testthat/test.SSURGO.R:8
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: suppressWarnings(httr::http_error(url))
  5: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  6: httr::http_error(url)
  7: http_error.character(url)
  8: http_error(HEAD(x, ...))
  9: HEAD(x, ...)
  10: request_perform(req, hu$handle$handle)
  11: request_fetch(req$output, req$url, handle)
  12: request_fetch.write_memory(req$output, req$url, handle)
  13: curl::curl_fetch_memory(url, handle = handle)
  
  ── 2. Failure: The SSURGO datasets are available at the correct URL (@test.SSURG
  `suppressWarnings(curl::curl(url) %>% readLines(n = 1))` threw an error.
  Message: Timeout was reached: Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
  Class:   simpleError/error/condition
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 25 SKIPPED: 0 FAILED: 2
  1. Error: The SSURGO inventory dataset is available at the correct URL (@test.SSURGO.R#8) 
  2. Failure: The SSURGO datasets are available at the correct URL (@test.SSURGO.R#32) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  In codeBufCode(cb, cntxt) :
    closing unused connection 3 (https://websoilsurvey.sc.egov.usda.gov/DSD/Download/Cache/SSA/wss_SSA_CO670_[2017-09-06].zip)
  Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 70-72 (lifeExpectancy.Rmd) 
Error: processing vignette 'lifeExpectancy.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
Package suggested but not available for checking: ‘multipanelfigure’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    fonts   6.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    fonts   7.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 168-169 (formattable-data-frame.Rmd) 
Error: processing vignette 'formattable-data-frame.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R   5.8Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
    doc    1.6Mb
Package unavailable to check Rd xrefs: ‘RMark’
Packages suggested but not available for checking: ‘RWeka’ ‘FSelector’
Package unavailable to check Rd xrefs: ‘FSelector’
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(FSelectorRcpp)
  > library(Matrix)
  > library(Rcpp)
  > library(RcppArmadillo)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > library(entropy)
  
  Attaching package: 'entropy'
  
  The following object is masked from 'package:FSelectorRcpp':
  
      discretize
  
  > library(lintr)
  > 
  > test_check("FSelectorRcpp")
  ── 1. Error: (unknown) (@test-cutoff.R#2)  ─────────────────────────────────────
  there is no package called 'FSelector'
  1: library(FSelector) at testthat/test-cutoff.R:2
  2: stop(txt, domain = NA)
  
  ── 2. Error: (unknown) (@test-discretize.R#2)  ─────────────────────────────────
  there is no package called 'FSelector'
  1: library(FSelector) at testthat/test-discretize.R:2
  2: stop(txt, domain = NA)
  
  ── 3. Error: (unknown) (@test-information_gain.R#2)  ───────────────────────────
  there is no package called 'FSelector'
  1: library(FSelector) at testthat/test-information_gain.R:2
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 22 SKIPPED: 0 FAILED: 3
  1. Error: (unknown) (@test-cutoff.R#2) 
  2. Error: (unknown) (@test-discretize.R#2) 
  3. Error: (unknown) (@test-information_gain.R#2) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 42-45 (benchmarks_discretize.Rmd) 
Error: processing vignette 'benchmarks_discretize.Rmd' failed with diagnostics:
there is no package called 'RWeka'
Execution halted
installed size is  5.1Mb
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    examples   4.6Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    data  16.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 604-605 (futureheatwaves.Rmd) 
Error: processing vignette 'futureheatwaves.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.4Mb
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    extdata   1.7Mb
    libs      1.9Mb
Error in re-building vignettes:
  ...
Warning in packageDescription("gputools") :
  no package 'gputools' was found
Error: processing vignette 'gcbd.Rnw' failed with diagnostics:
at gcbd.Rnw:860, subscript out of bounds
Execution halted
installed size is  5.9Mb
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Package suggested but not available for checking: ‘reactome.db’
installed size is  5.5Mb
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    doc        1.5Mb
    examples   1.9Mb
    vign       1.4Mb
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    data  27.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.1-2 (2017-12-21) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

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

    backsolve, forwardsolve

Loading required package: maps
See www.image.ucar.edu/~nychka/Fields for
 a vignette and other supplements. 
New output format of RFsimulate: S4 object of class 'RFsp';
for a bare, but faster array format use 'RFoptions(spConform=FALSE)'.

     PLEASE NOTE:  The components "delsgs" and "summary" of the
 object returned by deldir() are now DATA FRAMES rather than
 matrices (as they were prior to release 0.0-18).
 See help("deldir").
 
     PLEASE NOTE: The process that deldir() uses for determining
 duplicated points has changed from that used in version
 0.0-9 of this package (and previously). See help("deldir").


Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 93-95 (zoningSimu.Rmd) 
Error: processing vignette 'zoningSimu.Rmd' failed with diagnostics:
dim(X) must have a positive length
Execution halted
Running examples in ‘gesis-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_study_groups
> ### Title: Get a dataframe with all available groups of studies
> ### Aliases: get_study_groups
> 
> ### ** Examples
> 
> groups <- get_study_groups()
Error in open.connection(x, "rb") : 
  Timeout was reached: Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
Calls: get_study_groups -> read_html -> read_html.default
Execution halted
Running ‘testthat.R’ [3s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(gesis)
  > 
  > test_check("gesis")
  ── 1. Error: get_study_groups() works (@test-availability.R#4)  ────────────────
  Timeout was reached: Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
  1: get_study_groups() at testthat/test-availability.R:4
  2: read_html(url)
  3: read_html.default(url)
  4: suppressWarnings(read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options))
  5: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  6: read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options)
  7: read_xml.character(x, encoding = encoding, ..., as_html = TRUE, options = options)
  8: read_xml.connection(con, encoding = encoding, ..., as_html = as_html, base_url = x, 
         options = options)
  9: open(x, "rb")
  10: open.connection(x, "rb")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2 SKIPPED: 0 FAILED: 1
  1. Error: get_study_groups() works (@test-availability.R#4) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  In as.list(elist) :
    closing unused connection 3 (https://dbk.gesis.org/dbksearch/gdesc.asp?db=e)
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 60-61 (gesis.Rmd) 
Error: processing vignette 'gesis.Rmd' failed with diagnostics:
Timeout was reached: Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for ‘ggdmc’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/ripley/R/Lib32/ggdmc/libs/ggdmc.so':
  ld.so.1: R: fatal: relocation error: file /home/ripley/R/Lib32/ggdmc/libs/ggdmc.so: symbol GOMP_parallel: referenced symbol not found
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot58901fba01.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot58901fba01.png': No such file or directory
Quitting from lines 28-33 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running ‘testthat.R’ [32s/36s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ggplot2)
  > 
  > test_check("ggplot2")
  ── 1. Failure: inherits timezone from data (@test-scale-date.R#18)  ────────────
  sc$timezone not equal to NULL.
  Types not compatible: character is not NULL
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 804 SKIPPED: 1 FAILED: 1
  1. Failure: inherits timezone from data (@test-scale-date.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘RSelenium’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 125-126 (ggsdc.Rmd) 
Error: processing vignette 'ggsdc.Rmd' failed with diagnostics:
Process terminated
Execution halted
Package which this enhances but not available for checking: ‘BRugs’
Running examples in ‘glmnet-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot.cv.glmnet
> ### Title: plot the cross-validation curve produced by cv.glmnet
> ### Aliases: plot.cv.glmnet
> ### Keywords: models regression
> 
> ### ** Examples
> 
> set.seed(1010)
> n=1000;p=100
> nzc=trunc(p/10)
> x=matrix(rnorm(n*p),n,p)
> beta=rnorm(nzc)
> fx= (x[,seq(nzc)] %*% beta)
> eps=rnorm(n)*5
> y=drop(fx+eps)
> px=exp(fx)
> px=px/(1+px)
> ly=rbinom(n=length(px),prob=px,size=1)
> cvob1=cv.glmnet(x,y)
Error in intI(j, n = x@Dim[2], dn[[2]], give.dn = FALSE) : 
  'NA' indices are not (yet?) supported for sparse Matrices
Calls: cv.glmnet ... NextMethod -> predict.glmnet -> [ -> [ -> subCsp_cols -> intI
Execution halted
Running examples in ‘glmnetUtils-Ex.R’ failed
The error most likely occurred in:

> ### Name: cv.glmnet
> ### Title: Formula interface for elastic net cross-validation with
> ###   cv.glmnet
> ### Aliases: cv.glmnet cv.glmnet.default cv.glmnet.formula
> ###   predict.cv.glmnet.formula coef.cv.glmnet.formula
> ###   print.cv.glmnet.formula
> 
> ### ** Examples
> 
> cv.glmnet(mpg ~ ., data=mtcars)
Call:
cv.glmnet.formula(formula = mpg ~ ., data = mtcars)

Model fitting options:
    Sparse model matrix: FALSE
    Use model.frame: FALSE
    Number of crossvalidation folds: 10
    Alpha: 1
    Deviance-minimizing lambda: 0.7295713  (+1 SE): 1.535678
> 
> cv.glmnet(Species ~ ., data=iris, family="multinomial")
Error in apply(nz, 1, median) : dim(X) must have a positive length
Calls: cv.glmnet -> cv.glmnet.formula -> <Anonymous> -> apply
Execution halted
Running ‘testthat.R’ [35s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv(R_TESTS="")  # needed for cluster creation to work
  > 
  > library(testthat)
  > library(glmnetUtils)
  > 
  > test_check("glmnetUtils")
  ── 1. Error: parallel foreach works (@test2_cv_glmnet.R#72)  ───────────────────
  dim(X) must have a positive length
  1: cv.glmnet(x, y, family = "multinomial", nfolds = 5, parallel = TRUE) at testthat/test2_cv_glmnet.R:72
  2: cv.glmnet.default(x, y, family = "multinomial", nfolds = 5, parallel = TRUE)
  3: glmnet::cv.glmnet(x, y, ...)
  4: apply(nz, 1, median)
  5: stop("dim(X) must have a positive length")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 118 SKIPPED: 1 FAILED: 1
  1. Error: parallel foreach works (@test2_cv_glmnet.R#72) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘gnmf/libs/gnmf.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘FactorMatrix.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘FactorMatrix.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 34-35 (installation-and-authentication.Rmd) 
Error: processing vignette 'installation-and-authentication.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.5Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R   5.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Running ‘testthat.R’ [33m/11m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(grf)
  > 
  > test_check("grf")
Installation failed.
See ‘/home/ripley/R/packages/tests32/GSCAD.Rcheck/00install.out’ for details.
installed size is 126.4Mb
  sub-directories of 1Mb or more:
    java  124.8Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    data   9.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 122-128 (Basic_use.Rmd) 
Error: processing vignette 'Basic_use.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/hdf5r.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Loading required package: viridis
Loading required package: viridisLite

======================
Welcome to heatmaply version 0.14.1

Type citation('heatmaply') for how to cite the package.
Type ?heatmaply for the main documentation.

The github page is: https://github.com/talgalili/heatmaply/
Please submit your suggestions and bug-reports at: https://github.com/talgalili/heatmaply/issues
Or contact: <tal.galili@gmail.com>
======================

Quitting from lines 88-90 (heatmaply.Rmd) 
Error: processing vignette 'heatmaply.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    doc          13.8Mb
    htmlwidgets   2.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Highcharts (www.highcharts.com) is a Highsoft software product which is
not free for commercial and Governmental use
Quitting from lines 45-46 (charting-data-frames.Rmd) 
Error: processing vignette 'charting-data-frames.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package which this enhances but not available for checking: ‘RProtoBuf’
Package unavailable to check Rd xrefs: ‘RProtoBuf’
Package required but not available: ‘bamsignals’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   2.6Mb
File ‘hSDM/libs/hSDM.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘useful.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Objects: ‘hSDM.Nmixture.o’, ‘hSDM.Nmixture.iCAR.o’, ‘hSDM.ZIB.o’,
      ‘hSDM.ZIB.iCAR.alteration.o’, ‘hSDM.ZIB.iCAR.o’, ‘hSDM.ZIP.o’,
      ‘hSDM.ZIP.iCAR.alteration.o’, ‘hSDM.ZIP.iCAR.o’,
      ‘hSDM.binomial.o’, ‘hSDM.binomial.iCAR.o’, ‘hSDM.poisson.o’,
      ‘hSDM.poisson.iCAR.o’, ‘hSDM.siteocc.o’, ‘hSDM.siteocc.iCAR.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
    doc    1.1Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    data  12.9Mb
    doc    1.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'https://arxiv.org/e-print/1406.4806v1'
Content type 'application/x-eprint-tar' length 29273 bytes (28 KB)
==================================================
downloaded 28 KB

Quitting from lines 162-165 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required but not available: ‘FSelector’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Running examples in ‘IAPWS95-Ex.R’ failed
The error most likely occurred in:

> ### Name: TDh
> ### Title: Temperature, Function of Density and Enthalpy
> ### Aliases: TDh
> 
> ### ** Examples
> 
> D <- 838.025
> h <- 977.181624
> TDh(D,h)
Installation failed.
See ‘/home/ripley/R/packages/tests32/icd.Rcheck/00install.out’ for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   2.7Mb
Running examples in ‘ifa-Ex.R’ failed
The error most likely occurred in:

> ### Name: ifa.bic
> ### Title: A function to compute the BIC
> ### Aliases: ifa.bic
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> data(memory)

 *** caught segfault ***
address a61a78f8, cause 'memory not mapped'

Traceback:
 1: sub(".*\\.", "", x)
 2: fileExt(file)
 3: data(memory)
An irrecoverable exception occurred. R is aborting now ...
Packages required but not available: ‘rpf’ ‘OpenMx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   4.0Mb
Package required but not available: ‘PythonInR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    help   1.2Mb
    libs   6.4Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    doc       4.9Mb
    extdata   1.2Mb
    include   2.9Mb
    libs      5.2Mb
Running examples in ‘Inflation-Ex.R’ failed
The error most likely occurred in:

> ### Name: INFL.core_tf
> ### Title: Computes the triple filter core inflation
> ### Aliases: INFL.core_tf
> ### Keywords: core filter triple
> 
> ### ** Examples
> 
> ipca <- ipca_sub
> INFL.core_tf(subits.var=ipca$ipca_ts, weights = ipca$weights_ts)
Unsupported platform: SunOS 5.10
For this platform, the path to the binary executable of X-13
has to be manually specified. See ?seasonal for details.
No path to the binary executable of X-13 specified.

You can set 'X13_PATH' manually if you intend to use your own
binaries. See ?seasonal for details.

Error in checkX13(fail = TRUE, fullcheck = FALSE, htmlcheck = FALSE) : 
  Process terminated
Calls: INFL.core_tf -> <Anonymous> -> checkX13
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 26-27 (internet-archive.Rmd) 
Error: processing vignette 'internet-archive.Rmd' failed with diagnostics:
Timeout was reached: Resolving timed out after 10000 milliseconds
Execution halted
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
Running examples in ‘iqspr-Ex.R’ failed
The error most likely occurred in:

> ### Name: viewstr
> ### Title: view 2D structures from SMILES string vector
> ### Aliases: viewstr
> 
> ### ** Examples
> 
> viewstr(c("c1ccc2ccc3c(NCCN(C)C)cc(nc3c2c1)", "c1ccc2ccc3c(NCCN(CC)CCCl)cc(nc3c2c1)",
+  "c1ccc2ccc3c(NC(CC)CC)cc(nc3c2c1)", "c1ccc2ccc3c(c2c1)ncc(c3NCCNCC=CCCCC)"))
Error in .jnew("org/guha/rcdk/view/RcdkDepictor", as.integer(width), as.integer(height),  : 
  java.lang.UnsupportedClassVersionError: org/guha/rcdk/view/RcdkDepictor : Unsupported major.minor version 52.0
Calls: viewstr -> get.depictor -> .jnew -> .External
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 89-91 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
RcallMethod: cannot determine object class
Execution halted
Package required but not available: ‘xergm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    dict  19.5Mb
Package suggested but not available for checking: ‘RProtoBuf’
Package suggested but not available for checking: ‘semPlot’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: shiny
Loading required package: shinythemes
Loading required package: plyr
Quitting from lines 37-53 (kgc-fine.Rmd) 
Error: processing vignette 'kgc-fine.Rmd' failed with diagnostics:
cannot allocate vector of size 640.7 Mb
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-13
Loading this package had a fatal error status code 1
Loading log:
Loading required package: Rcpp
Error: package or namespace load failed for ‘knor’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/ripley/R/Lib32/knor/libs/knor.so':
  ld.so.1: R: fatal: relocation error: file /home/ripley/R/Lib32/knor/libs/knor.so: symbol GOMP_parallel: referenced symbol not found
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    java   6.2Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R   7.4Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(KRIG)
  > 
  > test_check("KRIG")
  ── 1. Failure: Same result sequencial and parallel code (@test1.R#15)  ─────────
  `kw` not equal to `nw`.
  1/1 mismatches
  [1] 12817 - 6408 == 6408
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Failure: Same result sequencial and parallel code (@test1.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Quitting from lines 120-123 (copper_mining_2d.Rmd) 
Error: processing vignette 'copper_mining_2d.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   3.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    2.2Mb
    help   1.2Mb
Running ‘config.R’
  Running ‘testthat.R’
Running the tests in ‘tests/config.R’ failed.
Complete output:
  > mac_dir <- "~/Documents/Rtest/"
  > win_dir <- "C:/Rtest"
  > linux_dir <- "~/Documents/Rtest"
  > 
  > switch(Sys.info()['sysname'],
  +        "Darwin" = {working_dir <- mac_dir},
  +        "Windows" = {working_dir <- win_dir},
  +        "Linux" = {working_dir <- linux_dir})
  > 
  > rds_file_name <- "./ranListSmall.rds"
  > llo_file_name <- "./ranListSmall.llo"
  > repeat_time <- 20
  > original <- FALSE
  > compress <- TRUE
  > 
  > # rds_file_name <- "./ranListMid.rds"
  > # llo_file_name <- "./ranListMid.llo"
  > # repeat_time <- 20
  > # original <- FALSE
  > # compress <- TRUE
  > 
  > options(list(largeList.report.progress = FALSE))
  > 
  > if (dir.exists(working_dir)) {
  +   setwd(working_dir)
  +   if (file.exists(rds_file_name)) {
  +     library(futile.logger)
  +     ready_to_test <- TRUE
  +   } else {
  +     ready_to_test <- FALSE
  +   }
  + } else {
  +   ready_to_test <- FALSE
  + }
  Error in dir.exists(working_dir) : object 'working_dir' not found
  Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc            1.1Mb
    testdata       2.1Mb
    vignettedata   2.3Mb
Running examples in ‘largeVis-Ex.R’ failed
The error most likely occurred in:

> ### Name: as.dendrogram.hdbscan
> ### Title: as.dendrogram.hdbscan
> ### Aliases: as.dendrogram.hdbscan
> 
> ### ** Examples
> 
> data(iris)
> vis <- largeVis(t(iris[,1:4]), K = 20, sgd_batches = 1, threads = 1)
Error: C stack usage  194866496 is too close to the limit

error: Mat::col(): index out of bounds

error: Mat::col(): index out of bounds
terminate called after throwing an instance of 'std::logic_error'
  what():  Mat::col(): index out of bounds
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
largeVis was compiled with 32-bit types. This will limit the size of the datasets it can process. Consider recompiling with -DARMA_64BIT_WORD
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in unit(c(t, r, b, l), unit) : NAs introduced by coercion
Error: C stack usage  309095744 is too close to the limit

error: Mat::col(): index out of bounds

error: Mat::col(): index out of bounds
terminate called after throwing an instance of 'std::logic_error'
  what():  Mat::col(): index out of bounds
installed size is  5.1Mb
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    doc   5.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 40-43 (Intro_to_lavaanPlot.Rmd) 
Error: processing vignette 'Intro_to_lavaanPlot.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required but not available: ‘semPlot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    geojson  11.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 67-77 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.1Mb
File ‘leaps/libs/leaps.so’:
  Found ‘__f90_esfw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Object: ‘leaps.o’
  Found ‘__f90_eslw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Object: ‘leaps.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 26.2Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs     24.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 272-273 (Understanding_lime.Rmd) 
Error: processing vignette 'Understanding_lime.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R          1.3Mb
    doc        1.8Mb
    testdata   1.7Mb
Package suggested but not available for checking: ‘Rsymphony’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 15-33 (README.Rmd) 
Error: processing vignette 'README.Rmd' failed with diagnostics:
object 'params' not found
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 18-23 (lspline.Rmd) 
Error: processing vignette 'lspline.Rmd' failed with diagnostics:
object 'params' not found
Execution halted
Packages required but not available: ‘OpenMx’ ‘semPlot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    TS_files     6.0Mb
    base_files   6.5Mb
Packages suggested but not available for checking: ‘rsvg’ ‘tesseract’
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
Packages unavailable to check Rd xrefs: ‘rsvg’, ‘tesseract’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 77-80 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
there is no package called 'rsvg'
Execution halted
Running ‘testthat.R’ [15s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > test_check("MALDIrppa")
  Loading required package: MALDIrppa
  Loading required package: MALDIquant
  
  This is MALDIquant version 1.17
  Quantitative Analysis of Mass Spectrometry Data
   See '?MALDIquant' for more information about this package.
  
  Loading required package: signal
  
  Attaching package: 'signal'
  
  The following objects are masked from 'package:stats':
  
      filter, poly
  
  Loading required package: robustbase
  Loading required package: wmtsa
  Loading required package: lattice
  ── 1. Failure: detectOutliers returns expected results (@test_all.R#23)  ───────
  sum(detectOutliers(peaks)) not equal to 63.
  1/1 mismatches
  [1] 64 - 63 == 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 19 SKIPPED: 0 FAILED: 1
  1. Failure: detectOutliers returns expected results (@test_all.R#23) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot37611587e10.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot37611587e10.png': No such file or directory
Quitting from lines 95-96 (manhattanly.Rmd) 
Error: processing vignette 'manhattanly.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot3d4317ed5550.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot3d4317ed5550.png': No such file or directory
Quitting from lines 61-68 (manipulateWidgets.Rmd) 
Error: processing vignette 'manipulateWidgets.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 32.8Mb
  sub-directories of 1Mb or more:
    mapdata  32.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: igraph

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 57-64 (mapfuser.Rmd) 
Error: processing vignette 'mapfuser.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 95-100 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.2Mb
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    mapdata   4.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    java   3.4Mb
File ‘maxent/libs/maxent.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘sgd.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in (function (filename = "Rplot%03d.png", width = 480, height = 480,  :
  cairo error 'invalid value (typically too big) for the size of the input (surface, pattern, etc.)'
Quitting from lines 39-41 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
unable to start device 'png'
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   2.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   6.0Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/meanr.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
Package required but not available: ‘OpenMx’

Package suggested but not available for checking: ‘semPlot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   1.1Mb
    doc    1.5Mb
    libs   1.5Mb
    misc   1.1Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mhde_article.tex' failed.
Messages:
/usr/local/bin/texi2dvi: biber failed
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/miceFast.Rcheck/00install.out’ for details.
File ‘MigClim/libs/MigClim.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Objects: ‘genclust.o’, ‘migrate.o’, ‘src_cell.o’, ‘validate.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Objects: ‘genclust.o’, ‘migrate.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 21-25 (MINVALintroduction.Rmd) 
Error: processing vignette 'MINVALintroduction.Rmd' failed with diagnostics:
there is no package called 'sybilSBML'
Execution halted
Running examples in ‘mitml-Ex.R’ failed
The error most likely occurred in:

> ### Name: anova.mitml.result
> ### Title: Compare several nested models
> ### Aliases: anova.mitml.result
> ### Keywords: methods
> 
> ### ** Examples
> 
> require(lme4)
Loading required package: lme4
Loading required package: Matrix
> data(studentratings)
> 
> fml <- ReadDis + SES ~ ReadAchiev + (1|ID)
> imp <- panImpute(studentratings, formula=fml, n.burn=1000, n.iter=100, m=5)
Running burn-in phase ...
Creating imputed data set ( 1 / 5 ) ...
Creating imputed data set ( 2 / 5 ) ...
Creating imputed data set ( 3 / 5 ) ...
Creating imputed data set ( 4 / 5 ) ...
Creating imputed data set ( 5 / 5 ) ...
Error in pan::pan(gy, subj = gclus, gpred, xcol, zcol, prior, seed = rns[ii +  : 
  NA/NaN/Inf in foreign function call (arg 20)
Calls: panImpute -> <Anonymous>
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 87-98 (pitch_plotting.Rmd) 
Error: processing vignette 'pitch_plotting.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages suggested but not available for checking: ‘FSelector’ ‘RWeka’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   5.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    2.4Mb
Running ‘testthat.R’ [14s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(Momocs)
  This is Momocs 1.2.2
  
  Attaching package: 'Momocs'
  
  The following object is masked from 'package:stats':
  
      filter
  
  The following object is masked from 'package:base':
  
      table
  
  > 
  > test_check("Momocs")
  ── 1. Error: filter works fine (@test-nse.R#62)  ───────────────────────────────
  bad value
  1: expect_true(x_lite$fac %>% sapply(nlevels) %>% ==1 %>% all) at testthat/test-nse.R:62
  2: quasi_label(enquo(object), label)
  3: force(quo)
  4: enquo(object)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 159 SKIPPED: 1 FAILED: 1
  1. Error: filter works fine (@test-nse.R#62) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
Package which this enhances but not available for checking: ‘MonetDBLite’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.6Mb
File ‘MRwarping/libs/MRwarping.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘interfaceRC_warp.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 30-37 (msaR.Rmd) 
Error: processing vignette 'msaR.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/MultiBD.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/multinet.Rcheck/00install.out’ for details.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    java  14.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    2.9Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    extdata  16.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 112-115 (using-nauf.Rmd) 
Error: processing vignette 'using-nauf.Rmd' failed with diagnostics:
'a' must be a numeric matrix
Execution halted
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.5Mb
Running examples in ‘ncdump-Ex.R’ failed
The error most likely occurred in:

> ### Name: NetCDF
> ### Title: Information about a NetCDF file, in convenient form.
> ### Aliases: NetCDF
> 
> ### ** Examples
> 
> rnc <- NetCDF(system.file("extdata", "S2008001.L3m_DAY_CHL_chlor_a_9km.nc", package= "ncdump"))
Error in R_nc4_open: NetCDF: HDF error
Error in ncdf4::nc_open(x) : 
  Error in nc_open trying to open file /home/ripley/R/Lib32/ncdump/extdata/S2008001.L3m_DAY_CHL_chlor_a_9km.nc
Calls: NetCDF -> <Anonymous>
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ncdump)
  > 
  > test_check("ncdump")
  Error in R_nc4_open: NetCDF: HDF error
  ── 1. Error: (unknown) (@testbasic.r#6)  ───────────────────────────────────────
  Error in nc_open trying to open file /home/ripley/R/Lib32/ncdump/extdata/S2008001.L3m_DAY_CHL_chlor_a_9km.nc
  1: NetCDF(ifile) at testthat/testbasic.r:6
  2: ncdf4::nc_open(x)
  3: stop(paste("Error in nc_open trying to open file", filename))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@testbasic.r#6) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘ncmeta-Ex.R’ failed
The error most likely occurred in:

> ### Name: nc_att
> ### Title: NetCDF attributes
> ### Aliases: nc_att nc_att nc_att.NetCDF nc_att nc_att.character
> 
> ### ** Examples
> 
> f <- system.file("extdata", "S2008001.L3m_DAY_CHL_chlor_a_9km.nc", package = "ncmeta")
> nc_att(f, 0, 0)
Error: NetCDF: HDF error
Execution halted
Running examples in ‘NCutYX-Ex.R’ failed
The error most likely occurred in:

> ### Name: ancut
> ### Title: Cluster the Columns of Y into K Groups with the Help of External
> ###   Features X.
> ### Aliases: ancut
> 
> ### ** Examples
> 
> #This sets up the initial parameters for the simulation.
> library(MASS)#for mvrnorm
> library(fields)
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.1-2 (2017-12-21) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: ‘spam’

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

    backsolve, forwardsolve

Loading required package: maps
See www.image.ucar.edu/~nychka/Fields for
 a vignette and other supplements. 
> n=30 #Sample size
> B=50 #Number of iterations in the simulated annealing algorithm.
> L=10000 #Temperature coefficient.
> p=50 #Number of columns of Y.
> q=p #Number of columns of X.
> h1=0.15
> h2=0.25
> 
> S=matrix(0.2,q,q)
> S[1:(q/2),(q/2+1):q]=0
> S[(q/2+1):q,1:(q/2)]=0
> S=S-diag(diag(S))+diag(q)
> 
> mu=rep(0,q)
> 
> W0=matrix(1,p,p)
> W0[1:(p/2),1:(p/2)]=0
> W0[(p/2+1):p,(p/2+1):p]=0
> Denum=sum(W0)
> 
> B2=matrix(0,q,p)
> for (i in 1:(p/2)){
+    B2[1:(q/2),i]=runif(q/2,h1,h2)
+    in1=sample.int(q/2,6)
+    B2[-in1,i]=0
+ }
> 
> for (i in (p/2+1):p){
+    B2[(q/2+1):q,i]=runif(q/2,h1,h2)
+    in2=sample(seq(q/2+1,q),6)
+    B2[-in2,i]=0
+ }
> 
> X=mvrnorm(n, mu, S)
> Z=X%*%B2
> Y=Z+matrix(rnorm(n*p,0,1),n,p)
> #Our method
> Res=ancut(Y=Y,X=X,B=B,L=L,alpha=0,ncv=3)
Error in if (J2 > J) { : missing value where TRUE/FALSE needed
Calls: ancut
Execution halted
File ‘NeatMap/libs/NeatMap.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘nMDS_R.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘nMDS_R.o’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘RSiena’
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 use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    CppCode   1.2Mb
    R         3.5Mb
    include   5.3Mb
    tests     1.3Mb
Running ‘anova.gls.R’
  Running ‘augPred_lab.R’ [47s/69s]
  Running ‘augPredmissing.R’
  Running ‘coef.R’
  Comparing ‘coef.Rout’ to ‘coef.Rout.save’ ... OK
  Running ‘contrMat.R’
  Running ‘data.frame.R’
  Running ‘deparse.R’
  Running ‘deviance.R’
  Running ‘fitted.R’
  Running ‘getData.R’
  Running ‘gls.R’
  Running ‘lmList.R’
  Running ‘lme.R’
  Comparing ‘lme.Rout’ to ‘lme.Rout.save’ ... OK
  Running ‘missing.R’
  Comparing ‘missing.Rout’ to ‘missing.Rout.save’ ... OK
  Running ‘nlme.R’
  Running ‘nlme2.R’
  Running ‘predict.lme.R’
  Running ‘sigma-fixed-etc.R’ [37s/43s]
Running the tests in ‘tests/sigma-fixed-etc.R’ failed.
Last 13 lines of output:
  > ##------------------------------------------------------ REML ---
  > method <- "REML"
  > cat("\nFixed sigma= ",sigma,"  estimation method ", method,"\n")
  
  Fixed sigma=  1   estimation method  REML 
  > t7.fix.REML.lme <- lme( current ~voltage + I(voltage^2), data = Wafer,
  +                        random = list(Wafer = pdDiag(~voltage + I(voltage^2)),
  +                                      Site  = pdDiag(~voltage + I(voltage^2)) ),
  +                        control = lmeControl(sigma = 1),
  +                        method = method)
  Error in lme.formula(current ~ voltage + I(voltage^2), data = Wafer, random = list(Wafer = pdDiag(~voltage +  : 
    nlminb problem, convergence error code = 1
    message = false convergence (8)
  Calls: lme -> lme.formula
  Execution halted
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    data      4.4Mb
    doc       1.2Mb
    reports   3.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'vignette_get_nltt_values.Rmd' failed with diagnostics:
(converted from warning) Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Execution halted
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    doc  12.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 192-194 (NormalizeMets_vignette.Rmd) 
Error: processing vignette 'NormalizeMets_vignette.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
Execution halted
installed size is 39.1Mb
  sub-directories of 1Mb or more:
    extdata  39.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
File ‘obliclus/libs/obliclus.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘random_cluster_C.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘random_cluster_C.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    help   2.2Mb
Package required but not available: ‘rpf’

Package suggested but not available for checking: ‘rpf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    java     1.3Mb
    models   6.1Mb
Running ‘testthat.R’ [28s/85s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > test_check("openxlsx")
  Loading required package: openxlsx
  ── 1. Error: loadWorkbook from different sources (@test-read_sources.R#49)  ────
  subscript out of bounds
  1: expect_true(all.equal.Workbook(wb_url, wb_file), "Loading from URL vs local not equal") at testthat/test-read_sources.R:49
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: all.equal.Workbook(wb_url, wb_file)
  5: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  9: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  10: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  11: attr.all.equal(target, current, ...)
  12: mode(current)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 505 SKIPPED: 2 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘OriGen/libs/OriGen.so’:
  Found ‘__f90_close’, possibly from ‘close’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__f90_esfr’, possibly from ‘read’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__f90_open’, possibly from ‘open’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__f90_rewind’, possibly from ‘rewind’ (Fortran)
    Object: ‘OriGen.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    nifti   4.1Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 185-198 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(oxcAAR)
  > 
  > test_check("oxcAAR")
  sh: /home/ripley/R/packages/tests32/oxcAAR.Rcheck/tests/testthat/ox_output.js: cannot execute
  ── 1. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_util
  `quickSetupOxcal()` threw an error.
  Message: argument is of length zero
  Class:   simpleError/error/condition
  
  ── 2. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_util
  dir.exists("OxCal/bin/") isn't true.
  
  ── 3. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_util
  `%in%`(...) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 94 SKIPPED: 0 FAILED: 3
  1. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_utility_functions.R#30) 
  2. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_utility_functions.R#31) 
  3. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_utility_functions.R#32) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 24-30 (basic-usage.Rmd) 
Error: processing vignette 'basic-usage.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
Running examples in ‘P2C2M-Ex.R’ failed
The error most likely occurred in:

> ### Name: p2c2m.complete
> ### Title: Execute the complete P2C2M pipeline via a single command
> ### Aliases: p2c2m.complete
> 
> ### ** Examples
> 
> ## Example of the minimal data requirements to run P2C2M
> 
> # The absolute path to the input directory is set
> inPath <- system.file("extdata", "sim.E.003.small/", package="P2C2M")
> 
> # The name of the xml-file generated by BEAUTi and located in 
> # "inPath" is set
> inFile <- "sim.E.003.small.xml"
> 
> # Posterior predictive simulations with a setting of 2 simulation 
> # replicates are preformed
> sim.E.003.small <- p2c2m.complete(inPath, inFile, num.reps=2, save.metadata=TRUE)
Error in python.exec(code, get.exception) : cannot import name izip
Calls: p2c2m.complete -> p2c2m.readstarb -> <Anonymous> -> python.exec
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 196-217 (progressive_packing.Rmd) 
Error: processing vignette 'progressive_packing.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data        1.6Mb
    localdata   3.1Mb
Info message:
Couldn't find 'pandoc'!
Pandoc version is set to '1.16', use `set_pandoc_version` to change the settings if necessary.
File ‘ParallelForest/libs/ParallelForest.so’:
  Found ‘__f90_close’, possibly from ‘close’ (Fortran)
    Object: ‘random_utils.o’
  Found ‘__f90_esfw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Object: ‘classification.o’
  Found ‘__f90_eslw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Object: ‘classification.o’
  Found ‘__f90_open’, possibly from ‘open’ (Fortran)
    Object: ‘random_utils.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘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 use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    extdata   9.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.2Mb
*** caught segfault ***
address 5f746e65, cause 'memory not mapped'

Traceback:
 1: dyn.load(file, DLLpath = DLLpath, ...)
 2: library.dynam(lib, package, package.lib)
 3: loadNamespace(name)
 4: doTryCatch(return(expr), name, parentenv, handler)
 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6: tryCatchList(expr, classes, parentenv, handlers)
 7: tryCatch(loadNamespace(name), error = function(e) stop(e))
 8: getNamespace(package)
 9: withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessage"))
10: suppressMessages(getNamespace(package))
11: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
12: suppressWarnings(suppressMessages(getNamespace(package)))
13: tools:::.check_code_usage_in_package(package = "pcaL1")
An irrecoverable exception occurred. R is aborting now ...
Running examples in ‘pcaL1-Ex.R’ failed
The error occurred in:


R version 3.4.4 Patched (2018-03-15 r74414) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-pc-solaris2.10 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> pkgname <- "pcaL1"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> library('pcaL1')

 *** caught segfault ***
address 6c, cause 'memory not mapped'

Traceback:
 1: dyn.load(file, DLLpath = DLLpath, ...)
 2: library.dynam(lib, package, package.lib)
 3: loadNamespace(package, lib.loc)
 4: doTryCatch(return(expr), name, parentenv, handler)
 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6: tryCatchList(expr, classes, parentenv, handlers)
 7: tryCatch({    attr(package, "LibPath") <- which.lib.loc    ns <- loadNamespace(package, lib.loc)    env <- attachNamespace(ns, pos = pos, deps)}, error = function(e) {    P <- if (!is.null(cc <- conditionCall(e)))         paste(" in", deparse(cc)[1L])    else ""    msg <- gettextf("package or namespace load failed for %s%s:\n %s",         sQuote(package), P, conditionMessage(e))    if (logical.return)         message(paste("Error:", msg), domain = NA)    else stop(msg, call. = FALSE, domain = NA)})
 8: library("pcaL1")
An irrecoverable exception occurred. R is aborting now ...
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    data   2.4Mb
Running examples in ‘penaltyLearning-Ex.R’ failed
The error most likely occurred in:

> ### Name: modelSelectionC
> ### Title: Exact model selection function
> ### Aliases: modelSelectionC
> 
> ### ** Examples
> 
> 
> library(penaltyLearning)
> data(neuroblastoma, package="neuroblastoma", envir=environment())
> pro <- subset(neuroblastoma$profiles, profile.id==1 & chromosome=="X")
> max.segments <- 20
> fit <- Segmentor3IsBack::Segmentor(pro$logratio, 2, max.segments)
Error in cumsum(datasize)[breaks[k, 1:k]] : 
  only 0's may be mixed with negative subscripts
Calls: <Anonymous> -> Segmentor.default
Execution halted
Running examples in ‘pense-Ex.R’ failed
The error most likely occurred in:

> ### Name: coef.pense
> ### Title: Extract Model Coefficients
> ### Aliases: coef.pense
> 
> ### ** Examples
> 
> # Generate data with highly correlated groups of variables and some outliers
> set.seed(12345)
> n <- 50
> n_out <- 3
> p <- 20
> x <- 1 + matrix(rnorm(n * p), ncol = p)
> x[, 2] <- x[, 1] + rnorm(n, sd = 0.01)
> x[, 3] <- x[, 1] + rnorm(n, sd = 0.01)
> x[, 5] <- x[, 4] + rnorm(n, sd = 0.01)
> x[, 6] <- x[, 4] + rnorm(n, sd = 0.01)
> 
> y <- x %*% c(rep(c(2, 5), each = 3), numeric(p - 6)) + rnorm(n)
> 
> y[seq_len(n_out)] <- rnorm(n_out, -100, sd = 3)
> 
> # Compute the PENSE estimator
> set.seed(1234)
> est_en <- pense(x, y, alpha = 0.5, warm_reset = 1, cv_k = 3)

 *** caught segfault ***
address 0, cause 'memory not mapped'

Traceback:
 1: .Call(C_enpy_exact, xtr, y, alpha, lambda, options, en_options)
 2: enpy_exact(x, y, alpha, lambda, options, en_options)
 3: enpy(std_data$xs, std_data$yc, alpha, lambda, delta = pense_options$bdp,     cc = pense_options$cc, options = initest_options, en_options = en_options)
 4: pense_init_cold(x = x_train, y = y_train, lambda = job$lambda,     ...)
 5: FUN(X[[i]], ...)
 6: cluster$lapply(jobs_cold_est, get_cold_est, alpha = alpha, standardize = standardize,     pense_options = options, initest_options = init_options,     en_options = en_options)
 7: doTryCatch(return(expr), name, parentenv, handler)
 8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9: tryCatchList(expr, classes, parentenv, handlers)
10: tryCatch({    cold_inits <- cluster$lapply(jobs_cold_est, get_cold_est,         alpha = alpha, standardize = standardize, pense_options = options,         initest_options = init_options, en_options = en_options)}, error = function(e) {    cluster$stopCluster()    stop(e)})
11: pense(x, y, alpha = 0.5, warm_reset = 1, cv_k = 3)
An irrecoverable exception occurred. R is aborting now ...
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      4.5Mb
    data   3.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
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 use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot1dc76da666ce.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot1dc76da666ce.png': No such file or directory
Quitting from lines 20-27 (Advanced_Usage.Rmd) 
Error: processing vignette 'Advanced_Usage.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot660e342a5502.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot660e342a5502.png': No such file or directory
Quitting from lines 65-68 (v01-introduction.Rmd) 
Error: processing vignette 'v01-introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Packages suggested but not available for checking: ‘Rserve’ ‘RSelenium’
Running ‘testthat.R’ [32s/36s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pmap)
  > 
  > set.seed(101)
  > 
  > test_check("pmap")
  ── 1. Error: render_pmap_file() should be able to render to a file (@test_render
  there is no package called 'rsvg'
  1: render_pmap_file(p, file_name, format = format) at testthat/test_render_pmap_file.R:15
  2: DiagrammeR::export_graph(p, file_name = file_name, file_type = format, width = width, 
         height = height)
  3: rsvg::rsvg_pdf
  4: getExportedValue(pkg, name)
  5: asNamespace(ns)
  6: getNamespace(ns)
  7: tryCatch(loadNamespace(name), error = function(e) stop(e))
  8: tryCatchList(expr, classes, parentenv, handlers)
  9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  10: value[[3L]](cond)
  
  ── 2. Error: render_pmap_file() should be able to guess file format (@test_rende
  there is no package called 'rsvg'
  1: render_pmap_file(p, file_name) at testthat/test_render_pmap_file.R:32
  2: DiagrammeR::export_graph(p, file_name = file_name, file_type = format, width = width, 
         height = height)
  3: rsvg::rsvg_pdf
  4: getExportedValue(pkg, name)
  5: asNamespace(ns)
  6: getNamespace(ns)
  7: tryCatch(loadNamespace(name), error = function(e) stop(e))
  8: tryCatchList(expr, classes, parentenv, handlers)
  9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  10: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 247 SKIPPED: 0 FAILED: 2
  1. Error: render_pmap_file() should be able to render to a file (@test_render_pmap_file.R#15) 
  2. Error: render_pmap_file() should be able to guess file format (@test_render_pmap_file.R#32) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
Running examples in ‘pmhtutorial-Ex.R’ failed
The error most likely occurred in:

> ### Name: particleFilterSVmodel
> ### Title: Bootstrap particle filter for state estimate in a simple
> ###   stochastic volatility model
> ### Aliases: particleFilterSVmodel
> ### Keywords: ts
> 
> ### ** Examples
> 
> # Get the data from Quandl
> library("Quandl")
Loading required package: xts
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

> d <- Quandl("NASDAQOMX/OMXS30", start_date="2012-01-02", 
+             end_date="2014-01-02", type="zoo")
Error: { "quandl_error": { "code": "QELx04", "message": "You have exceeded the API speed limit. Please slow down your requests by reducing the number of requests made at the same time." } }
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Package suggested but not available for checking: ‘ROI.plugin.symphony’
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    java   5.7Mb
File ‘powell/libs/powell.so’:
  Found ‘printf’, possibly from ‘printf’ (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 use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Packages suggested but not available for checking:
  ‘gurobi’ ‘lpsymphony’ ‘Rsymphony’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 31-43 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
Running ‘testthat.R’ [4s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(processx)
  > 
  > test_check("processx")
  
   *** caught segfault ***
  address 31000018, cause 'memory not mapped'
Running examples in ‘profile-Ex.R’ failed
The error most likely occurred in:

> ### Name: read_rprof
> ### Title: File I/O for profiler data
> ### Aliases: read_rprof read_pprof write_rprof write_pprof
> 
> ### ** Examples
> 
> rprof_file <- system.file("samples/rprof/1.out", package = "profile")
> ds <- read_rprof(rprof_file)
> ds
Profile data: 22 samples
> pprof_file <- tempfile("profile", fileext = ".pb.gz")
> write_pprof(ds, pprof_file)
Error: Package RProtoBuf is required to read pprof files.
Execution halted
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   7.4Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   2.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    dict   5.3Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc        4.8Mb
    examples   2.4Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
Running examples in ‘pyinit-Ex.R’ failed
The error most likely occurred in:

> ### Name: pyinit
> ### Title: PY (Pena-Yohai) initial estimates for S-estimates of regression
> ### Aliases: pyinit
> 
> ### ** Examples
> 
> # generate a simple synthetic data set for a linear regression model
> # with true regression coefficients all equal to one "(1, 1, 1, 1, 1)"
> set.seed(123)
> x <- matrix(rnorm(100*4), 100, 4)
> y <- rnorm(100) + rowSums(x) + 1
> # add masked outliers
> a <- svd(var(x))$v[,4]
> x <- rbind(x, t(outer(a, rnorm(20, mean=4, sd=1))))
> y <- c(y, rnorm(20, mean=-2, sd=.2))
> 
> # these outliers are difficult to find
> plot(lm(y~x), ask=FALSE)
> 
> # use pyinit to obtain estimated regression coefficients
> tmp <- pyinit(x=x, y=y, resid_keep_method='proportion', psc_keep = .5, resid_keep_prop=.5)

 *** caught segfault ***
address 0, cause 'memory not mapped'

Traceback:
 1: .Call(C_initpy, t(x), y, ctrl$maxit, ctrl$eps, ctrl$resid_keep_thresh,     ctrl$resid_keep_prop, ctrl$psc_keep, ctrl$delta, ctrl$mscale_cc,     ctrl$mscale_maxit, ctrl$mscale_tol, ctrl$mscale_rho_fun)
 2: pyinit(x = x, y = y, resid_keep_method = "proportion", psc_keep = 0.5,     resid_keep_prop = 0.5)
An irrecoverable exception occurred. R is aborting now ...
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    data  12.9Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R         1.9Mb
    contrib   3.7Mb
    doc       3.3Mb
    libs      1.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 83-117 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 92-106 (wilcox1973.Rmd) 
Error: processing vignette 'wilcox1973.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
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 use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘qVarSel/libs/qVarSel.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘qVarSelH.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘qVarSelH.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘R2Cuba-Ex.R’ failed
The error most likely occurred in:

> ### Name: R2Cuba-package
> ### Title: Multidimensional Numerical Integration
> ### Aliases: R2Cuba-package R2Cuba
> ### Keywords: package
> 
> ### ** Examples
> 
> integrand <- function(arg, weight) {
+   x <- arg[1]
+   y <- arg[2]
+   z <- arg[3]
+   ff <- sin(x)*cos(y)*exp(z);
+ return(ff)
+ } # end integrand
> NDIM <-3
> NCOMP <- 1
> vegas(NDIM, NCOMP, integrand, rel.tol=1e-3,  abs.tol=1e-12)
Iteration 1:  1000 integrand evaluations so far
[1] 0.664916 +- 0.0138647  	chisq 0 (0 df)

 *** caught segfault ***
address fd080ee5, cause 'invalid permissions'

Traceback:
 1: .C("Rvegas", as.integer(ndim), as.integer(ncomp), ffintegrand,     new.env(), as.double(lower), as.double(upper), as.double(prdbounds),     as.double(rel.tol), as.double(abs.tol), as.integer(flags$mersenne.seed),     as.integer(nbatch), as.integer(gridno), as.integer(lesflags),     as.integer(min.eval), as.integer(max.eval), as.integer(nstart),     as.integer(nincrease), as.character(state.file), neval = as.integer(neval),     fail = as.integer(fail), integral = as.double(integral),     error = as.double(error), prob = as.double(prob), NAOK = TRUE)
 2: vegas(NDIM, NCOMP, integrand, rel.tol = 0.001, abs.tol = 1e-12)
An irrecoverable exception occurred. R is aborting now ...
Package unavailable to check Rd xrefs: ‘BRugs’
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    app   6.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   1.5Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    htmlwidgets   6.6Mb
Running examples in ‘ramidst-Ex.R’ failed
The error most likely occurred in:

> ### Name: dbn_generator
> ### Title: Generates a random dynamic Bayesian network
> ### Aliases: dbn_generator
> 
> ### ** Examples
> 
> d <- dbn_generator(3,2,2)
Error in .jfindClass(as.character(class)) : class not found
Calls: dbn_generator -> J -> jclassName -> .jfindClass
Execution halted
Running examples in ‘RandomFields-Ex.R’ failed
The error most likely occurred in:

> ### Name: RMave
> ### Title: Space-time moving average model
> ### Aliases: RMave
> ### Keywords: spatial models
> 
> ### ** Examples
> 
> RFoptions(seed=0) ## *ANY* simulation will have the random seed 0; set
> ##                   RFoptions(seed=NA) to make them all random again
> 
> ## Example of an evaluation of the ave2-covariance function
> ## in three different ways
> ## ---------------------------------------------------------
> ## some parameters A and z
> A <- matrix(c(2,1,1,2),ncol=2)
> z <- c(1,2)
> ## h for evalutation
> h <- c(1,2)
> ## some abbreviations
> E <- matrix(c(1,0,0,1),ncol=2)
> B <- A %*% h %*% t(h) %*% A
> phi <- function(t){return(RFcov(RMwhittle(1), t))}
> ## ---------------------------------------------------------
> ## the following should yield the same value 3 times
> ## (also for other choices of A,z and h)
> z1 <- RFcov( model=RMave(RMwhittle(1),A=A,z=z) , x=t(c(h,0)) )
> z2 <- RFcov( model=RMave(RMwhittle(1),A=A,z=z,spacetime=FALSE) , x=t(h) )
> z3 <- ( (det(E+2*B))^(-1/2) ) *
+  phi( sqrt( sum(h*h)/2 + (t(z) %*% h)^2 *
+  ( 1-2*t(h) %*% A %*% solve(E+2*B) %*% A %*% h) ) )
> ##
> stopifnot(abs(z1-z2)<1e-12, abs(z2-z3)<1e-12)
Error: abs(z2 - z3) < 1e-12 is not TRUE
Execution halted
Running examples in ‘rapidraker-Ex.R’ failed
The error most likely occurred in:

> ### Name: rapidrake
> ### Title: Rapid RAKE
> ### Aliases: rapidrake
> 
> ### ** Examples
> 
> rapidrake(txt = "some text that has great keywords")
Error in .jfindClass(as.character(class)) : class not found
Calls: rapidrake ... <Anonymous> -> <Anonymous> -> jclassName -> .jfindClass
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.5Mb
Running examples in ‘rbcb-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_all_currencies
> ### Title: All currency values
> ### Aliases: get_all_currencies
> 
> ### ** Examples
> 
> get_all_currencies("2017-03-10")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
Calls: get_all_currencies ... request_fetch -> request_fetch.write_memory -> <Anonymous> -> .Call
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/rCBA.Rcheck/00install.out’ for details.
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    cont  23.4Mb
Running examples in ‘rcdk-Ex.R’ failed
The error most likely occurred in:

> ### Name: eval.desc
> ### Title: Evaluate a Molecular Descriptor
> ### Aliases: eval.desc
> ### Keywords: programming
> 
> ### ** Examples
> 
> smiles <- c('CCC', 'c1ccccc1', 'CC(=O)C')
> mols <- sapply(smiles, parse.smiles)
> 
> dnames <- get.desc.names('constitutional')
Error in .jcall("org/guha/rcdk/descriptors/DescriptorUtilities", "[Ljava/lang/String;",  : 
  RcallMethod: cannot determine object class
Calls: get.desc.names -> .jcall
Execution halted
Error in re-building vignettes:
  ...
Loading required package: rcdklibs
Loading required package: rJava

Error: processing vignette 'rcdk.Rnw' failed with diagnostics:
 chunk 14 
Error in .jcall("org/guha/rcdk/util/Misc", "V", "setProperty", molecule,  : 
  RcallMethod: cannot determine object class
Execution halted
Running examples in ‘rchallenge-Ex.R’ failed
The error most likely occurred in:

> ### Name: icon
> ### Title: HTML code for icons. Currently only supports Font Awesome icons.
> ### Aliases: icon
> 
> ### ** Examples
> 
> rmd <- '
+ ```{r}
+ library(rchallenge)
+ ```
+ <link rel="stylesheet" 
+  href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css">
+ `r icon("fa-user")`
+ `r icon("fa-user fa-lg")`
+ `r icon("fa-user fa-2x")`
+ `r icon("fa-user fa-3x")`
+ `r icon("fa-user fa-3x fa-border")`
+ '
> file <- tempfile()
> cat(rmd, file=file)
> writeLines(readLines(file))

```{r}
library(rchallenge)
```
<link rel="stylesheet" 
 href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css">
`r icon("fa-user")`
`r icon("fa-user fa-lg")`
`r icon("fa-user fa-2x")`
`r icon("fa-user fa-3x")`
`r icon("fa-user fa-3x fa-border")`
> rmarkdown::render(file)
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.1Mb
    po    2.2Mb
Running ‘testthat.R’ [5s/86s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rcongresso)
  > 
  > test_check("rcongresso")
  ── 1. Failure: Dimensoes do dataframe (@test_votacoes.R#54)  ───────────────────
  dim(votos_pec241) not equal to c(478, 10).
  1/2 mismatches
  [1] 500 - 478 == 22
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 66 SKIPPED: 0 FAILED: 1
  1. Failure: Dimensoes do dataframe (@test_votacoes.R#54) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 62-65 (introducao-rcongresso.Rmd) 
Error: processing vignette 'introducao-rcongresso.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    include   4.8Mb
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    include  25.2Mb
Running examples in ‘RcppBlaze-Ex.R’ failed
The error most likely occurred in:

> ### Name: fastLmPure
> ### Title: linear model fitting function based on RcppBlaze
> ### Aliases: fastLmPure
> 
> ### ** Examples
> 
> # according to fastLm example in RcppArmadillo
> data(trees, package="datasets")
> flm <- fastLmPure(cbind(1, log(trees$Girth)), log(trees$Volume), 0)

 *** caught segfault ***
address fd164580, cause 'memory not mapped'

Traceback:
 1: .Call(`_RcppBlaze_fastLmPure`, X, y, type)
 2: fastLmPure(cbind(1, log(trees$Girth)), log(trees$Volume), 0)
An irrecoverable exception occurred. R is aborting now ...
Running examples in ‘RcppCCTZ-Ex.R’ failed
The error most likely occurred in:

> ### Name: toTz
> ### Title: Shift datetime object from one timezone to another
> ### Aliases: toTz
> 
> ### ** Examples
> 
> toTz(Sys.time(), "America/New_York", "Europe/London")
Error in toTz(Sys.time(), "America/New_York", "Europe/London") : 
  Bad 'from' timezone
Calls: toTz -> .Call
Execution halted
Running ‘simpleTests.R’
Running the tests in ‘tests/simpleTests.R’ failed.
Complete output:
  > 
  > library(RcppCCTZ)
  > 
  > ord <- "America/Chicago"
  > lax <- "America/Los_Angeles"
  > lga <- "America/New_York"
  > htr <- "Europe/London"
  > utc <- "UTC"
  > 
  > now <- ISOdatetime(2016, 11, 29, 12, 00, 00, tz="UTC")
  > 
  > format(toTz(now, utc, lax), tz=lax)
  Error in toTz(now, utc, lax) : Bad 'to' timezone
  Calls: format -> toTz -> .Call
  Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/RcppCWB.Rcheck/00install.out’ for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    include   7.2Mb
Running examples in ‘RcppGetconf-Ex.R’ failed
The error most likely occurred in:

> ### Name: getAll
> ### Title: Return all System Configuration Settings
> ### Aliases: getAll
> 
> ### ** Examples
> 
> head(getAll(), 30)
Error in getAll() : Memory allocation error
Calls: head -> getAll -> .Call
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: RcppGSL
Installation failed.
See ‘/home/ripley/R/packages/tests32/RcppHoney.Rcheck/00install.out’ for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    include   1.5Mb
    lib       3.0Mb
    libs      1.2Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/RcppMsgPack.Rcheck/00install.out’ for details.
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    include   8.9Mb
    libs     14.9Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc       3.2Mb
    include   6.6Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    include   3.9Mb
    lib       5.8Mb
    libs      1.7Mb
Running examples in ‘Rcrawler-Ex.R’ failed
The error most likely occurred in:

> ### Name: LinkExtractor
> ### Title: LinkExtractor
> ### Aliases: LinkExtractor
> 
> ### ** Examples
> 
> 
> pageinfo<-LinkExtractor(url="http://www.glofile.com", ExternalLInks = TRUE)
Error in LinkExtractor(url = "http://www.glofile.com", ExternalLInks = TRUE) : 
  object 'Extlinks' not found
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
── Attaching packages ────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 2.2.1     ✔ purrr   0.2.4
✔ tibble  1.4.2     ✔ dplyr   0.7.4
✔ tidyr   0.8.0     ✔ stringr 1.3.0
✔ readr   1.1.1     ✔ forcats 0.3.0
── Conflicts ───────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Linking to GEOS 3.6.2, GDAL 2.2.3, proj.4 4.9.3

Attaching package: 'units'

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

    %*%

Quitting from lines 122-147 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rdist)
  > 
  > test_check("rdist")
  ── 1. Failure: euclidean metric works as expected (@test-euclidean.R#12)  ──────
  `dist_mat` not equivalent to pdist(x).
  14/10000 mismatches (average diff: 1.84e-08)
  [203]  0 - 1.49e-08 == -1.49e-08
  [2122] 0 -      NaN ==       NaN
  [2627] 0 -      NaN ==       NaN
  [3940] 0 -      NaN ==       NaN
  [4950] 0 - 2.11e-08 == -2.11e-08
  [5859] 0 -      NaN ==       NaN
  [6061] 0 -      NaN ==       NaN
  [6667] 0 - 1.49e-08 == -1.49e-08
  [6869] 0 - 1.49e-08 == -1.49e-08
  ...
  
  ── 2. Failure: euclidean metric works as expected (@test-euclidean.R#13)  ──────
  `dist_mat` not equivalent to cdist(x, x).
  14/10000 mismatches (average diff: 1.84e-08)
  [203]  0 - 1.49e-08 == -1.49e-08
  [2122] 0 -      NaN ==       NaN
  [2627] 0 -      NaN ==       NaN
  [3940] 0 -      NaN ==       NaN
  [4950] 0 - 2.11e-08 == -2.11e-08
  [5859] 0 -      NaN ==       NaN
  [6061] 0 -      NaN ==       NaN
  [6667] 0 - 1.49e-08 == -1.49e-08
  [6869] 0 - 1.49e-08 == -1.49e-08
  ...
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 63 SKIPPED: 0 FAILED: 2
  1. Failure: euclidean metric works as expected (@test-euclidean.R#12) 
  2. Failure: euclidean metric works as expected (@test-euclidean.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘RSelenium’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
Error in re-building vignettes:
  ...
Quitting from lines 16-19 (rDVR-basics.Rmd) 
Error: processing vignette 'rDVR-basics.Rmd' failed with diagnostics:
there is no package called 'RSelenium'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot344172d910ad.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot344172d910ad.png': No such file or directory
Quitting from lines 22-26 (mapDWD.Rmd) 
Error: processing vignette 'mapDWD.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-17 (recexcavAAR-vignette-1.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-1.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
Execution halted
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.9Mb
Error in re-building vignettes:
  ...
Quitting from lines 13-18 (short_intro.Rmd) 
Error: processing vignette 'short_intro.Rmd' failed with diagnostics:
there is no package called 'semPlot'
Execution halted
Package suggested but not available for checking: ‘Rsymphony’

Package which this enhances but not available for checking: ‘Rcplex’
Package suggested but not available for checking: ‘sodium’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    java   6.0Mb
Running examples in ‘reprex-Ex.R’ failed
The error most likely occurred in:

> ### Name: un-reprex
> ### Title: Un-render a reprex
> ### Aliases: un-reprex reprex_invert reprex_clean reprex_rescue
> 
> ### ** Examples
> 
> ## a rendered reprex can be inverted, at least approximately
> x <- reprex({
+   #' Some text
+   #+ chunk-label-and-options-cannot-be-recovered, message = TRUE
+   (x <- 1:4)
+   #' More text
+   y <- 2:5
+   x + y
+ }, show = FALSE)
Error in reprex_(r_file) : 
Cannot render this code.
Error : pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Calls: reprex -> reprex_
Execution halted
Running examples in ‘respirometry-Ex.R’ failed
The error most likely occurred in:

> ### Name: calc_MO2
> ### Title: Calculate metabolic rate
> ### Aliases: calc_MO2
> 
> ### ** Examples
> 
> # get O2 data
> file <- system.file('extdata', 'witrox_file.txt', package = 'respirometry')
> o2_data <- na.omit(import_witrox(file, split_channels = TRUE)$CH_4)
Warning in strsplit(raw, split = "\r\n", fixed = T) :
  input string 1 is invalid UTF-8
Error in grep("Date &Time [", f[1:20], fixed = TRUE):length(f) : 
  argument of length 0
Calls: na.omit -> import_witrox
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 75-77 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
Python shared library '' not found, Python bindings not loaded.
Execution halted
Running examples in ‘revgeo-Ex.R’ failed
The error most likely occurred in:

> ### Name: revgeo
> ### Title: Reverse Geocoding with the Photon Geocoder for OpenStreetMap,
> ###   Google Maps, and Bing.
> ### Aliases: revgeo
> ### Keywords: geocode reverse
> 
> ### ** Examples
> 
> revgeo(longitude=-77.0229529, latitude=38.89283435)
[1] "Getting geocode data from Photon: http://photon.komoot.de/reverse?lon=-77.0229529&lat=38.89283435"
Running ‘testthat.R’ [4s/132s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("rglobi")
  Loading required package: rglobi
  ── 1. Failure: interactions subsetted by adding additional information all inter
  dim(unique(rbind(rattusaves, rattus))) not equal to dim(unique(rattus)).
  1/2 mismatches
  [1] 632 - 628 == 4
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 32 SKIPPED: 2 FAILED: 1
  1. Failure: interactions subsetted by adding additional information all interaction types include observations (@test-globi.R#70) 
  
  Error: testthat unit tests failed
  Execution halted
Package unavailable to check Rd xrefs: ‘Rsymphony’
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc     4.1Mb
    fonts   1.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 17-19 (WebGL.Rmd) 
Error: processing vignette 'WebGL.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
Execution halted
Packages suggested but not available for checking: ‘pmg’ ‘rggobi’
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    extra  10.2Mb
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help  10.6Mb
    libs   3.1Mb
File ‘RGtk2/libs/RGtk2.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_new_custom_connection’,
    ‘Rf_EncodeInteger’, ‘Rf_EncodeLogical’, ‘Rf_EncodeReal’,
    ‘Rf_formatInteger’, ‘Rf_formatLogical’, ‘Rf_formatReal’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc   9.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 34-47 (intro_rhandsontable.Rmd) 
Error: processing vignette 'intro_rhandsontable.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/rinform.Rcheck/00install.out’ for details.
File ‘RInside/libs/RInside.so’:
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLdo1’, ‘R_ReplDLLinit’,
    ‘R_RunExitFinalizers’, ‘R_SetParams’, ‘R_SignalHandlers’,
    ‘R_TempDir’, ‘Rf_endEmbeddedR’, ‘Rf_initEmbeddedR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
Running examples in ‘RJafroc-Ex.R’ failed
The error most likely occurred in:

> ### Name: PlotRsmOperatingCharacteristics
> ### Title: RSM predicted operating characteristics, ROC pdfs and different
> ###   FOMs possible with FROC data
> ### Aliases: PlotRsmOperatingCharacteristics
> 
> ### ** Examples
> 
> ## Following example is for mu = 2, lambda = 1, nu = 0.6, in one treatment and   
> ## mu = 3, lambda = 1.5, nu = 0.8, in the other treatment. 20% of the diseased 
> ## cases have a single lesion, 40% have two lesions, 10% have 3 lesions, 
> ## and 30% have 4 lesions.  
> lesDistr <- rbind(c(1, 0.2), c(2, 0.4), c(3, 0.1), c(4, 0.3))
> 
> ## On cases with one lesion the weights are 1, on cases with 2 lesions the weights
> ## are 0.4 and 0.6, on cases with three lesions the weights are 0.2, 0.3 and 0.5, and
> ## on cases with 4 lesions the weights are 0.3, 0.4, 0.2 and 0.1: 
> lesionWeights <- rbind(c(1.0, -Inf, -Inf, -Inf), 
+                        c(0.4,  0.6, -Inf, -Inf), 
+                        c(0.2,  0.3,  0.5, -Inf), 
+                        c(0.3,  0.4, 0.2,  0.1))
> ret <- PlotRsmOperatingCharacteristics(mu = c(2, 3), lambda = c(1, 1.5), nu = c(0.6, 0.8),
+    lesDistr = lesDistr, lesionWeights = lesionWeights, 
+    legendPosition = "bottom", nlfRange = c(0, 1), llfRange = c(0, 1))
Error in PlotRsmOperatingCharacteristics(mu = c(2, 3), lambda = c(1, 1.5),  : 
  Line 4 of lesion weights matrix should be summed up to 1.
Execution halted
Note: information on .o files is not available
File ‘/home/ripley/R/Lib32/rJava/libs/rJava.so’:
  Found ‘exit’, possibly from ‘exit’ (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 use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    java  11.2Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    datasets   9.0Mb
installed size is 46.5Mb
  sub-directories of 1Mb or more:
    exe  46.5Mb
Running examples in ‘RKEEL-Ex.R’ failed
The error most likely occurred in:

> ### Name: Alatasetal_A
> ### Title: Alatasetal_A KEEL Association Rules Algorithm
> ### Aliases: Alatasetal_A R6_Alatasetal_A
> ### Keywords: association rules
> 
> ### ** Examples
> 
> 
> #Load KEEL dataset iris
> dat<-loadKeelDataset("iris")
/home/ripley/R/Lib32/RKEELdata/datasets/> 
> #Create algorithm
> algorithm <- Alatasetal_A(dat)
> 
> #Run algorithm
> algorithm$run()
Executing algorithm...
java -jar RunKeel.jar/tmp/RtmpmtaqWW/experiment_2018-03-17_02-12-062656/results/KEELToPMML/TSTAlatasetal_A/result0s0file0.pmml
Error! Error in private$readOutputs(paste0(private$mainPath, "/results/KEELToPMML/TST", : Results were not stored. Execution error.
> 
> #Rules in format arules
> algorithm$rules
NULL
> 
> #Show a number of rules
> algorithm$showRules(2)
Error! Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘inspect’ for signature ‘"NULL"’
> 
> #Return a data.frame with all interest measures of set rules
> algorithm$getInterestMeasures()
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘quality’ for signature ‘"NULL"’
Calls: <Anonymous> -> <Anonymous> -> <Anonymous>
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      1.0Mb
    extdata   3.1Mb
Found the following significant warnings:
  "lib/vec.c", line 29: warning: improper pointer/integer combination: op "="
See ‘/home/ripley/R/packages/tests32/rlang.Rcheck/00install.out’ for details.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rlas)
  > 
  > test_check("rlas")
  Error: std::bad_alloc
  ── 1. Failure: streaming works with extra bytes (@test-readlas.R#58)  ──────────
  `las1` not equal to `las2`.
  Different number of rows
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 31 SKIPPED: 0 FAILED: 1
  1. Failure: streaming works with extra bytes (@test-readlas.R#58) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘Rlibeemd-Ex.R’ failed
The error most likely occurred in:

> ### Name: ceemdan
> ### Title: CEEMDAN decomposition
> ### Aliases: ceemdan
> 
> ### ** Examples
> 
> imfs <- ceemdan(UKgas, threads = 1)
Error reported by gsl_linalg_solve_tridiag: tried to divide by zero
Error reported by gsl_linalg_solve_tridiag: tried to divide by zero
Error reported by gsl_linalg_solve_tridiag: tried to divide by zero
> # trend extraction
> ts.plot(UKgas, imfs[, ncol(imfs)], col = 1:2, 
+         main = "Quarterly UK gas consumption", ylab = "Million therms")
> 
> # CEEMDAN for logarithmic demand, note that increasing ensemble size 
> # will produce smoother results
> imfs <- ceemdan(log(UKgas), ensemble_size = 50, threads = 1)
Error reported by gsl_linalg_solve_tridiag: tried to divide by zero
> plot(ts.union("log(obs)" = log(UKgas), Seasonal = imfs[, 1], 
+      Irregular = rowSums(imfs[, 2:5]), Trend = imfs[, 6]), 
+      main = "Quarterly UK gas consumption")
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 in plot.window(...) : need finite 'ylim' values
Calls: plot ... plotts -> plot.default -> localWindow -> plot.window
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Luminescence
Loading required package: magrittr
Welcome to the R package Luminescence version 0.8.2 [Built: 2018-03-16 19:42:52 UTC]
A fluvially transported quartz grain at night: 'Always look at the bright side of life.'

Attaching package: 'RLumModel'

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

    model_LuminescenceSignals

Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 125-154 (RLumModel_-_Simulating_luminescence_in_Al2O3.Rmd) 
Error: processing vignette 'RLumModel_-_Simulating_luminescence_in_Al2O3.Rmd' failed with diagnostics:
subscript out of bounds
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 50-54 (rmapshaper.Rmd) 
Error: processing vignette 'rmapshaper.Rmd' failed with diagnostics:
Cannot open data source
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/RMariaDB.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    rmd   6.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    java   4.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: pwr
Loading required package: psych
Loading required package: RColorBrewer
Loading required package: plotrix

Attaching package: 'plotrix'

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

    rescale

Loading required package: rmcorr
Loading required package: lme4
Loading required package: Matrix
Loading required package: ggplot2

Attaching package: 'ggplot2'

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

    %+%, alpha

Loading required package: merTools
Loading required package: arm
Loading required package: MASS

arm (Version 1.9-3, built: 2016-11-21)

Working directory is /home/ripley/R/packages/tests32/rmcorr.Rcheck/vign_test/rmcorr/vignettes


Attaching package: 'arm'

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

    rescale

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

    logit, rescale, sim

Loading required package: dplyr

Attaching package: 'dplyr'

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

    select

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'merTools'

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

    ICC

Warning in rmcorr(sub, newX, newY, exampleMat) :
  'sub' coerced into a factor
Warning in rmcorr(sub, newX, newY, exampleMat) :
  'sub' coerced into a factor
Warning in rmcorr(sub, newX, newY, exampleMat2) :
  'sub' coerced into a factor
Warning in rmcorr(sub, newX, newY, exampleMat3) :
  'sub' coerced into a factor
Quitting from lines 523-595 (Combined_paper_figures.Rmd) 
Error: processing vignette 'Combined_paper_figures.Rmd' failed with diagnostics:
Starting values violate bounds
Execution halted
File ‘RMC/libs/RMC.so’:
  Found ‘__1cDstdEcout_’, 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 use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    java  12.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ape
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
No ENTREZ API key provided
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Struthioniformes'

Quitting from lines 85-86 (metadata.Rmd) 
Error: processing vignette 'metadata.Rmd' failed with diagnostics:
'{"error":"API key invalid","api-key":"","type":"invalid","status":"unknown"}' does not exist in current working directory ('/home/ripley/R/packages/tests32/RNeXML.Rcheck/vign_test/RNeXML/vignettes').
Execution halted
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    R   9.8Mb
Running examples in ‘robust-Ex.R’ failed
The error most likely occurred in:

> ### Name: overlaidDenPlot.fdfm
> ### Title: Overlaid Density Plot
> ### Aliases: overlaidDenPlot.fdfm
> ### Keywords: hplot
> 
> ### ** Examples
> 
>   data(los, package="robustbase")
>   los.fm <- fit.models(c(Robust = "fitdstnRob", MLE = "fitdstn"),
+                          x = los, densfun = "gamma")

 *** caught segfault ***
address 1, cause 'memory not mapped'

Traceback:
 1: .Fortran("rlcretabi", b1 = as.double(b1), b2 = as.double(b2),     kk = as.integer(k), la = as.integer(2), a = as.double(A),     maxta = as.integer(maxta), maxtc = as.integer(maxtc), maxit = as.integer(maxit),     til = as.double(til), tol = as.double(tol), alpha1 = as.double(alpha1),     alpha2 = as.double(alpha2), monit = as.integer(0), tab = tab,     tpar = double(6), PACKAGE = "robust")
 2: Tabgamma(b1, b2, alpha1, alpha2, k, A, maxta, maxtc, maxit, til,     tol)
 3: gammaRob(x, ...)
 4: fitdstnRob(x = los, densfun = "gamma")
 5: eval(model.call, sys.parent())
 6: eval(model.call, sys.parent())
 7: fit.models(c(Robust = "fitdstnRob", MLE = "fitdstn"), x = los,     densfun = "gamma")
An irrecoverable exception occurred. R is aborting now ...
Installation failed.
See ‘/home/ripley/R/packages/tests32/ROI.plugin.clp.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ROI.plugin.symphony’

Package which this enhances but not available for checking: ‘ROI.plugin.cplex’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 47-57 (meta-analysis.Rmd) 
Error: processing vignette 'meta-analysis.Rmd' failed with diagnostics:
Timeout was reached: Operation timed out after 3287 milliseconds with 0 out of 0 bytes received
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/rpf.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/rpg.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 51-53 (rpivotTableIntroduction.Rmd) 
Error: processing vignette 'rpivotTableIntroduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    extdata  10.9Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/RPostgres.Rcheck/00install.out’ for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
Package required but not available: ‘wdman’

Package suggested but not available for checking: ‘Rcompression’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/ripley/R/packages/tests32/Rserve.Rcheck/00install.out’ for details.
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 use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Installation failed.
See ‘/home/ripley/R/packages/tests32/RSiena.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
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


Attaching package: ‘rsolr’

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

    ftable

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

    grouping


Error: processing vignette 'intro.Rnw' failed with diagnostics:
 chunk 3 (label = SolrFrame) 
Error in value[[3L]](cond) : 
  Failed to retrieve schema. rsolr requires schema via REST or as XML from the admin module.
Execution halted
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    2.6Mb
    libs  10.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 2-15 (./children/SETTINGS-knitr.txt) 
Quitting from lines NA-15 (./children/SETTINGS-knitr.txt) 
Error: processing vignette 'aov.Rmd' failed with diagnostics:
object 'params' not found
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs        4.8Mb
    unitTests   1.0Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/rsunlight.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    include   5.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
Running examples in ‘RxnSim-Ex.R’ failed
The error most likely occurred in:

> ### Name: RxnSim-package
> ### Title: Functions to compute chemical reaction and molecular similarity
> ### Aliases: RxnSim-package RxnSim rxnsim
> 
> ### ** Examples
> 
> ## Not run: Reaction similarity
> rs.compute('CCCO>>CCC=O', 'CC(O)C>>CC(=O)C')
Error in .jcall("org/guha/rcdk/util/Misc", "Ljava/lang/Object;", "getProperty",  : 
  RcallMethod: cannot determine object class
Calls: rs.compute ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data          1.0Mb
    sample_data   2.7Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/s2.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 34-35 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.8Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(scriptexec)
  > 
  > test_check("scriptexec")
  ── 1. Failure: examples: all examples (@test_api_stability.R#156)  ─────────────
  output$status not equal to 0.
  1/1 mismatches
  [1] 1 - 0 == 1
  
  ── 2. Failure: examples: all examples (@test_api_stability.R#157)  ─────────────
  is_string_exists("test_api_stability.R", output$output) not equal to TRUE.
  1 element mismatch
  
  ── 3. Failure: examples: all examples (@test_api_stability.R#162)  ─────────────
  output$status not equal to 0.
  1/1 mismatches
  [1] 1 - 0 == 1
  
  ── 4. Failure: execute: valid command (@test_execute.R#13)  ────────────────────
  output$status not equal to 0.
  1/1 mismatches
  [1] 1 - 0 == 1
  
  ── 5. Failure: execute: valid commands (@test_execute.R#18)  ───────────────────
  output$status not equal to 0.
  1/1 mismatches
  [1] 1 - 0 == 1
  
  ── 6. Failure: execute: runner provided (@test_execute.R#64)  ──────────────────
  output$status not equal to 0.
  1/1 mismatches
  [1] 1 - 0 == 1
  
  ── 7. Failure: execute: print_commands (@test_execute.R#69)  ───────────────────
  output$status not equal to 0.
  1/1 mismatches
  [1] 1 - 0 == 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 62 SKIPPED: 0 FAILED: 7
  1. Failure: examples: all examples (@test_api_stability.R#156) 
  2. Failure: examples: all examples (@test_api_stability.R#157) 
  3. Failure: examples: all examples (@test_api_stability.R#162) 
  4. Failure: execute: valid command (@test_execute.R#13) 
  5. Failure: execute: valid commands (@test_execute.R#18) 
  6. Failure: execute: runner provided (@test_execute.R#64) 
  7. Failure: execute: print_commands (@test_execute.R#69) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data            1.5Mb
    vignette_data   2.1Mb
Running examples in ‘Segmentor3IsBack-Ex.R’ failed
The error most likely occurred in:

> ### Name: BestSegmentation
> ### Title: BestSegmentation
> ### Aliases: BestSegmentation
> ### Keywords: R-package PDPA Segmentation
> 
> ### ** Examples
> 
> require(Segmentor3IsBack);
> N=2000 
> x=rnbinom(3*N,size=1.3,prob=rep(c(0.7,0.2,0.01),each=N));
> res=Segmentor(data=x,model=3,Kmax=10, keep=TRUE);  
Error in cumsum(datasize)[breaks[k, 1:k]] : 
  only 0's may be mixed with negative subscripts
Calls: Segmentor -> Segmentor.default
Execution halted
Package suggested but not available for checking: ‘OpenMx’
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    6.2Mb
    libs   1.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data        1.7Mb
    sequences   2.1Mb
Running examples in ‘seqminer-Ex.R’ failed
The error most likely occurred in:

> ### Name: annotateGene
> ### Title: Annotate a test variant
> ### Aliases: annotateGene
> 
> ### ** Examples
> 
> param <- list(reference = system.file("tabanno/test.fa", package = "seqminer"),
+               geneFile = system.file("tabanno/test.gene.txt", package = "seqminer"))
> param <- makeAnnotationParameter(param)
> print(param)
$reference
[1] "/home/ripley/R/Lib32/seqminer/tabanno/test.fa"

$geneFile
[1] "/home/ripley/R/Lib32/seqminer/tabanno/test.gene.txt"

$geneFileFormat
[1] "refFlat"

$codonFile
[1] "/home/ripley/R/Lib32/seqminer/tabanno/codon.txt"

$priorityFile
[1] "/home/ripley/R/Lib32/seqminer/tabanno/priority.txt"

$upstreamRange
[1] 50

$downstreamRange
[1] 50

$spliceIntoExon
[1] 3

$spliceIntoIntron
[1] 8

$bed
NULL

$genomeScore
NULL

$tabix
NULL

$indexOutput
[1] FALSE

$inputFormat
[1] "vcf"

$checkReference
[1] TRUE

> annotateGene(param, c("1", "1"), c(3, 5) , c("A", "C"), c("G", "C"))
Load reference genome /home/ripley/R/Lib32/seqminer/tabanno/test.fa...
DONE: 1 chromosomes and 74 bases are loaded.
Load codon file /home/ripley/R/Lib32/seqminer/tabanno/codon.txt...
DONE: codon file loaded.
Load priority file /home/ripley/R/Lib32/seqminer/tabanno/priority.txt...
DONE: 25 priority annotation types loaded.
Load gene file /home/ripley/R/Lib32/seqminer/tabanno/test.gene.txt...
DONE: 3 gene loaded from /home/ripley/R/Lib32/seqminer/tabanno/test.gene.txt.

 *** caught segfault ***
address 0, cause 'memory not mapped'

Traceback:
 1: .Call("annotateGene", param, chrom, position, ref, alt, PACKAGE = "seqminer")
 2: annotateGene(param, c("1", "1"), c(3, 5), c("A", "C"), c("G",     "C"))
An irrecoverable exception occurred. R is aborting now ...
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    doc     10.5Mb
    sqlite   1.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 195-198 (sf5.Rmd) 
Error: processing vignette 'sf5.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    www   9.9Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    www   7.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    semantic   6.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 89-90 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.7Mb
Error in re-building vignettes:
  ...
Loading required package: rcdklibs
Loading required package: rJava

Error: processing vignette 'SimuChemPC_vignette.Rnw' failed with diagnostics:
 chunk 2 
Error in .jcall("org/guha/rcdk/util/Misc", "[Lorg/openscience/cdk/interfaces/IAtomContainer;",  : 
  RcallMethod: cannot determine object class
Execution halted
Running ‘testthat.R’ [11s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(skimr)
  
  Attaching package: 'skimr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  > 
  > test_check("skimr")
  ── 1. Failure: Skimr kable prints as expected, 32-bit windows (@test-skim_print.
  input[16] not equal to "|Petal.Width  |0       |150      |150 |1.2  |0.76 |0.1 |0.3 |1.3    |1.8 |2.5  |▇▁▁▃▃▃▂▂ |".
  1/1 mismatches
  x[1]: "|Petal.Width  |0       |150      |150 |1.2  |0.76 |0.1 |0.3 |1.3    |1.8 
  x[1]: |2.5  |▇▁▁▅▃▃▂▂ |"
  y[1]: "|Petal.Width  |0       |150      |150 |1.2  |0.76 |0.1 |0.3 |1.3    |1.8 
  y[1]: |2.5  |▇▁▁▃▃▃▂▂ |"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 328 SKIPPED: 1 FAILED: 1
  1. Failure: Skimr kable prints as expected, 32-bit windows (@test-skim_print.R#104) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: magrittr
Loading required package: data.table
skm_mls: skm solver via skm_mls_cpp ...

skm_mls: auto_create g w.r.t first letter of s_name.

skm_mls: optimizing on k <1> ...

skm_mls: optimizing on k <1> ... done.

skm_mls: optimizing on k <2> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <2> ... done.

skm_mls: optimizing on k <3> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <3> ... done.

skm_mls: optimizing on k <4> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <4> ... done.

skm_mls: optimizing on k <5> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <5> ... done.

skm_mls: optimizing on k <6> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <6> ... done.

skm_mls: optimizing on k <7> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: encounter better solution at jk <18> run based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <7> ... done.

skm_mls: optimizing on k <8> ...
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Running examples in ‘SMCP-Ex.R’ failed
The error most likely occurred in:

> ### Name: SMCP
> ### Title: Smoothed minimax concave penalization (SMCP) method for
> ###   genome-wide association studies.
> ### Aliases: SMCP sp
> ### Keywords: model fitting
> 
> ### ** Examples
> 
> x=matrix(rnorm(100*20),100,20)
> y=rnorm(100)
> fit=SMCP(x,y,0.3,0.3,3)
> #solution path for this data
> s.p=sp(x,y,0.3,10,0.05,3)
Error in SMCP(x, y, alpha, delta * i, gamma) : 
  NA/NaN/Inf in foreign function call (arg 6)
Calls: sp -> SMCP
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
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

Identifing all possible orderings..
Total run time: 2.06 secs
Identifing all possible orderings..
Total run time: 2.17 secs
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot59c425d429cf.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot59c425d429cf.png': No such file or directory
Quitting from lines 346-347 (SourceSet.Rmd) 
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

Loading required package: quickPlot
Loading required package: reproducible

Attaching package: 'reproducible'

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

    %>%

Loading required package: RColorBrewer
Loading required package: raster
Loading required package: sp
Loading required package: grid

Attaching package: 'grid'

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

    gpar

Quitting from lines 357-361 (ii-modules.Rmd) 
Error: processing vignette 'ii-modules.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot55cd2ad2ac.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot55cd2ad2ac.png': No such file or directory
Quitting from lines 20-30 (intro_sparkline.Rmd) 
Error: processing vignette 'intro_sparkline.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'SparkR'

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

    cov, filter, lag, na.omit, predict, sd, var, window

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

    as.data.frame, colnames, colnames<-, drop, endsWith,
    intersect, rank, rbind, sample, startsWith, subset, summary,
    transform, union

Picked up _JAVA_OPTIONS: -XX:-UsePerfData 
Exception in thread "main" java.lang.UnsupportedClassVersionError: org/apache/spark/launcher/Main : Unsupported major.minor version 52.0
	at java.lang.ClassLoader.defineClass1(Native Method)
	at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
	at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
	at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
	at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
	at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)
Quitting from lines 65-67 (sparkr-vignettes.Rmd) 
Error: processing vignette 'sparkr-vignettes.Rmd' failed with diagnostics:
JVM is not ready after 10 seconds
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/spass.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/spatialwarnings.Rcheck/00install.out’ for details.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    R      5.2Mb
    doc    5.0Mb
    help   5.0Mb
    libs   1.3Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.9Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
Running examples in ‘sptemExp-Ex.R’ failed
The error most likely occurred in:

> ### Name: extractVNC4
> ### Title: Extract Values for Point from NC4 Image
> ### Aliases: extractVNC4
> ### Keywords: ~kwd1 ~kwd2
> 
> ### ** Examples
> 
> 
> data("samplepnt")
> nc4File=file.path(system.file(package = "sptemExp"), "extdata", "ancdata.nc4")
> ncin0=ncdf4::nc_open(nc4File)
Error in R_nc4_open: NetCDF: HDF error
Error in ncdf4::nc_open(nc4File) : 
  Error in nc_open trying to open file /home/ripley/R/Lib32/sptemExp/extdata/ancdata.nc4
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    lsndata   2.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    include   5.7Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   5.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R          2.1Mb
    datasets   2.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 111-114 (introducing-stplanr.Rmd) 
Error: processing vignette 'introducing-stplanr.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Building shared library for Rcpp code chunk...
make: Warning: Ignoring DistributedMake -j option
make: Warning: Ignoring DistributedMake -j option
make: Fatal error: Don't know how to make target `fileb8129a01a6c.o'
Current working directory /tmp/Rtmp0paiWf/sourceCpp-i386-pc-solaris2.10-0.12.16/sourcecpp_b8190f7d7
`/home/ripley/R/cc/etc/Makeconf' is up to date.
`/home/ripley/R/cc/etc/Makeconf' is up to date.
Quitting from lines 60-85 (strider.Rmd) 
Error: processing vignette 'strider.Rmd' failed with diagnostics:
Error occurred building shared library.
Execution halted
installed size is 33.0Mb
  sub-directories of 1Mb or more:
    libs  32.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 61-64 (stRvignette.Rmd) 
Error: processing vignette 'stRvignette.Rmd' failed with diagnostics:
Process terminated
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/subprocess.Rcheck/00install.out’ for details.
Running examples in ‘subspaceMOA-Ex.R’ failed
The error most likely occurred in:

> ### Name: DSC_HDDStream
> ### Title: Density-based Projected Clustering over High-Dimensional Data
> ### Aliases: DSC_HDDStream
> 
> ### ** Examples
> 
> dsc <- DSC_HDDStream()
Error in rJava::.jcall("moa/r_interface/OneStageClusterer", returnSig = "Lmoa/r_interface/RCompatibleDataStreamClusterer;",  : 
  RcallMethod: cannot determine object class
Calls: DSC_HDDStream -> <Anonymous>
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    help   1.0Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   1.9Mb
    doc    2.9Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 540-542 (survtmle_intro.Rmd) 
Error: processing vignette 'survtmle_intro.Rmd' failed with diagnostics:
'names' attribute [3] must be the same length as the vector [2]
Execution halted
Running examples in ‘svd-Ex.R’ failed
The error most likely occurred in:

> ### Name: extmat
> ### Title: External matrices operations.
> ### Aliases: is.extmat extmat.ncol extmat.nrow extmat ematmul
> 
> ### ** Examples
> 
> ## Not run: 
> ##D library(Matrix)
> ##D f <- function(v) as.numeric(A %*% v) # Convert Matrix object back to vector
> ##D tf <- function(v) as.numeric(tA %*% v) # Convert Matrix object back to vector
> ##D 
> ##D e <- new.env()
> ##D assign("A", USCounties, e)
> ##D assign("tA", t(USCounties), e)
> ##D environment(f) <- e
> ##D environment(tf) <- e
> ##D 
> ##D m <-extmat(f, tf, nrow(USCounties), ncol(USCounties))
> ##D system.time(v1 <- propack.svd(m, neig = 10))
> ##D #   user  system elapsed 
> ##D #  0.252   0.007   0.259 
> ##D system.time(v2 <- propack.svd(as.matrix(USCounties), neig = 10))
> ##D #   user  system elapsed 
> ##D #  8.563   0.027   8.590 
> ## End(Not run)
> 
> # The largest eigenvalue and the corresponding eigenvector of a Hilbert matrix
> h <- outer(1:5000, 1:5000, function(i, j) 1 / (i + j - 1))
> v1 <- trlan.eigen(h, neig = 1)
> # Same, but using complex numbers
> v2 <- ztrlan.eigen(h, neig = 1)

 *** caught segfault ***
address 1f0, cause 'memory not mapped'

Traceback:
 1: .Call("ztrlan_eigen", X, neig, opts, lambda, U)
 2: ztrlan.eigen(h, neig = 1)
An irrecoverable exception occurred. R is aborting now ...
File ‘svmpath/libs/svmpath.so’:
  Found ‘__f90_close’, possibly from ‘close’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘__f90_eifr’, possibly from ‘read’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi30spec.o’, ‘mi36mps.o’, ‘mi40bfil.o’
  Found ‘__f90_esfr’, possibly from ‘read’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi30spec.o’, ‘mi35mps.o’,
      ‘mi36mps.o’, ‘mi40bfil.o’
  Found ‘__f90_esfw’, possibly from ‘print’ (Fortran), ‘write’
    (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’
  Found ‘__f90_open’, possibly from ‘open’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘__f90_rewind’, possibly from ‘rewind’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi10unix.o’, ‘mi35mps.o’, ‘mi40bfil.o’

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

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

> ### Name: nullModel
> ### Title: SwapClass null model
> ### Aliases: nullModel
> 
> ### ** Examples
> 
> MAT=matrix(sample(0:3,50*20,replace=TRUE,prob=c(.7,.1,.1,.1)),ncol=20)
> 
> #Generation of null communities
> NULL_MATS=nullModel(MAT)

 *** caught segfault ***
address fe1a07f0, cause 'memory not mapped'

Traceback:
 1: .Primitive(".C")(<pointer: fe1a07f0>, mat0 = as.double(mat0),     mat = as.double(mat), nsim = as.integer(nsim), recursive = as.integer(recursive),     nr = as.integer(nr), nc = as.integer(nc), Kb = as.integer(Kb),     Kt = as.integer(Kt), strata = as.integer(strata), perms = as.double(perms))
 2: swapClass_swapC(mat0 = as.double(mat0), mat = as.double(mat),     nsim = as.integer(nsim), recursive = as.integer(recursive *         1), nr = as.integer(nr), nc = as.integer(nc), Kb = as.integer(burnin),     Kt = as.integer(thin), strata = as.integer(strata), perms = as.double(perms))
 3: swapClass_swapC(mat0 = as.double(mat0), mat = as.double(mat),     nsim = as.integer(nsim), recursive = as.integer(recursive *         1), nr = as.integer(nr), nc = as.integer(nc), Kb = as.integer(burnin),     Kt = as.integer(thin), strata = as.integer(strata), perms = as.double(perms))
 4: nullModel(MAT)
An irrecoverable exception occurred. R is aborting now ...
*** caught segfault ***
address 63203220, cause 'memory not mapped'

Traceback:
 1: dyn.load(file, DLLpath = DLLpath, ...)
 2: library.dynam(lib, package, package.lib)
 3: loadNamespace(p)
 4: withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessage"))
 5: suppressMessages(loadNamespace(p))
 6: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
 7: suppressWarnings(suppressMessages(loadNamespace(p)))
 8: doTryCatch(return(expr), name, parentenv, handler)
 9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch(suppressWarnings(suppressMessages(loadNamespace(p))),     error = function(e) e)
12: tools:::.check_packages_used(package = "sybil")
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.3Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    sql   8.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    3.9Mb
Package suggested but not available for checking: ‘btergm’

Packages which this enhances but not available for checking:
  ‘RSiena’ ‘xergm’
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    3.8Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   8.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    rda    4.1Mb
Package suggested but not available for checking: ‘Rblpapi’
Package unavailable to check Rd xrefs: ‘Rblpapi’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

sh: nproc:  not found
Quitting from lines 111-113 (Tigger-Vignette.Rmd) 
Error: processing vignette 'Tigger-Vignette.Rmd' failed with diagnostics:
error in running command: 'Illegal seek'
Execution halted
Running examples in ‘TimeMachine-Ex.R’ failed
The error most likely occurred in:

> ### Name: mu.mle
> ### Title: Maximum-Likelihood Estimation of the Mutation Rate
> ### Aliases: mu.mle
> 
> ### ** Examples
> 
> # Load example dataset
> data(pdm)
> transitions <- full.transitions(pdm$unitary.transitions, pdm$loci)
> pi <- stationary.dist(transitions)
> 
> mu.int <- c(0.1, 10)
> samples <- 10
> 
> # MLE of the mutation rate for a single target population size
> n <- 10
> mle.res <- mu.mle(transitions, pi, pdm$population, n, mu.int, samples)
Error: C stack usage  189030512 is too close to the limit
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc         3.8Mb
    rmarkdown   1.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    3.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-26 (toOrdinal.Rmd) 
Error: processing vignette 'toOrdinal.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
File ‘tpr/libs/tpr.so’:
  Found ‘__1cDstdEcerr_’, 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 use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Loading required package: trackdem

Error: processing vignette 'tutorial.Rnw' failed with diagnostics:
 chunk 10 (label = trackParticlesHidden) 
Error : cannot allocate vector of size 824.0 Mb
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    2.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: ggplot2

Attaching package: 'trackeR'

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

    append

Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=57.157231,-2.104296&zoom=13&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false
Quitting from lines 96-97 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running examples in ‘treatSens-Ex.R’ failed
The error most likely occurred in:

> ### Name: treatSens.BART
> ### Title: Dual-Parameter Sensitivity Analysis Using BART
> ### Aliases: treatSens.BART
> 
> ### ** Examples
> 
> N <- 250                      # number of observations
> 
> zetay <- 0.5                  # coefficient on U in the outcome model
> zetaz <- 0.5                  # coefficient on U in the treatment model
> betaz <- c(0.75, -0.5,  0.25) # coefficients of X in the treatment model
> betay <- c(0.5,   1.0, -1.5)  # coefficients of X in the outcome model
> tau   <- 0.25                 # treatment effect
> 
> set.seed(725)
> X <- matrix(rnorm(3 * N), N)  # covariates
> 
> U  <- rbinom(N, 1, 0.5)                        # unmeasured confounder
> ps <- pnorm(X %*% betaz + zetaz * (U - 0.5)) # propensity score
> Z  <- rbinom(N, 1, ps)                         # treatment variable
> epsilon <- rnorm(N, 0.0, 2.0)                  # error term
> 
> Y0 <- X %*% betay + zetay * (U - 0.5) + epsilon       # potential outcome(Z=0)
> Y1 <- X %*% betay + zetay * (U - 0.5) + tau + epsilon # potential outcome(Z=1)
> Y  <- Y0 * (1 - Z) + Y1 * Z                             # realization of potential outcome
> 
> # sensitivity analysis
> out.bin <- treatSens.BART(Y ~ Z + X, nsim = 3, nthin = 2, nburn = 0,
+                           spy.range = c(0, 4), spz.range = c(-2 , 2), grid.dim = c(5, 3),
+                           standardize = FALSE, verbose = TRUE)
Binary U with binomial distribution is assumed.
Error in .Object$initialize(...) : adaptive radix tree not aligned
Calls: treatSens.BART ... new -> initialize -> initialize -> <Anonymous> -> .Call
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ape
Loading required package: ade4
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'

   /// adegenet 2.1.1 is loaded ////////////

   > overview: '?adegenet'
   > tutorials/doc/questions: 'adegenetWeb()' 
   > bug reports/feature requests: adegenetIssues()



Attaching package: 'adegenet'

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

    AICc

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

    .render.server.info

Quitting from lines 139-141 (DengueVignette.Rmd) 
Error: processing vignette 'DengueVignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/trialr.Rcheck/00install.out’ for details.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(trustOptim)
  > 
  > test_check("trustOptim")
  Beginning optimization
  
  Iteration has terminated
  
  iter            f           nrm_gr                     status
    50       0.000000       0.000000                    Success
  
  Beginning optimization
  
  Iteration has terminated
  
  iter            f           nrm_gr                     status
   128       0.000000       0.000000                    Success
  
  Beginning optimization
  
  Iteration has terminated
  
  iter            f           nrm_gr                     status
   287       0.000000       0.000000Radius of trust region is less than stop.trust.radius
  
  ── 1. Failure: Rosenbrock (@test_rosenbrock.R#67)  ─────────────────────────────
  opt0\$status does not match "Success".
  Actual value: "Radius of trust region is less than stop\.trust\.radius"
  
  Beginning optimization
  
  Iteration has terminated
  
  iter            f           nrm_gr                     status
    65       0.000000       0.000000                    Success
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 15 SKIPPED: 0 FAILED: 1
  1. Failure: Rosenbrock (@test_rosenbrock.R#67) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘TSEtools-Ex.R’ failed
The error most likely occurred in:

> ### Name: mcPrt
> ### Title: Matrix Conversion in Portfolio
> ### Aliases: mcPrt
> 
> ### ** Examples
> 
> fpath<-system.file("extdata", "sample.csv", package="TSEtools")
> asset0<-getTSE(fpath)$assets
proceeding...
SSPF1 compeleted! 
Last observations:
            Open  High   Low Close Volume  <NA>
2018-03-14 10034 10034 10034 10034   2540 10034

proceeding...
KMND1 compeleted! 
Last observations:
           Open High  Low Close Volume <NA>
2018-03-18 9901 9998 9900  9905  21000 9900

proceeding...
FPAF1 compeleted! 
Last observations:
            Open  High   Low Close  Volume  <NA>
2018-03-18 10045 10045 10011 10025 6530249 10044


 SSPF1 KMND1 FPAF1 are assigned!
> rtn<-mcPrt(asset0, sub="2016::", pstvRtn=TRUE, L=5)$return
Values in % base lag= 5 :
      meanReturn volatility sharpRatio
FPAF1          0       1.98       0.18

> 
> 
> 
> ### * <FOOTER>
> ###
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  1.411 0.092 51.503 0 0 
> grDevices::dev.off()
Error in grDevices::dev.off() : 
  cannot shut down device 1 (the null device)
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
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.
'getSymbols' currently uses auto.assign=TRUE by default, but will
use auto.assign=FALSE in 0.5-0. You will still be able to use
'loadSymbols' to automatically load data. getOption("getSymbols.env")
and getOption("getSymbols.auto.assign") will still be checked for
alternate defaults.

This message is shown once per session and may be disabled by setting 
options("getSymbols.warning4.0"=FALSE). See ?getSymbols for details.

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

This message is shown once per session and may be disabled by setting
options("getSymbols.yahoo.warning"=FALSE).
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot449c3a2d69bb.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot449c3a2d69bb.png': No such file or directory
Quitting from lines 37-64 (TSstudio_Intro.Rmd) 
Error: processing vignette 'TSstudio_Intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    doc         5.5Mb
    dummydata   1.5Mb
    libs        1.9Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/unrtf.Rcheck/00install.out’ for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc   8.2Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    data  14.9Mb
installed size is 29.8Mb
  sub-directories of 1Mb or more:
    data  29.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    extdata   6.5Mb
Running examples in ‘utiml-Ex.R’ failed
The error most likely occurred in:

> ### Name: ctrl
> ### Title: CTRL model for multi-label Classification
> ### Aliases: ctrl
> 
> ### ** Examples
> 
> model <- ctrl(toyml, "RANDOM")
Error in ctrl(toyml, "RANDOM") : 
  There are no installed package 'FSelector' to use CTRL multi-label classifier
Execution halted
Running ‘testthat.R’ [19s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(utiml)
  Loading required package: mldr
  > 
  > test_check("utiml")
  ── 1. Error: CTRL (@test_brclassifiers.R#94)  ──────────────────────────────────
  There are no installed package 'FSelector' to use CTRL multi-label classifier
  1: ctrl(train, "RANDOM") at testthat/test_brclassifiers.R:94
  2: stop(paste("There are no installed package 'FSelector' to use CTRL", "multi-label classifier"))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1061 SKIPPED: 21 FAILED: 1
  1. Error: CTRL (@test_brclassifiers.R#94) 
  
  Error: testthat unit tests failed
  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 use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 24-36 (intro_to_vegalite.Rmd) 
Error: processing vignette 'intro_to_vegalite.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    1.3Mb
    help   2.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 157-163 (using_visdat.Rmd) 
Error: processing vignette 'using_visdat.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc           4.8Mb
    htmlwidgets   4.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 22-27 (Introduction-to-visNetwork.Rmd) 
Error: processing vignette 'Introduction-to-visNetwork.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    extdata  11.3Mb
Found the following significant warnings:
  "predict.c", line 112: warning: improper pointer/integer combination: op "<"
See ‘/home/ripley/R/packages/tests32/VLMC.Rcheck/00install.out’ for details.
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 use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   3.9Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/wand.Rcheck/00install.out’ for details.
Running examples in ‘WaterML-Ex.R’ failed
The error most likely occurred in:

> ### Name: AddMethods
> ### Title: AddMethods
> ### Aliases: AddMethods
> ### Keywords: waterml
> 
> ### ** Examples
> 
> user <- "admin"
> pass <- "password"
> server <- "http://worldwater.byu.edu/app/index.php/default/services/cuahsi_1_1.asmx"
> #make random site codes
> random_description <- sprintf("R Test Method %04d",sample(1:10000, 1))
> random_link <- "http://example.com"
> my_methods <- data.frame(
+   MethodDescription = random_description,
+   MethodLink = random_link
+ )
> 
> added_methods <- AddMethods(server, username=user, password=pass,
+                                 methods=my_methods)
[1] "{\n \"user\": \"admin\",\n\"password\": \"password\",\n\"MethodDescription\": \"R Test Method 2656\",\n\"MethodLink\": \"http://example.com\",\n\"VariableID\":      0 \n}"
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Connection timed out after 10010 milliseconds
Calls: AddMethods ... request_fetch -> request_fetch.write_memory -> <Anonymous> -> .Call
Execution halted
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc  12.3Mb
Package required but not available: ‘subprocess’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    client  10.1Mb
    doc      1.1Mb
Package suggested but not available for checking: ‘iptools’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 37-39 (wordcloud.Rmd) 
Error: processing vignette 'wordcloud.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    data  13.4Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  11.9Mb
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
Quitting from lines 884-890 (WRS2.Rnw) 
Error: processing vignette 'WRS2.Rnw' failed with diagnostics:
could not find function "mediation"
Execution halted
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    data  14.3Mb
Package required but not available: ‘x12’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/ripley/R/packages/tests32/x12.Rcheck/00install.out’ for details.
Package unavailable to check Rd xrefs: ‘RSiena’
Package required but not available: ‘btergm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    java  19.3Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    java  10.9Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    exampleData   1.5Mb
    examples      4.6Mb
Running examples in ‘XRJulia-Ex.R’ failed
The error most likely occurred in:

> ### Name: JuliaFunction-class
> ### Title: Proxy Objects in R for Julia Functions
> ### Aliases: JuliaFunction JuliaFunction-class
> ###   initialize,JuliaFunction-method
> 
> ### ** Examples
> 
> if(findJulia(test = TRUE)) {
+   set.seed(228)
+   x <- matrix(rnorm(1000),20,5)
+   xm <- juliaSend(x)
+   svdJ <- JuliaFunction("svdfact")
+   sxm <- svdJ(xm)
+   sxm
+ }
sh: no:  not found
Error in base::system(cmd, intern = TRUE) : 
  error in running command: 'Illegal seek'
Calls: findJulia -> testJSON -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
date	lon	lat	lowLon	higLon	lowLat	higLat
4/23/2003	203.899	19.664	203.899	203.899	19.664	19.664
4/24/2003	204.151	19.821	203.912597	204.389403	18.78051934	20.86148066
4/30/2003	203.919	20.351	203.6793669	204.1586331	18.79728188	21.90471812
5/1/2003	204.229	20.305	203.9943343	204.4636657	18.90440013	21.70559987
Quitting from lines 1055-1057 (Usingxtractomatic.Rmd) 
Error: processing vignette 'Usingxtractomatic.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running examples in ‘yhat-Ex.R’ failed
The error most likely occurred in:

> ### Name: aps
> ### Title: All Possible Subsets Regression
> ### Aliases: aps
> ### Keywords: models regression
> 
> ### ** Examples
> 
>   ## APS regression predicting miles per gallon based 
>   ## on vehicle weight, type of 
>   ## carborator, & number of engine cylinders
>      apsOut<-aps(mtcars,"mpg",list("wt","carb","cyl"))
> 
>   ## APS regression predicting paragraph comprehension based 
>   ## on thre verbal tests: general info, sentence comprehension,
>   ## & word classification
>  
>   ## Use HS dataset in MBESS 
>      require ("MBESS")
Loading required package: MBESS
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘MBESS’
>      data(HS.data)
Warning in data(HS.data) : data set ‘HS.data’ not found
>   ## APS
>      apsOut<-aps(HS.data,"paragrap",list("general","sentence",
+                                          "wordc"))
Error in is.data.frame(x) : object 'HS.data' not found
Calls: aps -> colnames -> is.data.frame
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/zstdr.Rcheck/00install.out’ for details.
Running examples in ‘ApacheLogProcessor-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: read.multiple.apache.access.log
> ### Title: Reads multiple files of apache web server.
> ### Aliases: read.multiple.apache.access.log
> 
> ### ** Examples
> 
> path <- system.file("examples", package="ApacheLogProcessor")
> path <- paste(path, "/", sep="")
> 
> #read multiple gziped logs with the prefix m_access_log_combined_
> dfLog <- read.multiple.apache.access.log(path, "m_access_log_combined_")
[1] "Starting the log processing. This may take a long time..."
[1] "Processing file  m_access_log_combined_1.log.gz"
[1] "Unziping  m_access_log_combined_1.log.gz"
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/ApacheLogProcessor/examples/m_access_log_combined_1.log': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: read.multiple.apache.access.log -> write -> cat -> file
Execution halted
Running examples in ‘ASIP-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: arvi
> ### Title: Atmospherically Resistant Vegetation Index
> ### Aliases: arvi
> 
> ### ** Examples
> 
> library (raster)
Loading required package: sp
> library (rgdal)
rgdal: version: 1.2-18, (SVN revision 718)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.2.3, released 2017/11/20
 Path to GDAL shared files: /usr/share/gdal/2.2
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 5.0.0, March 1st, 2018, [PJ_VERSION: 500]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.2-7 
> # Finding the path of the sample satellite image directory.
> # User may define paths directly like "/home/ur_folder" or "C:/ur_folder"
> path <- system.file ("TM_sample", package = "ASIP")
> shapefil <- paste0 (path, "/test.shp")
> arvi (directory = path, crop = "y", ext2crop = shapefil)
OGR data source with driver: ESRI Shapefile 
Source: "/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/ASIP/TM_sample/test.shp", layer: "test"
with 1 features
It has 1 fields
Integer64 fields read as strings:  id 
Error in .local(.Object, ...) : Dataset copy failed
Calls: arvi ... <Anonymous> -> new -> initialize -> initialize -> .local -> .Call
Execution halted
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-release-gcc/Work/PKGS/audio.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: orthopolynom
Loading required package: polynom
Loading required package: VGAM
Loading required package: stats4
Loading required package: splines
Killed
Running examples in ‘biclique-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bi.format
> ### Title: Add number of vertices and edges to the input file
> ### Aliases: bi.format
> 
> ### ** Examples
> 
> bi.format(system.file("extdata", "example2.el", package = "biclique"))
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/biclique/extdata/example2.el': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: bi.format -> cat -> file
Execution halted
Error in re-building vignettes:
  ...
Loading required package: ggmap
Loading required package: ggplot2
Loading required package: RCurl
Loading required package: bitops
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=Chicago,%20IL&sensor=false
Warning: geocode failed with status OVER_QUERY_LIMIT, location = "Chicago, IL"
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=New%20York&sensor=false
Warning: geocode failed with status OVER_QUERY_LIMIT, location = "New York"
Quitting from lines 16-23 (getting-started.Rmd) 
Error: processing vignette ‘getting-started.Rmd’ failed with diagnostics:
undefined columns selected
Execution halted
Running ‘testthat.R’ [10m/12m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(clusternomics)
  > 
  > test_check("clusternomics")
  Killed
Running examples in ‘CREAM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CREAM
> ### Title: CREAM is the main function for CORE identification
> ### Aliases: CREAM
> 
> ### ** Examples
> 
> CREAM(system.file("extdata", "A549_Chr21.bed", package = "CREAM"),
+ system.file("extdata", "A549_Chr21_COREs.bed", package = "CREAM"),
+ MinLength = 1000, peakNumMin = 2)
[1] "Please make sure there is no overlap between the input genomic regions. Overlap between the input regions may cause error."
[1] "Identifying window size for each Order"
[1] "Identifying COREs"
[1] "Filtering clusters of low order"
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/CREAM/extdata/A549_Chr21_COREs.bed': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: CREAM -> write.table -> file
Execution halted
Running ‘testthat.R’ [6s/57s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(curl)
  > 
  > test_check("curl")
  This is libcurl version 7.58.0 with GnuTLS/3.5.18 
  Using test server: http://hb.opencpu.org 
  ── 1. Error: IDN domain names (@test-idn.R#8)  ─────────────────────────────────
  SSL: certificate subject name (www.malmo.se) does not match target host name 'www.xn--malm-8qa.se'
  1: expect_is(curl::curl_fetch_memory(enc2utf8(malmo))$status_code, "integer") at testthat/test-idn.R:8
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: curl::curl_fetch_memory(enc2utf8(malmo))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 171 SKIPPED: 0 FAILED: 1
  1. Error: IDN domain names (@test-idn.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Cyclops.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 78-85 (Introduction_to_datasus.Rmd) 
Error: processing vignette ‘Introduction_to_datasus.Rmd’ failed with diagnostics:
invalid ‘nrow’ value (too large or NA)
Execution halted
Error in re-building vignettes:
  ...
Loading required package: Rcpp

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Joining, by = "gene"
Joining, by = "cell"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "cell"
Joining, by = c("cell", "capture")
Have 35 cells after filtering
Joining, by = "cell"
Have 20 genes after filtering
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "cell"
Joining, by = c("cell", "capture")
Compiling model
the number of chains is less than 1; sampling not done
Saving compiled model to /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/DeLorean/extdata/exact-sizes.rds
Quitting from lines 145-146 (DeLorean.Rmd) 
Error: processing vignette ‘DeLorean.Rmd’ failed with diagnostics:
cannot open the connection
Execution halted
Running examples in ‘EasyStrata-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EasyStrata
> ### Title: Function to run EasyStrata (v8.6).
> ### Aliases: EasyStrata
> 
> ### ** Examples
> 
> extDataDir=system.file("extdata", package="EasyStrata")
> ## Example Pipeline:
> ecfPipe=paste(extDataDir,"example_pipeline.ecf",sep="/")
> EasyStrata(ecfPipe)
Warning message:
In file(fileLog, open = "a") :
  cannot open file '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/EasyStrata/extdata/example_pipeline.ecf.out': Read-only file system
Execution halted
Running ‘testthat.R’ [1s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ECctmc)
  > 
  > test_check("ECctmc")
  ── 1. Failure: Modified rejection sampling and uniformization target the same di
  t.test(MR_res[k, ], Unif_res[k, ])$p.value < 0.1 isn't false.
  
  ── 2. Failure: Modified rejection sampling and uniformization target the same di
  t.test(MR_res[k, ], Unif_res[k, ])$p.value < 0.1 isn't false.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 5 SKIPPED: 0 FAILED: 2
  1. Failure: Modified rejection sampling and uniformization target the same distribution (@test_simfcns.R#36) 
  2. Failure: Modified rejection sampling and uniformization target the same distribution (@test_simfcns.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: iteration 7 invokes undefined behavior [-Waggressive-loop-optimizations]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/expoRkit.Rcheck/00install.out’ for details.
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-release-gcc/Work/PKGS/FastRWeb.Rcheck/00install.out’ for details.
Running examples in ‘MAGNAMWAR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: FormatMCLFastas
> ### Title: Format all raw GenBank fastas to single OrthoMCL compatible
> ###   fasta file
> ### Aliases: FormatMCLFastas
> 
> ### ** Examples
> 
> 
> dir <- system.file('extdata', 'fasta_dir', package='MAGNAMWAR')
> dir <- paste(dir,'/',sep='')
> formatted_file <- FormatMCLFastas(dir)
Warning in file.remove(outfile) :
  cannot remove file '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/MAGNAMWAR/extdata/fasta_dir/MCLformatted_all.fasta', reason 'Read-only file system'
Writing out to /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/MAGNAMWAR/extdata/fasta_dir/MCLformatted_all.fasta 
Warning in file(description = file.out, open = open) :
  cannot open file '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/MAGNAMWAR/extdata/fasta_dir/MCLformatted_all.fasta': Read-only file system
Error in file(description = file.out, open = open) : 
  cannot open the connection
Calls: FormatMCLFastas -> <Anonymous> -> file
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/maGUI.Rcheck/00install.out’ for details.
Running examples in ‘MetaSubtract-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: meta.subtract
> ### Title: Subtracts GWAS results from one or more cohorts from the
> ###   meta-GWAS results
> ### Aliases: meta.subtract
> ### Keywords: Correct meta-GWAS results Leave-one-out
> 
> ### ** Examples
> 
> metafile="meta_results.txt"
> cohortfiles=c("cohort1_results.txt","cohort2_results.txt")
> # Subtract summary statistics of the two cohorts from the meta summary statistics in metafile.
> # Genomic control correction of the imported meta summary statistics will be undone using 
> # lambda.meta. Genomic control will be applied to the corrected meta summary statistics 
> # (gc_meta=TRUE by default) based on a lambda derived from the new meta summary statistics 
> # (calculate_lambda.meta=TRUE by default). The cohorts summary statistics will always be first 
> # corrected for genomic control before subtracting them from the meta summary statistics. By 
> # default, the lambda will be calculated from the data (calculate_lambdas.cohort=TRUE by default).
> m1<-meta.subtract(metafile=metafile, cohortfiles=cohortfiles, lambda.meta=1.046, 
+       dir=system.file("extdata", package="MetaSubtract"))
[1] "Mon Mar 19 17:19:11 2018"
Reading meta_results.txt 
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file 'MetaSubtract.log': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: meta.subtract -> write.table -> file
Execution halted
Error in re-building vignettes:
  ...
Use the user-defined lambda vector.
Using the criterion BIC to choose optimized penalty.
The chosen penalty throuth BIC is 3.6867.
The penalty term is selected automatically with 50 candidates.
Using the criterion BIC to choose optimized penalty.
The chosen penalty throuth BIC is 4.9895.
The penalty term is selected automatically with 50 candidates.
Using the criterion deviance to choose optimized penalty.
The chosen penalty throuth deviance is 2.4657.
trying URL ‘http://www.cs.columbia.edu/~andrews/mil/data/MIL-Data-2002-Musk-Corel-Trec9.tgz’
Content type 'application/x-gzip' length 6249673 bytes (6.0 MB)
==================================================
downloaded 6.0 MB

Warning in fread("MilData/Musk/musk1norm.svm", header = FALSE) :
  Starting data input on line 2 and discarding line 1 because it has too few or too many items to be column names or data: # Generated by musk_2_svm(/pro/webagents/stu/mil//experiments/musk//data/clean1.data, /pro/webagents/stu/mil//experiments/musk//generate_data/clean1.svm)
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Warning: 'switch' is deprecated.
Use 'strip.position' instead.
See help("Deprecated")
The penalty term is selected automatically with 100 candidates.
Using the criterion deviance to choose optimized penalty.
The chosen penalty throuth deviance is 3.5287.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Killed
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/MRMR.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [21s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > test_check("openxlsx")
  Loading required package: openxlsx
  ── 1. Error: loadWorkbook from different sources (@test-read_sources.R#49)  ────
  subscript out of bounds
  1: expect_true(all.equal.Workbook(wb_url, wb_file), "Loading from URL vs local not equal") at testthat/test-read_sources.R:49
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: all.equal.Workbook(wb_url, wb_file)
  5: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  9: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  10: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  11: attr.all.equal(target, current, ...)
  12: mode(current)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 505 SKIPPED: 2 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [7s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pxweb)
  pxweb: R tools for PX-WEB API.
  Copyright (C) 2014 Mans Magnusson, Leo Lahti, Love Hansson
  https://github.com/ropengov/pxweb
  
  New PXWEB API(s):
   - prognos.konj.se
   - data.ssb.no
   - pxweb.asub.ax
   - makstat.stat.gov.mk
   - data.csb.gov.lv
  
  Use update_pxweb_apis() to update the api catalogue.
  > test_check("pxweb")
  ── 1. Failure: pxweb_api_class (@test-pxweb_api_class.R#20)  ───────────────────
  NOT(success)
  
  ── 2. Failure: pxweb_api_class (@test-pxweb_api_class.R#22)  ───────────────────
  "foo.bar" %in% unlist(lapply(api_catalogue(), function(X) X$api)) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 98 SKIPPED: 16 FAILED: 2
  1. Failure: pxweb_api_class (@test-pxweb_api_class.R#20) 
  2. Failure: pxweb_api_class (@test-pxweb_api_class.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘R2GUESS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as.ESS.object
> ### Title: Compiles the main input and output files from a previous run of
> ###   'R2GUESS' and creates an ESS object.
> ### Aliases: as.ESS.object
> 
> ### ** Examples
> 
> dataX <- "data-X-C-CODE.txt"
> dataY <- "data-Y-ALL-C-CODE.txt"
> 
> path.input <- system.file("Input", package="R2GUESS")
> path.output <- system.file("Output", package="R2GUESS")
> path.par <- system.file("extdata", package="R2GUESS")
> file.par <- "Par_file_example_Hopx.xml"
> root.file.output <- "Example-GUESS-Y-Hopx"
> label.Y <- c("ADR","Fat","Heart","Kidney")
> my.env <- new.env()
> data(MAP.file,envir=my.env)
> MAP.file <- my.env$MAP.file
> modelY_Hopx <-as.ESS.object(dataY=dataY,dataX=dataX,path.input=path.input,
+     path.output=path.output,root.file.output=root.file.output,label.X=NULL,
+     label.Y=label.Y,path.par=path.par,file.par=file.par,MAP.file=MAP.file)
Warning in gzfile(file, "wb") :
  cannot open compressed file '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/R2GUESS/Output/Example-GUESS-Y-Hopx_output_best_visited_models.RData', probable reason 'Read-only file system'
Error in gzfile(file, "wb") : cannot open the connection
Calls: as.ESS.object -> get.best.models -> save -> gzfile
Execution halted
Running ‘testthat.R’ [4s/84s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rcongresso)
  > 
  > test_check("rcongresso")
  ── 1. Failure: Dimensoes do dataframe (@test_votacoes.R#54)  ───────────────────
  dim(votos_pec241) not equal to c(478, 10).
  1/2 mismatches
  [1] 500 - 478 == 22
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 66 SKIPPED: 0 FAILED: 1
  1. Failure: Dimensoes do dataframe (@test_votacoes.R#54) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RcppShark.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [5s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("rglobi")
  Loading required package: rglobi
  ── 1. Failure: interactions subsetted by adding additional information all inter
  dim(unique(rbind(rattusaves, rattus))) not equal to dim(unique(rattus)).
  1/2 mismatches
  [1] 632 - 628 == 4
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 32 SKIPPED: 2 FAILED: 1
  1. Failure: interactions subsetted by adding additional information all interaction types include observations (@test-globi.R#70) 
  
  Error: testthat unit tests failed
  Execution halted
Rjava.init.warning: stack size reduced from unlimited to 7947503 bytes after JVM initialization.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’
File ‘rJava/libs/rJava.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  libjson/Source/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-release-gcc/Work/PKGS/RJSONIO.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: ape
No ENTREZ API key provided
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Struthioniformes'

Quitting from lines 85-86 (metadata.Rmd) 
Error: processing vignette ‘metadata.Rmd’ failed with diagnostics:
'{"error":"API key invalid","api-key":"","type":"invalid","status":"unknown"}' does not exist in current working directory ('/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RNeXML.Rcheck/vign_test/RNeXML/vignettes').
Execution halted
Error in re-building vignettes:
  ...
Error : Oops, API did not return json after calling '§dldl  ':
        check your query - or api.oadoi.org may experience problems
Quitting from lines 177-178 (intro.Rmd) 
Error: processing vignette ‘intro.Rmd’ failed with diagnostics:
Oops, API did not return json after calling '10.1007/978-1-349-80976-9_6':
        check your query - or api.oadoi.org may experience problems
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for ‘Rpolyhedra’:
 .onLoad failed in loadNamespace() for ‘Rpolyhedra’, details:
  call: gzfile(file, mode)
  error: cannot open the connection
In addition: Warning message:
In gzfile(file, mode) :
  cannot open compressed file ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rpolyhedra/extdata/polyhedra.RDS’, probable reason ‘Read-only file system’
Execution halted
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pushSmetIntoIni
> ### Title: Pushes SMET object file into a 'meteoioini-class' object
> ### Aliases: pushSmetIntoIni
> 
> ### ** Examples
> 
> 
> ini <- as.meteoioini("test")
> 
> AA <- as.smet("test")
> BB <- as.smet("test")
> 
> 
> newini <- pushSmetIntoIni(AA,BB,ini=ini)
Warning in file(con, "w") :
  cannot open file '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/RSMET/temp/test_station.smet': Read-only file system
Error in file(con, "w") : cannot open the connection
Calls: pushSmetIntoIni -> lapply -> FUN -> print.smet -> <Anonymous> -> file
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/rsunlight.Rcheck/00install.out’ for details.
Running examples in ‘satscanMapper-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: satscanMapper
> ### Title: Function to map Results data produced by a SaTScan (TM) cluster
> ###   analysis
> ### Aliases: satscanMapper
> 
> ### ** Examples
> 
> ######
> #
> #  These examples focus on mapping the SaTScan (TM) data after the analysis
> #  has been completed.
> #  See the section on the CreateGeo4SS function for an example of how 
> #  to build a coordinates file (.geo) that matches the satscanMapper 
> #  boundary data.
> #
> ######
> 
> ######
> #
> #  Example # 1 - Mapping existing SaTScan (TM) results - "USStateLung" result files
> #     Make sure SaTScan (TM) results files are still located in the directories
> #     documented in the session saved (.prm) file.
> #
> #     This example maps data for the US States containing circular clusters.
> #
> #   Get location of .prm file and location to write mapping output files
> #
> 
> SSMInstDir <- system.file(package="satscanMapper", "extdata")
> 
> TT =c("Contiguous US States All Lung Cancer Mortality, 2004")
> 
> satscanMapper(resDir=SSMInstDir,                # path to .prm file location for output files. 
+                      prmFile  = "stateLung.prm", 
+                      title    = TT          )
Error in pdf(file = OutputFNpdf, width = vW, height = vH) : 
  cannot open file '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/satscanMapper/extdata/stateLung-R01.pdf'
Calls: satscanMapper -> pdf
Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

Loading required package: quickPlot
Loading required package: reproducible

Attaching package: 'reproducible'

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

    %>%

Warning in gzfile(file, mode) :
  cannot open compressed file ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/.snapshot.RDS’, probable reason ‘Read-only file system’
Quitting from lines 326-354 (ii-modules.Rmd) 
Error: processing vignette ‘ii-modules.Rmd’ failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

Loading required package: sp
loading reproducible     0.1.4
loading quickPlot        0.1.3
loading SpaDES.core      0.1.1
loading SpaDES.tools     0.1.1
loading SpaDES.addins    0.1.1

Default paths for SpaDES directories set to:
  cachePath:  /tmp/RtmpJQtZe5/SpaDES/cache
  inputPath:  /tmp/RtmpJQtZe5/SpaDES/inputs
  modulePath: /tmp/RtmpJQtZe5/SpaDES/modules
  outputPath: /tmp/RtmpJQtZe5/SpaDES/outputs
These can be changed using 'setPaths()'. See '?setPaths'.
Quitting from lines 48-61 (iii-cache.Rmd) 
Error: processing vignette ‘iii-cache.Rmd’ failed with diagnostics:
cannot open the connection
Execution halted
Running examples in ‘Stickbreaker-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sim.data.from.priors.for.mod.selection
> ### Title: Simulate data from priors for doing model selection
> ### Aliases: sim.data.from.priors.for.mod.selection
> 
> ### ** Examples
> 
>  n.muts <- 4
>  n.muts <- length(Khan.data[1,])-1
>  geno.matrix <- Khan.data[,seq(1, n.muts)]
>  fit.matrix <- as.matrix(Khan.data[,(n.muts+1)])
>  outdir <- system.file("extdata",package="Stickbreaker")
>  file.name <- paste("Training_simulated_priors_fit_data_", n.muts, "muts.txt", sep="")
>  outpath <- paste(outdir, file.name, sep="/")
>  sim.data.from.priors.for.mod.selection(n.muts,
+    c(0.05, 0.5),
+    c(0, 0.25),
+    c(4),
+    1,
+    c(0.1, 10),
+    1.1,
+    1,
+    c(2,1),
+    outpath,
+    50,
+    coe.sim.model="identical",
+    coe.dist.par=NA,
+    print.interval=NA)
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Stickbreaker/extdata/Training_simulated_priors_fit_data_5muts.txt': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: sim.data.from.priors.for.mod.selection -> write.table -> file
Execution halted
Error in re-building vignettes:
  ...
Installing package into '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages'
(as 'lib' is unspecified)
Quitting from lines 23-30 (summer-vignette.Rmd) 
Error: processing vignette ‘summer-vignette.Rmd’ failed with diagnostics:
unable to install packages
Execution halted
Error in re-building vignettes:
  ...
Loading required package: data.table
No methods found in package ‘RSQLite’ for request: ‘dbGetQuery’ when loading ‘tcpl’
tcpl (v1.2.2) loaded with the following settings:
  TCPL_DB:    /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/tcpl/sql/tcpldb.sqlite
  TCPL_USER:  NA
  TCPL_HOST:  NA
  TCPL_DRVR:  SQLite
Default settings stored in TCPL.conf. See ?tcplConf for more information.

Error: processing vignette ‘tcpl_Overview.Rnw’ failed with diagnostics:
 chunk 4 
Error in rsqlite_send_query(conn@ptr, statement) : 
  attempt to write a readonly database
Execution halted
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidyinftheo)
  > 
  > test_check("tidyinftheo")
  ── 1. Error: right number of columns given (@test-errors.R#10)  ────────────────
  argument "expr" is missing, with no default
  1: expect_length(tab %>% select(vs) %>% shannon_entropy(), 1) at testthat/test-errors.R:10
  2: quasi_label(enquo(object))
  3: eval_bare(get_expr(quo), get_env(quo))
  4: tab %>% select(vs) %>% shannon_entropy()
  5: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  6: eval(quote(`_fseq`(`_lhs`)), env, env)
  7: eval(quote(`_fseq`(`_lhs`)), env, env)
  8: `_fseq`(`_lhs`)
  9: freduce(value, `_function_list`)
  10: withVisible(function_list[[k]](value))
  11: function_list[[k]](value)
  12: shannon_entropy(.)
  13: reduce_data(.data, !(!enquo(X)), numvars = 1, na.rm = na.rm)
  14: tidyselect::vars_select(names(reduced_tab), !(!(!quos(...))))
  15: vars_select_eval(.vars, quos)
  16: map_lgl(quos, quo_is_helper)
  17: .f(.x[[i]], ...)
  18: extract_expr(quo)
  19: is_call(expr, paren_sym)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 37 SKIPPED: 0 FAILED: 1
  1. Error: right number of columns given (@test-errors.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘TSEtools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mcPrt
> ### Title: Matrix Conversion in Portfolio
> ### Aliases: mcPrt
> 
> ### ** Examples
> 
> fpath<-system.file("extdata", "sample.csv", package="TSEtools")
> asset0<-getTSE(fpath)$assets
proceeding...
SSPF1 compeleted! 
Last observations:
            Open  High   Low Close Volume  <NA>
2018-03-14 10034 10034 10034 10034   2540 10034

proceeding...
KMND1 compeleted! 
Last observations:
           Open  High  Low Close Volume  <NA>
2018-03-19 9980 10070 9980 10058  11530 10070

proceeding...
FPAF1 compeleted! 
Last observations:
            Open  High   Low Close   Volume  <NA>
2018-03-19 10065 10089 10062 10065 63085412 10065


 SSPF1 KMND1 FPAF1 are assigned!
> rtn<-mcPrt(asset0, sub="2016::", pstvRtn=TRUE, L=5)$return
Values in % base lag= 5 :
      meanReturn volatility sharpRatio
FPAF1          0       1.97       0.23

> 
> 
> 
> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
> base::cat("mcPrt", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> ### * <FOOTER>
> ###
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  1.387 0.027 7.131 0 0 
> grDevices::dev.off()
Error in grDevices::dev.off() : 
  cannot shut down device 1 (the null device)
Execution halted
Running examples in ‘WaterML-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AddMethods
> ### Title: AddMethods
> ### Aliases: AddMethods
> ### Keywords: waterml
> 
> ### ** Examples
> 
> user <- "admin"
> pass <- "password"
> server <- "http://worldwater.byu.edu/app/index.php/default/services/cuahsi_1_1.asmx"
> #make random site codes
> random_description <- sprintf("R Test Method %04d",sample(1:10000, 1))
> random_link <- "http://example.com"
> my_methods <- data.frame(
+   MethodDescription = random_description,
+   MethodLink = random_link
+ )
> 
> added_methods <- AddMethods(server, username=user, password=pass,
+                                 methods=my_methods)
[1] "{\n \"user\": \"admin\",\n\"password\": \"password\",\n\"MethodDescription\": \"R Test Method 2656\",\n\"MethodLink\": \"http://example.com\",\n\"VariableID\":      0 \n}"
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Connection timed out after 10001 milliseconds
Calls: AddMethods ... request_fetch -> request_fetch.write_memory -> <Anonymous> -> .Call
Execution halted
Running examples in ‘yCrypticRNAs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bam_to_reads
> ### Title: Convert BAM files into BED files containing the reads overlaping
> ###   the specified annotations.
> ### Aliases: bam_to_reads
> 
> ### ** Examples
> 
> bamfile <- system.file("extdata", "wt_rep1.bam", package = "yCrypticRNAs")
> data(annotations)
> bam_to_reads(bamfile, annotations)
Error in FUN(X[[i]], ...) : failed to build index
  file: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/yCrypticRNAs/extdata/wt_rep1.bam
Calls: bam_to_reads -> .index_bam
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 48-60 (yCrypticRNAs.Rmd) 
Error: processing vignette ‘yCrypticRNAs.Rmd’ failed with diagnostics:
failed to build index
  file: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/yCrypticRNAs/extdata/wt_rep1.bam
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/AbsFilterGSEA.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Quitting from lines 78-85 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
subscript out of bounds
Execution halted
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    R  14.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data       2.7Mb
    pictures   2.1Mb
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(testthat)
  > test_check("AnnotationBustR")
  Loading required package: AnnotationBustR
  -- 1. Error: More than max query works to find longest seq (@test_FindLongestSeq
  cannot open the connection
  1: ape::read.GenBank(as.vector(Achrist$V1)) at testthat/test_FindLongestSeq.R:217
  2: scan(file = URL, what = "", sep = "\n", quiet = TRUE)
  3: file(file, "r")
  
  == testthat results  ===========================================================
  OK: 7 SKIPPED: 1 FAILED: 1
  1. Error: More than max query works to find longest seq (@test_FindLongestSeq.R#217) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: 'AffymetrixDataTestFiles'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.5Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    bin   12.0Mb
    misc   2.1Mb
'library' or 'require' calls in package code:
  'cacheSweave' 'weaver'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'utils:::RtangleSetup'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'cacheSweave:::metaChunkName' 'cacheSweave:::metaSetCreationTime'
  'survival:::survmean' 'utils:::.SweaveValidFilenameRegexp'
  'utils:::RtangleFinish' 'utils:::RtangleRuncode'
  'utils:::SweaveParseOptions'
  See the note in ?`:::` about the use of this operator.
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.4/audio.Rcheck/00install.out' for details.
Running 'testthat.R' [15s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  9: auk_country(., country)
  10: auk_country.auk_ebd(., country)
  11: tolower(countrycode::countrycode_data$iso2c)
  12: countrycode::countrycode_data
  13: getExportedValue(pkg, name)
  14: stop(gettextf("'%s' is not an exported object from 'namespace:%s'", name, getNamespaceName(ns)), 
         call. = FALSE, domain = NA)
  
  == testthat results  ===========================================================
  OK: 197 SKIPPED: 13 FAILED: 2
  1. Error: auk_ebd prints method (@test_auk-ebd.r#66) 
  2. Error: auk_country (@test_filters.r#36) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.8Mb
installed size is 33.4Mb
  sub-directories of 1Mb or more:
    libs  33.0Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.8Mb
    libs   1.9Mb
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(baseballDBR)
  > 
  > test_check("baseballDBR")
  -- 1. Failure: (unknown) (@test-check_urls.R#25)  ------------------------------
  urlExists("http://www.fangraphs.com/guts.aspx?type=cn") isn't true.
  
  == testthat results  ===========================================================
  OK: 2 SKIPPED: 0 FAILED: 1
  1. Failure: (unknown) (@test-check_urls.R#25) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  In if (is.character(f) && !nzchar(f)) { :
    closing unused connection 3 (http://www.fangraphs.com/guts.aspx?type=cn)
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/BayClone2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/bayesCL.Rcheck/00install.out' for details.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   4.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R     1.6Mb
    doc   3.6Mb
File 'BayHap/libs/i386/BayHap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'mcmc.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'mcmc.o'
File 'BayHap/libs/x64/BayHap.dll':
  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.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 143.8Mb
  sub-directories of 1Mb or more:
    include  142.9Mb
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
             stop("Function ", name, " not found in environment ", environmentName(env), 
                 ".", call. = FALSE)
         mock(name = name, env = env, new = eval(new_values[[qual_name]], eval_env, eval_env))
     })
  4: FUN(X[[i]], ...)
  5: stop("Can't mock functions in base packages (", pkg_name, ")", call. = FALSE)
  
  == testthat results  ===========================================================
  OK: 26 SKIPPED: 0 FAILED: 3
  1. Error: canDownloadFiles (@test-download_files.R#9) 
  2. Error: canReturnEmptyDFWhenEmptyDownloadFiles (@test-download_files.R#27) 
  3. Error: canProcessYaml (@test-process_yaml.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'BioInstaller-Ex.R' failed
The error most likely occurred in:

> ### Name: install.bioinfo
> ### Title: Download and install biology software or database
> ### Aliases: install.bioinfo
> 
> ### ** Examples
> 
> db <- sprintf('%s/.BioInstaller', tempdir())
> set.biosoftwares.db(db)
> install.bioinfo('bwa', show.all.versions = TRUE)
INFO [2018-03-15 20:26:26] Fetching bwa versions....
Error in function (type, msg, asError = TRUE)  : 
  error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
Calls: install.bioinfo ... getURL -> curlPerform -> .Call -> <Anonymous> -> fun
Execution halted
Running 'testthat.R' [40s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  trying URL 'ftp://ftp.sjtu.edu.cn/pub/CPAN/clpa//index.html'
  ...
  downloaded 3574 bytes
  
  == testthat results  ===========================================================
  OK: 59 SKIPPED: 0 FAILED: 5
  1. Error: install.github (@test_install.R#10) 
  2. Error: install.bioinfo (@test_install.R#57) 
  3. Error: initial (@test_install_uilts.R#39) 
  4. Error: dependence (@test_install_uilts.R#88) 
  5. Error: git.download (@test_install_uilts.R#102) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/BonEV.Rcheck/00install.out' for details.
installed size is 72.0Mb
  sub-directories of 1Mb or more:
    include   2.7Mb
    lib      69.0Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
File 'brainwaver/libs/i386/brainwaver.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'connexity_small_world.o'
File 'brainwaver/libs/x64/brainwaver.dll':
  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.
Running 'test-all.R' [24s]
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  > #test_check("breathtestcore", filter = "plot_breathtestfit")
  > test_check("breathtestcore")
  Loading required package: breathtestcore
  -- 1. Failure: read_iris_csv returns with funny identification cleans up (@test_
  iconv(f$study) not equal to "GE-flüssig".
  1/1 mismatches
  x[1]: "GE-flÃ¼ssig"
  y[1]: "GE-flüssig"
  
  == testthat results  ===========================================================
  OK: 351 SKIPPED: 4 FAILED: 1
  1. Failure: read_iris_csv returns with funny identification cleans up (@test_read_iris_csv.R#51) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     2.2Mb
    doc   2.3Mb
plot,ANY-brob: no visible global function definition for 'plot.default'
plot,ANY-glub: no visible global function definition for 'plot.default'
plot,brob-ANY: no visible global function definition for 'plot.default'
plot,brob-missing: no visible global function definition for
  'plot.default'
plot,glub-ANY: no visible global function definition for 'plot.default'
plot,glub-missing: no visible global function definition for
  'plot.default'
Undefined global functions or variables:
  plot.default
Consider adding
  importFrom("graphics", "plot.default")
to your NAMESPACE file.
Running 'test-all.R' [31s]
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
         attr(value, "row.names") <- row.names
         attr(value, "class") <- "data.frame"
         value
     })(null.deviance = 83.2344746889857, `NA` = NULL, check.names = TRUE, fix.empty.names = TRUE, 
         stringsAsFactors = TRUE)
  8: stop(gettextf("arguments imply differing number of rows: %s", paste(unique(nrows), 
         collapse = ", ")), domain = NA)
  
  == testthat results  ===========================================================
  OK: 680 SKIPPED: 12 FAILED: 2
  1. Error: tidy works on gam models (@test-gam.R#6) 
  2. Error: glance works on gam models (@test-gam.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Running examples in 'cablecuttr-Ex.R' failed
The error most likely occurred in:

> ### Name: can_i_stream
> ### Title: Query CanIStream.It
> ### Aliases: can_i_stream can_i_stream_id can_i_stream_it
> 
> ### ** Examples
> 
> can_i_stream_id("4eb0173df5f8079d29000002", "purchase")
Error in as.POSIXlt.character(x, tz, ...) : 
  character string is not in a standard unambiguous format
Calls: can_i_stream_id ... as.POSIXct.default -> as.POSIXct -> as.POSIXlt -> as.POSIXlt.character
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    5.7Mb
    libs   1.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data     1.5Mb
    models   2.4Mb
Found the following Makefile(s) without a final LF:
  inst/doc/Makefile
Some 'make' programs ignore lines not ending in LF.
Files in the 'vignettes' directory newer than same file in 'inst/doc':
  'figure/glmnet-diagnostic.pdf', 'figure/roc-plot.pdf'
The following files look like leftovers/mistakes:
  'Causata-vignette.log'
Please remove them from your package.
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
Error in re-building vignettes:
  ...
Warning: running command '"pdflatex" -halt-on-error -interaction=batchmode "ciee.tex"' had status 1
! LaTeX Error: Unknown graphics extension: .tiff.

Error: processing vignette 'ciee.Rmd' failed with diagnostics:
Failed to compile ciee.tex. See ciee.log for more info.
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
    pdf   2.2Mb
Error in re-building vignettes:
  ...

    expand.grid

Loading required package: XML

Attaching package: 'XML'

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

    toHTML

Loading required package: GO.db

Loading required package: moe430a.db
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'moe430a.db'
Loading required package: RankAggreg
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "clValid.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.4.4/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.4.4/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'clValid.tex' failed

LaTeX errors:
!pdfTeX error: pdflatex.EXE (file ./clValid-022.pdf): PDF inclusion: required p
age does not exist <0>
 ==> Fatal error occurred, no output PDF file produced!
Execution halted
Running 'testthat.R' [25s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > 
  > test_check("codemetar")
  -- 1. Error: we can generate codemeta
                      from the root director
  unknown certificate check failure
  1: git2r::clone("https://github.com/codemeta/codemetar", "codemetar_copy", progress = FALSE) at testthat/test-cloned-repo.R:10
  2: git2r::clone("https://github.com/codemeta/codemetar", "codemetar_copy", progress = FALSE)
  
  == testthat results  ===========================================================
  OK: 32 SKIPPED: 12 FAILED: 1
  1. Error: we can generate codemeta
                      from the root directory of R source code on github (@test-cloned-repo.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: 'mogene10sttranscriptcluster.db'
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data      6.5Mb
    extdata   2.6Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   6.5Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.3Mb
'library' or 'require' call to 'parallel' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'car' 'ellipse' 'rJPSGCS'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/Cyclops.Rcheck/00install.out' for details.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   8.6Mb
Running 'test-all.R' [20s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("dcmr")
  Loading required package: dcmr
  -- 1. Failure: Test ScoreDCM outputs for Qmatrix with no interaction (@test_scor
  `rmse_class` is not strictly less than `tolerance`. Difference: 0.417
  
  == testthat results  ===========================================================
  OK: 119 SKIPPED: 0 FAILED: 1
  1. Failure: Test ScoreDCM outputs for Qmatrix with no interaction (@test_scoreDCM.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  -- 4. Failure: DCF reader works (@test-read.R#9)  ------------------------------
  desc$get("Author") not equal to c(Author = "Gábor Csárdi").
  1/1 mismatches
  x[1]: "GÃ¡bor CsÃ¡rdi"
  y[1]: "Gábor Csárdi"
  
  == testthat results  ===========================================================
  OK: 348 SKIPPED: 0 FAILED: 4
  1. Failure: get_maintainer is OK, too (@test-authors.R#171) 
  2. Failure: get works (@test-queries.R#9) 
  3. Failure: get_or_fail works (@test-queries.R#18) 
  4. Failure: DCF reader works (@test-read.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    help   1.3Mb
    libs   1.6Mb
Running 'has-devel.R' [3s]
  Running 'test-that.R' [104s]
Running the tests in 'tests/test-that.R' failed.
Last 13 lines of output:
      setup
  
  -- 1. Failure: remote_sha.github_remote returns expected value if remote does ex
  remote_sha(github_remote("hadley/devtools@v1.8.0")) not equal to "ad9aac7b9a522354e1ff363a86f389e32cec181b".
  1/1 mismatches
  x[1]: NA
  y[1]: "ad9aac7b9a522354e1ff363a86f389e32cec181b"
  
  
  == testthat results  ===========================================================
  OK: 400 SKIPPED: 10 FAILED: 1
  1. Failure: remote_sha.github_remote returns expected value if remote does exist (@test-remotes.r#75) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    5.1Mb
    libs   1.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    5.6Mb
    libs   1.4Mb
Running 'AESTest.R' [1s]
  Comparing 'AESTest.Rout' to 'AESTest.Rout.save' ... OK
  Running 'digestTest.R' [1s]
  Comparing 'digestTest.Rout' to 'digestTest.Rout.save' ... OK
  Running 'hmacTest.R' [1s]
  Comparing 'hmacTest.Rout' to 'hmacTest.Rout.save' ... OK
  Running 'load-unload.R' [0s]
  Running 'num2hexTest.R' [0s]
  Running 'sha1Test.R' [1s]
Running the tests in 'tests/sha1Test.R' failed.
Last 13 lines of output:
  +         sha1(matrix(integer(0))),
  +         sha1(matrix(numeric(0)))
  +     )
  + )
  > 
  > if (getRversion() < "3.5.0") {
  +     stopifnot(
  +         identical(
  +             sha1(serialize("e13485e1b995f3e36d43674dcbfedea08ce237bc", NULL)),
  +             "93ab6a61f1a2ad50d4bf58396dc38cd3821b2eaf"
  +         )
  +     )
  + }
  Error: identical(sha1(serialize("e13485e1b995f3e36d43674dcbfedea08ce237bc",  .... is not TRUE
  Execution halted
Running 'AESTest.R' [0s]
  Comparing 'AESTest.Rout' to 'AESTest.Rout.save' ... OK
  Running 'digestTest.R' [1s]
  Comparing 'digestTest.Rout' to 'digestTest.Rout.save' ... OK
  Running 'hmacTest.R' [0s]
  Comparing 'hmacTest.Rout' to 'hmacTest.Rout.save' ... OK
  Running 'load-unload.R' [0s]
  Running 'num2hexTest.R' [0s]
  Running 'sha1Test.R' [1s]
Running the tests in 'tests/sha1Test.R' failed.
Last 13 lines of output:
  +         sha1(matrix(integer(0))),
  +         sha1(matrix(numeric(0)))
  +     )
  + )
  > 
  > if (getRversion() < "3.5.0") {
  +     stopifnot(
  +         identical(
  +             sha1(serialize("e13485e1b995f3e36d43674dcbfedea08ce237bc", NULL)),
  +             "93ab6a61f1a2ad50d4bf58396dc38cd3821b2eaf"
  +         )
  +     )
  + }
  Error: identical(sha1(serialize("e13485e1b995f3e36d43674dcbfedea08ce237bc",  .... is not TRUE
  Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Running 'testthat.R' [15s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  3: eval_bare(get_expr(quo), get_env(quo))
  4: summarise(gdf, out = 1:2)
  5: summarise.tbl_df(gdf, out = 1:2)
  6: summarise_impl(.data, dots)
  
  == testthat results  ===========================================================
  OK: 2875 SKIPPED: 6 FAILED: 3
  1. Error: mutate() supports unquoted values (@test-mutate.r#721) 
  2. Failure: summarise() supports unquoted values (@test-summarise.r#980) 
  3. Error: summarise() supports unquoted values (@test-summarise.r#985) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  call dbDisconnect() when finished working with a connection 
  Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.1Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.2Mb
    libs   3.9Mb
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > 
  > test_check("ECctmc")
  -- 1. Failure: Modified rejection sampling and uniformization target the same di
  t.test(MR_res[k, ], Unif_res[k, ])$p.value < 0.1 isn't false.
  
  -- 2. Failure: Modified rejection sampling and uniformization target the same di
  t.test(MR_res[k, ], Unif_res[k, ])$p.value < 0.1 isn't false.
  
  == testthat results  ===========================================================
  OK: 5 SKIPPED: 0 FAILED: 2
  1. Failure: Modified rejection sampling and uniformization target the same distribution (@test_simfcns.R#36) 
  2. Failure: Modified rejection sampling and uniformization target the same distribution (@test_simfcns.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    xsd   5.4Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   3.4Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
'LinkingTo' field is unused: package has no 'src' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/FastRWeb.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Warning in parse(file = files, n = -1L) :
  invalid input found on input connection 'fivethirtyeight-Ex.R'
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),  : 
  Evaluation error: only replacement of elements is allowed.
Calls: forecasting_ga -> .Call
Execution halted
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    1.6Mb
    libs   1.5Mb
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    CATCH_CHECK( entrR[0] == fselector::entropy::numeric_entropy(x.begin(), x.end()) )
  with expansion:
    1.0114042647 == 1.0114042647
  
  ===============================================================================
  test cases: 2 | 1 passed | 1 failed
  assertions: 5 | 4 passed | 1 failed
  
  
  == testthat results  ===========================================================
  OK: 89 SKIPPED: 0 FAILED: 1
  1. Failure: Catch unit tests pass (@test-cpp.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    data  16.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   2.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      4.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/GB2.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.3Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:

======== End of example output (where/before crash/hang up occured ?) ========
Running examples in 'geotopbricks-Ex.R' failed
The error most likely occurred in:

> ### Name: create.geotop.inpts.keyword
> ### Title: Creates an 'geotop.inpts' files the keyword and their values of
> ###   a date.frame like the one returned by
> ###   'declared.geotop.inpts.keywords'
> ### Aliases: create.geotop.inpts.keyword
> 
> ### ** Examples
> 
> 
> library(geotopbricks)
> 
> #Simulation working path
> wpath <- 'http://www.rendena100.eu/public/geotopbricks/simulations/panola13_run2xC_test3'
> df <- declared.geotop.inpts.keywords(wpath=wpath)
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Das Zeitlimit für den Vorgang wurde erreicht.'
Error in file(con, "r") : cannot open the connection
Calls: declared.geotop.inpts.keywords -> <Anonymous> -> file
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    1.2Mb
    libs   1.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.7Mb
Running 'test-all.R' [5s]
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  8: git2r::fetch(gitrepo, name = "github", credentials = credentials)
  
  == testthat results  ===========================================================
  OK: 9 SKIPPED: 0 FAILED: 8
  1. Error: Install a single package (@test_install.R#8) 
  2. Error: Install a single package, removing old install (@test_install.R#14) 
  3. Error: Install a single package w/o vignettes (@test_install.R#19) 
  4. Error: Install from a branch (@test_install.R#25) 
  5. Error: Install from a commit ref (@test_install.R#36) 
  6. Error: Install from a tag (@test_install.R#42) 
  7. Error: Install from a pull request (@test_install.R#49) 
  8. Error: (unknown) (@test_internal.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg18.masked'
  'BSgenome.Hsapiens.UCSC.hg19.masked'
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  21.3Mb
File 'gnmf/libs/i386/gnmf.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'FactorMatrix.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'FactorMatrix.o'
File 'gnmf/libs/x64/gnmf.dll':
  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.
Error in re-building vignettes:
  ...
Loading required package: survival
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "ashg2012.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.4.4/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.4.4/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'ashg2012.tex' failed

LaTeX errors:
! LaTeX Error: File `D:/RCompile/recent/R-34\unhbox\voidb@x \penalty \@M \ {}1.
4/share/texmf/tex/latex/Sweave.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Execution halted
Running examples in 'GuardianR-Ex.R' failed
The error most likely occurred in:

> ### Name: get_guardian
> ### Title: Search Guardian API for news articles that match the criteria
> ### Aliases: get_guardian
> ### Keywords: IO utilities
> 
> ### ** Examples
> 
> ## Not run:
> results <- get_guardian("islamic+state", 
+ 	section="world",
+ 	from.date="2014-09-16", 
+ 	to.date="2014-09-16", 
+ 	api.key="3xzg2fk53jcdgaj5tbwqqhcz")
trying URL 'https://curl.haxx.se/ca/cacert.pem'
Warning in download.file(url = "https://curl.haxx.se/ca/cacert.pem", destfile = "cacert.perm") :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in download.file(url = "https://curl.haxx.se/ca/cacert.pem", destfile = "cacert.perm") : 
  cannot open URL 'https://curl.haxx.se/ca/cacert.pem'
Calls: get_guardian -> get_json -> download.file
Execution halted
installed size is 125.9Mb
  sub-directories of 1Mb or more:
    java  124.6Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Running 'testthat-all1q.R' [3s]
  Running 'testthat-all2q.R' [4s]
Running the tests in 'tests/testthat-all2q.R' failed.
Last 13 lines of output:
  
  == testthat results  ===========================================================
  OK: 2 SKIPPED: 0 FAILED: 9
  1. Failure: all_answered_questions return expected format (@test_2all_answered_questions.R#11) 
  2. Failure: all_answered_questions return expected format (@test_2all_answered_questions.R#12) 
  3. Failure: all_answered_questions return expected format (@test_2all_answered_questions.R#13) 
  4. Failure: all_answered_questions return expected format (@test_2all_answered_questions.R#14) 
  5. Failure: all_answered_questions return expected format (@test_2all_answered_questions.R#21) 
  6. Failure: all_answered_questions return expected format (@test_2all_answered_questions.R#22) 
  7. Failure: all_answered_questions return expected format (@test_2all_answered_questions.R#23) 
  8. Failure: all_answered_questions return expected format (@test_2all_answered_questions.R#24) 
  9. Failure: all_answered_questions return expected format (@test_2all_answered_questions.R#25) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 112-118 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
Argument 1 must have names
Execution halted
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
Running 'testthat.R' [24s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(harvestr)
  > foreach::registerDoSEQ()
  > test_check("harvestr")
  -- 1. Failure: caching in reap with long sample (@test-caching.R#76)  ----------
  all(t2[1] <= t1[1]) isn't true.
  
  == testthat results  ===========================================================
  OK: 104 SKIPPED: 5 FAILED: 1
  1. Failure: caching in reap with long sample (@test-caching.R#76) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    doc          13.7Mb
    htmlwidgets   1.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   1.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    data  12.8Mb
    doc    1.3Mb
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(hyphenatr)
  > 
  > test_check("hyphenatr")
  -- 1. Failure: we can do something (@test-hyphenatr.R#16)  ---------------------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "tÃ¤=gelÃ®ch"
  y[1]: "tä=gelîch"
  
  == testthat results  ===========================================================
  OK: 4 SKIPPED: 0 FAILED: 1
  1. Failure: we can do something (@test-hyphenatr.R#16) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(hyphenatr)
  > 
  > test_check("hyphenatr")
  -- 1. Failure: we can do something (@test-hyphenatr.R#16)  ---------------------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "tÃ¤=gelÃ®ch"
  y[1]: "tä=gelîch"
  
  == testthat results  ===========================================================
  OK: 4 SKIPPED: 0 FAILED: 1
  1. Failure: we can do something (@test-hyphenatr.R#16) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      1.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/ICSNP.Rcheck/00install.out' for details.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   5.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.5Mb
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  13.8Mb
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.9Mb
    include   2.8Mb
    libs     11.6Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R  10.7Mb
Error in re-building vignettes:
  ...
Warning in read.table(file = file, header = header, sep = sep, quote = quote,  :
  invalid input found on input connection 'D:\temp\RtmpQlv4tX\ex_data271b820e3cd9.csv2'
Warning in read.table(file = file, header = header, sep = sep, quote = quote,  :
  incomplete final line found by readTableHeader on 'D:\temp\RtmpQlv4tX\ex_data271b820e3cd9.csv2'
Quitting from lines 31-32 (incadoc.Rmd) 
Error: processing vignette 'incadoc.Rmd' failed with diagnostics:
cannot open URL 'http://www.cancercentrum.se/globalassets/cancerdiagnoser/lunga-och-lungsack/dokument/styrdokument.pdf'
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   6.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   2.2Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R   7.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/LAM.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/lavaan.survey.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    htmlwidgets   4.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      3.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  19: (function (dt, year, month, yday, mday, wday, hour, minute, second, tz = NULL, roll = FALSE, 
         week_start = 7L) 
     {
         .Call(`_lubridate_C_update_dt`, dt, year, month, yday, mday, wday, hour, minute, 
             second, tz, roll, week_start)
     })(year = integer(0), month = integer(0), yday = integer(0), mday = 18, wday = integer(0), 
         hour = 1, minute = 0, second = 0, dt = structure(1487289600, class = c("POSIXct", 
         "POSIXt"), tzone = ""), roll = FALSE, tz = "", week_start = 7)
  
  == testthat results  ===========================================================
  OK: 62 SKIPPED: 0 FAILED: 1
  1. Error: plot_i_hr_datetime produces a ggplot object (@test_viz_plot.R#73) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.0Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc        1.5Mb
    libs       2.1Mb
    testdata   1.5Mb
Running examples in 'lubridate-Ex.R' failed
The error most likely occurred in:

> ### Name: ymd
> ### Title: Parse dates with *y*ear, *m*onth, and *d*ay components
> ### Aliases: ymd ydm mdy myd dmy dym yq
> ### Keywords: chron
> 
> ### ** Examples
> 
> x <- c("09-01-01", "09-01-02", "09-01-03")
> ymd(x)
[1] "2009-01-01" "2009-01-02" "2009-01-03"
> x <- c("2009-01-01", "2009-01-02", "2009-01-03")
> ymd(x)
[1] "2009-01-01" "2009-01-02" "2009-01-03"
> ymd(090101, 90102)
[1] "2009-01-01" "2009-01-02"
> now() > ymd(20090101)
Warning in with_tz(Sys.time(), tzone) : Unrecognized time zone ''
Error in C_force_tz(time, tz = tzone, roll) : 
  CCTZ: Unrecognized output timezone: ""
Calls: >.POSIXt -> date_to_posix -> force_tz -> C_force_tz -> .Call
Execution halted
Running 'testthat.R' [28s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
         .Call(`_lubridate_C_update_dt`, dt, year, month, yday, mday, wday, hour, minute, 
             second, tz, roll, week_start)
     })(year = integer(0), month = integer(0), yday = integer(0), mday = 15, wday = integer(0), 
         hour = 23, minute = 22, second = 5, dt = structure(1521152572.42724, class = c("POSIXct", 
         "POSIXt"), tzone = ""), roll = FALSE, tz = "", week_start = 7)
  
  == testthat results  ===========================================================
  OK: 2442 SKIPPED: 4 FAILED: 4
  1. Failure: with_tz throws warning on unrecognized time zones (@test-timezones.R#82) 
  2. Failure: with_tz throws warning on unrecognized time zones (@test-timezones.R#83) 
  3. Failure: with_tz throws warning on unrecognized time zones (@test-timezones.R#84) 
  4. Error: Updateing on seconds doesn't affect hours (@test-update.R#414) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [27s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
         .Call(`_lubridate_C_update_dt`, dt, year, month, yday, mday, wday, hour, minute, 
             second, tz, roll, week_start)
     })(year = integer(0), month = integer(0), yday = integer(0), mday = 15, wday = integer(0), 
         hour = 23, minute = 23, second = 5, dt = structure(1521152600.56944, class = c("POSIXct", 
         "POSIXt"), tzone = ""), roll = FALSE, tz = "", week_start = 7)
  
  == testthat results  ===========================================================
  OK: 2442 SKIPPED: 4 FAILED: 4
  1. Failure: with_tz throws warning on unrecognized time zones (@test-timezones.R#82) 
  2. Failure: with_tz throws warning on unrecognized time zones (@test-timezones.R#83) 
  3. Failure: with_tz throws warning on unrecognized time zones (@test-timezones.R#84) 
  4. Error: Updateing on seconds doesn't affect hours (@test-update.R#414) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  y[1]: "£12.00"
  
  -- 2. Failure: Complex amounts can be converted (@test_conversion.R#8)  --------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "Â£12,000.00"
  y[1]: "£12,000.00"
  
  == testthat results  ===========================================================
  OK: 6 SKIPPED: 0 FAILED: 2
  1. Failure: Simple amounts can be converted (@test_conversion.R#4) 
  2. Failure: Complex amounts can be converted (@test_conversion.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 40.9Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs  34.0Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   2.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   3.9Mb
    libs      1.5Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.8Mb
    misc   1.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.7Mb
    libs   1.8Mb
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > 
  > test_check("Momocs")
  -- 1. Error: filter works fine (@test-nse.R#62)  -------------------------------
  bad value
  1: expect_true(x_lite$fac %>% sapply(nlevels) %>% ==1 %>% all) at testthat/test-nse.R:62
  2: quasi_label(enquo(object), label)
  3: force(quo)
  4: enquo(object)
  
  == testthat results  ===========================================================
  OK: 159 SKIPPED: 1 FAILED: 1
  1. Error: filter works fine (@test-nse.R#62) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(mortAAR)
  > 
  > test_check("mortAAR")
  -- 1. Failure: prep.life.table imports a data set correct (@test_input_functions
  names(example_life_table) not equal to c("Unbestimmt", "Weiblich", "Männlich", "All").
  1/4 mismatches
  x[3]: "MÃ¤nnlich"
  y[3]: "Männlich"
  
  == testthat results  ===========================================================
  OK: 78 SKIPPED: 0 FAILED: 1
  1. Failure: prep.life.table imports a data set correct (@test_input_functions.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/MRMR.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'amap' 'clValid' 'cluster' 'fpc' 'mzR' 'xcms'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'library' or 'require' calls to packages already attached by Depends:
  'amap' 'clValid' 'cluster' 'fpc' 'xcms'
  Please remove these calls from your code.
'library' or 'require' call to 'tcltk' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'mzR' 'xcms'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls to packages already attached by Depends:
  'MSeasy' 'tcltk'
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'grDevices' 'xcms'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Error in re-building vignettes:
  ...
pandoc.exe: Could not determine mime type for `https://raw.github.com/vincent-dk/msgl/master/fig1.png'
CallStack (from HasCallStack):
  error, called at src\Text\Pandoc\SelfContained.hs:156:35 in pandoc-1.19.2.1-3EiBhxep0x773HKxrkonLI:Text.Pandoc.SelfContained
Warning: running command '"D:/compiler/pandoc/pandoc" +RTS -K512m -RTS README.utf8.md --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output README.html --smart --email-obfuscation none --self-contained --standalone --section-divs --template "d:\RCompile\CRANpkg\lib\3.4\rmarkdown\rmd\h\default.html" --highlight-style pygments --css "d:\RCompile\CRANpkg\lib\3.4\rmarkdown\rmarkdown\templates\html_vignette\resources\vignette.css" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"' had status 1
Error: processing vignette 'README.Rmd' failed with diagnostics:
pandoc document conversion failed with error 1
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.7Mb
    libs   1.5Mb
Running 'testthat.R' [31s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
     {
         .Call(`_lubridate_C_update_dt`, dt, year, month, yday, mday, wday, hour, minute, 
             second, tz, roll, week_start)
     })(year = integer(0), month = integer(0), yday = integer(0), mday = 16, wday = integer(0), 
         hour = 5, minute = 30, second = 18.764552116394, dt = structure(1521174616.76455, class = c("POSIXct", 
         "POSIXt"), tzone = ""), roll = FALSE, tz = "", week_start = 7)
  
  == testthat results  ===========================================================
  OK: 67 SKIPPED: 0 FAILED: 3
  1. Error: character date handling: yyyy-mm-dd hh:mm:ss in past (@test-naptime.R#126) 
  2. Error: character date handling: yyyy-mm-dd hh:mm:ss in future (@test-naptime.R#136) 
  3. Error: Invalid Period throws error (@test-naptime.R#168) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Error in re-building vignettes:
  ...
Warning: running command '"pdflatex" -halt-on-error -interaction=batchmode "NEArender_vignette.tex"' had status 1
! Package pdftex.def Error: File `http://research.scilifelab.se/andrej_alexeyen
ko/downloads/test_data/aa.png' not found.

Error: processing vignette 'NEArender_vignette.Rmd' failed with diagnostics:
Failed to compile NEArender_vignette.tex. See NEArender_vignette.log for more info.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   2.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.1Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    CppCode   2.5Mb
    R         3.4Mb
    include   5.6Mb
    libs      1.8Mb
    tests     1.2Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.2Mb
Error in re-building vignettes:
  ...
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "nonrandom.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.4.4/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.4.4/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'nonrandom.tex' failed

LaTeX errors:
! LaTeX Error: File `sfmath.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

Execution halted
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    doc  12.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   2.4Mb
File 'obliclus/libs/i386/obliclus.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'random_cluster_C.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'random_cluster_C.o'
File 'obliclus/libs/x64/obliclus.dll':
  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.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    help   2.2Mb
    libs   1.3Mb
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    R        2.3Mb
    libs     5.9Mb
    models   4.8Mb
Running 'testthat.R' [36s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  5: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  9: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  10: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  11: attr.all.equal(target, current, ...)
  12: mode(current)
  
  == testthat results  ===========================================================
  OK: 505 SKIPPED: 2 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    nifti   3.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Loading required package: pathological
  -- 1. Failure: standardize_path works with missing files with ./ prefix (@test_s
  standardize_path(x) not equal to `expected`.
  1/2 mismatches
  x[1]: "D:/RCompile/CRANpkg/local/3.4/pathological.Rcheck/tests/testthat/test_dec
  x[1]: ompose_path.R"
  y[1]: "D:/Rcompile/CRANpkg/local/3.4/pathological.Rcheck/tests/testthat/test_dec
  y[1]: ompose_path.R"
  
  == testthat results  ===========================================================
  OK: 187 SKIPPED: 18 FAILED: 1
  1. Failure: standardize_path works with missing files with ./ prefix (@test_standardize_path.R#198) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    lib    5.8Mb
    libs   4.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.4Mb
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  8. Error: both dataframes return rows - test #5 (@test_joining.R#11) 
  9. Error: both dataframes return rows - test #3 (@test_joining.R#25) 
  1. ...
  
  Error: testthat unit tests failed
  In addition: Warning messages:
  1: closing unused connection 10 (https://www.onepetro.org/search?q="neural+network"&peer_reviewed=&published_between=on&from_year=1990&to_year=2000) 
  2: closing unused connection 8 (https://www.onepetro.org/search?q="neural+network"&peer_reviewed=&published_between=&from_year=&to_year=&start=0&rows=1000&dc_type=conference-paper) 
  3: closing unused connection 7 (https://www.onepetro.org/search?q="neural+network"&peer_reviewed=&published_between=&from_year=&to_year=&start=0&rows=1000&dc_type=journal-paper) 
  4: closing unused connection 10 (https://www.onepetro.org/search?q="neural+network"&peer_reviewed=&published_between=&from_year=&to_year=&dc_type=presentation) 
  5: closing unused connection 9 (https://www.onepetro.org/search?q="neural+network"&peer_reviewed=&published_between=&from_year=&to_year=&dc_type=journal-paper) 
  6: closing unused connection 8 (https://www.onepetro.org/search?q="mechanistic+performance"&peer_reviewed=&published_between=&from_year=&to_year=) 
  7: closing unused connection 7 (https://www.onepetro.org/search?q="neural+network"&peer_reviewed=&published_between=&from_year=&to_year=) 
  8: closing unused connection 6 (https://www.onepetro.org/search?q="neural+network"&peer_reviewed=&published_between=on&from_year=1970&to_year=1987) 
  Execution halted
Error in re-building vignettes:
  ...
pandoc-citeproc: Error parsing XML file plos-genetics.csl: HttpExceptionRequest Request {
  host                 = "www.zotero.org"
  port                 = 80
  secure               = False
  requestHeaders       = []
  path                 = "/styles/plos"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (ConnectionFailure getAddrInfo: does not exist (error 11001))
pandoc.exe: Error running filter pandoc-citeproc
Filter returned error status 1
Warning: running command '"D:/compiler/pandoc/pandoc" +RTS -K512m -RTS Simulation-and-LinearModel.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output Simulation-and-LinearModel.tex --table-of-contents --toc-depth 2 --template "d:\RCompile\CRANpkg\lib\3.4\rmarkdown\rmd\latex\default-1.17.0.2.tex" --highlight-style tango --latex-engine pdflatex --variable graphics=yes --variable "geometry:margin=1in" --filter pandoc-citeproc' had status 83
Error: processing vignette 'Simulation-and-LinearModel.Rmd' failed with diagnostics:
pandoc document conversion failed with error 83
Execution halted
Running examples in 'phuse-Ex.R' failed
The error most likely occurred in:

> ### Name: cvt_list2df
> ### Title: Convert list to data frame
> ### Aliases: cvt_list2df
> 
> ### ** Examples
> 
>   a <- "https://github.com/phuse-org/phuse-scripts/raw/master"
>   b <- "development/R/scripts"
>   c <- "Draw_Dist2_R.yml"
>   f1 <- paste(a,b,c, sep = '/')
>   r1 <- read_yml(f1)
>   r2 <- cvt_list2df(r1)
Error in a[[k1]] : subscript out of bounds
Calls: cvt_list2df -> typeof
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   1.6Mb
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  OK: 53 SKIPPED: 0 FAILED: 24
  1. Error: Creating a `col_is_character()` step is possible (@test-create_validation_steps.R#10) 
  2. Error: Creating a `col_is_date()` step is possible (@test-create_validation_steps.R#74) 
  3. Error: Creating a `col_is_factor()` step is possible (@test-create_validation_steps.R#138) 
  4. Error: Creating a `col_is_integer()` step is possible (@test-create_validation_steps.R#202) 
  5. Error: Creating a `col_is_logical()` step is possible (@test-create_validation_steps.R#266) 
  6. Error: Creating a `col_is_numeric()` step is possible (@test-create_validation_steps.R#330) 
  7. Error: Creating a `col_is_posix()` step is possible (@test-create_validation_steps.R#394) 
  8. Error: Creating a `col_vals_between()` step is possible (@test-create_validation_steps.R#458) 
  9. Error: Creating a `col_vals_not_between()` step is possible (@test-create_validation_steps.R#530) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: 'rcqp'

Package suggested but not available for checking: 'polmineR.sampleCorpus'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
File 'powell/libs/i386/powell.dll':
  Found 'printf', possibly from 'printf' (C)
    Object: 'powell.o'
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
    Object: 'powell.o'
File 'powell/libs/x64/powell.dll':
  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.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Packages which this enhances but not available for checking:
  'org.Ag.eg.db' 'org.Pt.eg.db' 'org.Rn.eg.db' 'org.Ss.eg.db'
  'org.Bt.eg.db' 'org.Ce.eg.db' 'org.Cf.eg.db' 'org.Dr.eg.db'
  'org.EcK12.eg.db' 'org.EcSakai.eg.db' 'org.Gg.eg.db' 'org.Mmu.eg.db'
  'org.Pf.plasmo.db' 'org.Xl.eg.db'
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   6.4Mb
    libs      1.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc        4.6Mb
    examples   2.2Mb
Error in re-building vignettes:
  ...
trying URL 'http://github.com/dobriban/pweight/raw/master/vignettes/iGWAS.cad.example.RData'
Quitting from lines 34-38 (iGWAS-DataExample.Rmd) 
Error: processing vignette 'iGWAS-DataExample.Rmd' failed with diagnostics:
cannot open URL 'http://github.com/dobriban/pweight/raw/master/vignettes/iGWAS.cad.example.RData'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 126-132 (Maps_and_Timeseries_Plots.Rmd) 
Error: processing vignette 'Maps_and_Timeseries_Plots.Rmd' failed with diagnostics:
cannot open URL 'http://maps.google.com/maps/api/staticmap?center=47,-118&zoom=7&size=640x640&maptype=roadmap&format=png32&sensor=true'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 112-113 (orthography_processing.Rmd) 
Error: processing vignette 'orthography_processing.Rmd' failed with diagnostics:
undefined columns selected
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   3.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   2.0Mb
File 'QUIC/libs/i386/QUIC.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'QUIC.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'QUIC.o'
File 'QUIC/libs/x64/QUIC.dll':
  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.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    Output   2.2Mb
    bin      9.3Mb
Package suggested but not available for checking: 'rcom'
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   6.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   2.8Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs   2.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    libs   1.8Mb
Running 'testthat.R' [111s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(testthat)
  > library(rcongresso)
  > 
  > test_check("rcongresso")
  -- 1. Failure: Dimensoes do dataframe (@test_votacoes.R#54)  -------------------
  dim(votos_pec241) not equal to c(478, 10).
  1/2 mismatches
  [1] 500 - 478 == 22
  
  == testthat results  ===========================================================
  OK: 66 SKIPPED: 0 FAILED: 1
  1. Failure: Dimensoes do dataframe (@test_votacoes.R#54) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    include   7.7Mb
    libs      1.8Mb
Error in re-building vignettes:
  ...
The top-level auxiliary file: RcppGSL-intro.aux
I couldn't open database file Rcpp.bib
---line 151 of file RcppGSL-intro.aux
 : \bibdata{Rcpp
 :              }
I'm skipping whatever remains of this command
The style file: jss.bst
I found no database files---while reading file RcppGSL-intro.aux
Warning--I didn't find a database entry for "GSL"
Warning--I didn't find a database entry for "JSS:Rcpp"
Warning--I didn't find a database entry for "Eddelbuettel:2013:Rcpp"
Warning--I didn't find a database entry for "CRAN:Rcpp"
Warning--I didn't find a database entry for "R:Main"
Warning--I didn't find a database entry for "CRAN:RcppArmadillo"
Warning--I didn't find a database entry for "Eddelbuettel+Sanderson:2013:RcppArmadillo"
Warning--I didn't find a database entry for "Sanderson:2010:Armadillo"
Warning--I didn't find a database entry for "CRAN:RcppEigen"
Warning--I didn't find a database entry for "JSS:RcppEigen"
Warning--I didn't find a database entry for "CRAN:inline"
Warning--I didn't find a database entry for "CRAN:Rcpp:Attributes"
(There were 2 error messages)
Warning: running command '"bibtex" "RcppGSL-intro.aux"' had status 1
Error: processing vignette 'RcppGSL-intro.Rmd' failed with diagnostics:
Failed to build the bibliography via bibtex
Execution halted